The ParlaMint corpora of parliamentary proceedings.

This paper presents the ParlaMint corpora containing transcriptions of the sessions of the 17 European national parliaments with half a billion words. The corpora are uniformly encoded, contain rich meta-data about 11 thousand speakers, and are linguistically annotated following the Universal Dependencies formalism and with named entities. Samples of the corpora and conversion scripts are available from the project's GitHub repository, and the complete corpora are openly available via the CLARIN.SI repository for download, as well as through the NoSketch Engine and KonText concordancers and the Parlameter interface for on-line exploration and analysis.

Understanding the Impacts of Online Mental Health Peer Support Forums: Realist Synthesis.

BACKGROUND: Online forums are widely used for mental health peer support. However, evidence of their safety and effectiveness is mixed. Further research focused on articulating the contexts in which positive and negative impacts emerge from forum use is required to inform innovations in implementation. OBJECTIVE: This study aimed to develop a realist program theory to explain the impacts of online mental health peer support forums on users. METHODS: We conducted a realist synthesis of literature published between 2019 and 2023 and 18 stakeholder interviews with forum staff. RESULTS: Synthesis of 102 evidence sources and 18 interviews produced an overarching program theory comprising 22 context-mechanism-outcome configurations. Findings indicate that users' perceptions of psychological safety and the personal relevance of forum content are foundational to ongoing engagement. Safe and active forums that provide convenient access to information and advice can lead to improvements in mental health self-efficacy. Within the context of welcoming and nonjudgmental communities, users may benefit from the opportunity to explore personal difficulties with peers, experience reduced isolation and normalization of mental health experiences, and engage in mutual encouragement. The program theory highlights the vital role of moderators in creating facilitative online spaces, stimulating community engagement, and limiting access to distressing content. A key challenge for organizations that host mental health forums lies in balancing forum openness and anonymity with the need to enforce rules, such as restrictions on what users can discuss, to promote community safety. CONCLUSIONS: This is the first realist synthesis of online mental health peer support forums. The novel program theory highlights how successful implementation depends on establishing protocols for enhancing safety and strategies for maintaining user engagement to promote forum sustainability. TRIAL REGISTRATION: PROSPERO CRD42022352528; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=352528.

Improving Peer Online Forums (iPOF): protocol for a realist evaluation of peer online mental health forums to inform practice and policy.

INTRODUCTION: Peer online mental health forums are commonly used and offer accessible support. Positive and negative impacts have been reported by forum members and moderators, but it is unclear why these impacts occur, for whom and in which forums. This multiple method realist study explores underlying mechanisms to understand how forums work for different people. The findings will inform codesign of best practice guidance and policy tools to enhance the uptake and effectiveness of peer online mental health forums. METHODS AND ANALYSIS: In workstream 1, we will conduct a realist synthesis, based on existing literature and interviews with approximately 20 stakeholders, to generate initial programme theories about the impacts of forums on members and moderators and mechanisms driving these. Initial theories that are relevant for forum design and implementation will be prioritised for testing in workstream 2.Workstream 2 is a multiple case study design with mixed methods with several online mental health forums differing in contextual features. Quantitative surveys of forum members, qualitative interviews and Corpus-based Discourse Analysis and Natural Language Processing of forum posts will be used to test and refine programme theories. Final programme theories will be developed through novel triangulation of the data.Workstream 3 will run alongside workstreams 1 and 2. Key stakeholders from participating forums, including members and moderators, will be recruited to a Codesign group. They will inform the study design and materials, refine and prioritise theories, and codesign best policy and practice guidance. ETHICS AND DISSEMINATION: Ethical approval was granted by Solihull Research Ethics Committee (IRAS 314029). Findings will be reported in accordance with RAMESES (Realist And MEta-narrative Evidence Syntheses: Evolving Standards) guidelines, published as open access and shared widely, along with codesigned tools. TRIAL REGISTRATION NUMBER: ISRCTN 62469166; the protocol for the realist synthesis in workstream one is prospectively registered at PROSPERO CRD42022352528.

De novo assembly of highly diverse viral populations.

BACKGROUND: Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. RESULTS: We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. CONCLUSIONS: We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon-gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology.