S. Nakagawa

Best Paper awards lack transparency, inclusivity, and support for Open Science

This paper surveys 222 Best Paper awards across disciplines and finds they lack transparency, inclusivity, and support for Open Science, with geographic and gender biases.

Keywords to success: a practical guide to maximise the visibility and impact of academic papers

The paper provides evidence-based recommendations to improve the discoverability and impact of academic papers through optimized use of keywords and abstract structure.

Comprehensive and quantitative analysis of intracellular structure polarization at the apical-basal axis in elongating Arabidopsis zygotes

The paper quantitatively analyzes intracellular structure polarization along the apical-basal axis in Arabidopsis zygotes and links compartmentalization to asymmetric cell division positioning.

Shell protein composition specified by NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles

The paper identifies how NEAT1 domains specify shell protein composition in paraspeckles, enabling their independence from nuclear speckles through phase separation.

The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle

This paper shows that the nuclear paraspeckle dynamically regulates inflammatory gene expression in macrophages, essential for controlling pathogen replication.

No general effects of advancing male age on ejaculates: a meta-analysis across the animal kingdom

This study conducts a meta-analysis of 1814 effect sizes from 379 studies to assess male reproductive senescence across species, finding no general pattern and highlighting taxonomic and methodological factors influencing results.

Taxonomy of interventions at academic institutions to improve research quality

This paper reviews and classifies interventions at academic institutions to improve research quality, reproducibility, and reduce waste by analyzing 11 peer-reviewed articles and 93 interventions.

SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant

This study identifies the S375F mutation in the Omicron spike protein as responsible for its reduced cleavage efficiency, fusogenicity, and rapid spread.

Sex differences in allometry for mouse phenotypic traits indicate that females are not scaled males

The paper quantifies sex differences in allometric relationships for 375 phenotypic traits in mice, finding that body weight differences do not fully explain sex differences in trait values.

NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data

The paper introduces NeoRdRp, a dataset of RNA-dependent RNA polymerase (RdRp) HMM profiles for identifying RNA viruses from metatranscriptomic data, showing improved detection compared to existing methods.

Ineffective neutralization of the SARS-CoV-2 Mu variant by convalescent and vaccine sera

This study shows that Mu variant is highly resistant to neutralization by convalescent and vaccine sera compared to other variants.

SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance

The paper investigates the SARS-CoV-2 Lambda variant, finding it more infectious due to specific mutations and better immune evasion, contributing to its spread in South America.

Planned missing data design: stronger inferences, increased research efficiency and improved animal welfare in ecology and evolution

This paper introduces planned missing data design (PMDD) as a strategy to improve statistical power, animal welfare, and research efficiency in ecology and evolution with high missing data rates.

Identification of the cell-type-specific ER membrane protein Tanmp expressed in hypothalamic tanycytes and subsets of neurons

The paper identifies Tanmp, an ER membrane protein specifically expressed in hypothalamic tanycytes and some neurons, and reports its association with mitochondrial ATPase.

SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances viral fusogenicity and pathogenicity

This study shows the P681R mutation in the SARS-CoV-2 spike protein enhances fusogenicity and pathogenicity in the Delta variant compared to the prototypic virus.

An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity

This study identifies two SARS-CoV-2 mutations, L452R and Y453F, that evade HLA-restricted cellular immunity and increase viral infectivity.

MinION™, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting

The paper demonstrates that MinION sequencing enables rapid, high-resolution analysis of vaginal microbiota in a clinical setting, identifying species-level profiles associated with health and disease.

Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene

The paper investigates how mutations in the nsp14 gene of SARS-CoV-2 affect genomic diversity and evolution, finding that the P203L mutation increases evolutionary rate and genomic variation.

Paternal hypoxia exposure primes offspring for increased hypoxia resistance

This study shows that paternal hypoxia exposure increases offspring hypoxia tolerance through upregulated hemoglobin genes, without detectable methylation changes.

Low Repeatability of Aversive Learning in Zebrafish (Danio rerio)

This study finds low repeatability of aversive learning in zebrafish, suggesting weak individual differences or genetic variance depletion due to selection pressure.

Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer

This study develops a method to rapidly profile drug-resistant bacteria using DNA-binding dyes and nanopore sequencing.

A novel RyR1 inhibitor prevents and rescues sudden death in a mouse model of malignant hyperthermia and heat stroke

This study introduces a novel RyR1 inhibitor that prevents and rescues MH and heat stroke in mouse models, offering improved solubility and clearance compared to dantrolene.

Sexual conflict mediated by ecological sex differences can generate diverse patterns of transgenerational plasticity

The paper uses an individual-based model to show that sexual conflict can lead to diverse sex-specific transgenerational plasticity patterns, including non-adaptive responses.

Activity-specificity trade-off gives PI5P4Kβ a nucleotide preference to function as a GTP-sensing kinase.

This study identifies the TRNVF motif as responsible for PI5P4Kβ's GTP binding and extended specificity to ITP and XTP, showing how its GTP preference allows it to function as a GTP sensor despite low cellular concentrations of ITP and XTP.

Sex and Power: sexual dimorphism in trait variability and its eco-evolutionary and statistical implications

The paper tests sex differences in trait variability using mouse data, finding trait-dependent patterns that challenge existing hypotheses and highlight eco-evolutionary and statistical implications.

SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant

This paper shows that SARS-CoV-2 ORF3b is a potent interferon antagonist, with a naturally occurring longer variant enhancing its anti-interferon activity in severe COVID-19 cases.

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

This study compares full-length and short-read 16S rRNA gene sequencing using MinION and conventional methods to assess species-level resolution in human gut microbiota.

Consistent trade-offs in ecosystem services between land covers with different production intensities

The paper quantifies ecosystem service supply across different land covers in New Zealand, finding consistent trade-offs between high-intensity production and extensive/no production land covers, but no distinct patterns for forest cover.

Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam

The paper characterizes blaNDM-1-carrying plasmids in Vietnamese Enterobacterales isolates, identifying horizontal plasmid transfer and resistance gene co-occurrence.

Conditional repeatability and the variance explained by reaction norm variation in random slope models

The paper introduces conditional repeatability as a measure of between-individual variation in response to environmental gradients, providing equations and recommendations for its calculation and reporting.