Community, Time, and (Con)text: A Dynamical Systems Analysis of Online Communication and Community Health among Open-Source Software Communities.

Free and open-source software projects have become essential digital infrastructure over the past decade. These projects are largely created and maintained by unpaid volunteers, presenting a potential vulnerability if the projects cannot recruit and retain new volunteers. At the same time, their development on open collaborative development platforms provides a nearly complete record of the community's interactions; this affords the opportunity to study naturally occurring language dynamics at scale and in a context with massive real-world impact. The present work takes a dynamical systems view of language to understand the ways in which communicative context and community membership shape the emergence and impact of language use-specifically, sentiment and expressions of gratitude. We then present evidence that these language dynamics shape newcomers' likelihood of returning, although the specific impacts of different community responses are crucially modulated by the context of the newcomer's first contact with the community.

Sublexical cues affect degraded speech processing: insights from fMRI.

In natural listening situations, speech perception is often impaired by degraded speech sounds arriving at the ear. Contextual speech information can improve the perception of degraded speech and modify neuronal responses elicited by degraded speech. However, most studies on context effects on neural responses to degraded speech confounded lexico-semantic and sublexical cues. Here, we used fMRI to investigate how prior sublexical speech (e.g. pseudowords cues) affects neural responses to degraded sublexical speech and hence its processing and recognition. Each trial consisted of three consecutively presented pseudowords, of which the first and third were identical and degraded. The second pseudoword was always presented in clear form and either matched or did not match the degraded pseudowords. Improved speech processing through sublexical processing was associated with BOLD activation increases in frontal, temporal, and parietal regions, including the primary auditory cortex (PAC), posterior superior temporal cortex, angular gyrus, supramarginal gyrus, middle temporal cortex, and somato-motor cortex. These brain regions are part of a speech processing network and are involved in lexico-semantic processing. To further investigate the adaptive changes in PAC, we conducted a bilateral region of interest analysis on PAC subregions. PAC ROIs showed bilaterally increased activation in the match condition compared with the mismatch condition. Our results show that the perception of unintelligible degraded speech is improved and the neuronal population response is enhanced after exposure to intact sublexical cues. Furthermore, our findings indicate that the processing of clear meaningless sublexical speech preceding degraded speech could enhance the activity in the brain regions that belong to the cortical speech processing network previously reported in studies investigating lexico-semantic speech.

Gender bias in academia: A lifetime problem that needs solutions.

Despite increased awareness of the lack of gender equity in academia and a growing number of initiatives to address issues of diversity, change is slow, and inequalities remain. A major source of inequity is gender bias, which has a substantial negative impact on the careers, work-life balance, and mental health of underrepresented groups in science. Here, we argue that gender bias is not a single problem but manifests as a collection of distinct issues that impact researchers' lives. We disentangle these facets and propose concrete solutions that can be adopted by individuals, academic institutions, and society.

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity.

The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2's unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.

MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis.

The development of the Brain Imaging Data Structure (BIDS; Gorgolewski et al., 2016) gave the neuroscientific community a standard to organize and share data. BIDS prescribes file naming conventions and a folder structure to store data in a set of already existing file formats. Next to rules about organization of the data itself, BIDS provides standardized templates to store associated metadata in the form of Javascript Object Notation (JSON) and tab separated value (TSV) files. It thus facilitates data sharing, eases metadata querying, and enables automatic data analysis pipelines. BIDS is a rich system to curate, aggregate, and annotate neuroimaging databases.

Decoding spectrotemporal features of overt and covert speech from the human cortex.

Auditory perception and auditory imagery have been shown to activate overlapping brain regions. We hypothesized that these phenomena also share a common underlying neural representation. To assess this, we used electrocorticography intracranial recordings from epileptic patients performing an out loud or a silent reading task. In these tasks, short stories scrolled across a video screen in two conditions: subjects read the same stories both aloud (overt) and silently (covert). In a control condition the subject remained in a resting state. We first built a high gamma (70-150 Hz) neural decoding model to reconstruct spectrotemporal auditory features of self-generated overt speech. We then evaluated whether this same model could reconstruct auditory speech features in the covert speech condition. Two speech models were tested: a spectrogram and a modulation-based feature space. For the overt condition, reconstruction accuracy was evaluated as the correlation between original and predicted speech features, and was significant in each subject (p < 10(-5); paired two-sample t-test). For the covert speech condition, dynamic time warping was first used to realign the covert speech reconstruction with the corresponding original speech from the overt condition. Reconstruction accuracy was then evaluated as the correlation between original and reconstructed speech features. Covert reconstruction accuracy was compared to the accuracy obtained from reconstructions in the baseline control condition. Reconstruction accuracy for the covert condition was significantly better than for the control condition (p < 0.005; paired two-sample t-test). The superior temporal gyrus, pre- and post-central gyrus provided the highest reconstruction information. The relationship between overt and covert speech reconstruction depended on anatomy. These results provide evidence that auditory representations of covert speech can be reconstructed from models that are built from an overt speech data set, supporting a partially shared neural substrate.

Combined process automation for large-scale EEG analysis.

Epileptogenesis is a dynamic process producing increased seizure susceptibility. Electroencephalography (EEG) data provides information critical in understanding the evolution of epileptiform changes throughout epileptic foci. We designed an algorithm to facilitate efficient large-scale EEG analysis via linked automation of multiple data processing steps. Using EEG recordings obtained from electrical stimulation studies, the following steps of EEG analysis were automated: (1) alignment and isolation of pre- and post-stimulation intervals, (2) generation of user-defined band frequency waveforms, (3) spike-sorting, (4) quantification of spike and burst data and (5) power spectral density analysis. This algorithm allows for quicker, more efficient EEG analysis.