Evaluated articles

eLife Assessment

This fundamental study describes patterns of anatomical connectivity between the cortex and the thalamus using magnetic resonance imaging data in humans and non-human primates. The measures are related to numerous other modalities to develop a robust understanding of the organisation of the system. The authors provide convincing evidence that there is a difference between sensory and association cortices in terms of their connectivity with the thalamus, which may have downstream effects on brain function. This work will be of interest to neuroscientists interested in the organization and dynamics of cortico-thalamic circuits.

eLife Assessment:

This fundamental study substantially advances our understanding of the role of different-sized soil invertebrates in shaping the rates of leaf litter decomposition, using an experiment across seasons along an aridity gradient. The authors provide compelling evidence that the summed effects of all invertebrates (with large-sized invertebrates being more active in summer and small-sized invertebrates in winter) on decomposition rates result in similar levels of leaf litter decomposition across seasons. The work will be of broad relevance to ecosystem ecologists interested in soil food webs, and researchers interested in modeling carbon cycles to understand global warming.

eLife assessment

This study presents important findings on the differential activity of noradrenergic and dopaminergic input to dorsal hippocampus CA1 in head-fixed mice traversing a runway in a virtual environment that is familiar or novel. The data are rigorously analysed, and the observed divergence in the dynamics of activity in the dopaminergic and noradrenergic axons is solid. Future studies, using specific manipulations of the two distinct midbrain inputs combined with behavioral testing, are required to strengthen the claim that distinct signals to the hippocampus cause distinct behavioral effects.

eLife Assessment

This important study introduces a new cortical circuit model for predictive processing. Simulations effectively illustrate that, with appropriate synaptic plasticity, a canonical layer 2/3 cortical circuit - comprising two classes of interneurons providing subtractive and divisive inhibition - can generate uncertainty-modulated prediction errors by pyramidal neurons. The model is compelling; although it relies on many assumptions and has not yet been compared directly to data, the model does align with empirical observations and yields a range of testable predictions. The study is expected to be of great interest to those involved in cortical and predictive processing research.

eLife Assessment

TDP-43 mislocalization is a key feature of some neurodegenerative diseases, but cellular models are lacking. The authors endogenously-tagged TDP-43 with a C-terminal GFP tag in human iPSCs, followed by expression of an intrabody-NES that targeted GFP to the cytosol. They convincingly report physical mislocalization and functional depletion of TDP-43, as measured by microscopy and RNAseq. This method will be valuable to investigators studying the biological consequences of TDP-43 mislocalization and the methodology is in line with the current state-of-the-art.

eLife assessment

This manuscript presents an important analysis of the role that the nucleosome acidic patch plays in SWR1-catalyzed histone exchange. This manuscript contains convincing data which significantly expands our understanding of the complex process of H2A.Z deposition by SWR1 and therefore would be of interest to a broad readership.

eLife assessment

This study presents a rather valuable finding on the RBM7 function in spicing regulation and uncharacterized role of MFGE8 splicing alteration in breast cancer metastasis. The evidence supporting the claims of the authors is solid. The work will be of broad interest to clinicians, medical researchers and scientists working on breast cancer.

eLife assessment

This useful study utilizes proteomics analysis across a large panel of 51 cancer cell lines to elucidate mechanisms underlying the sensitivity of cancer cells to high-dose vitamin C (Ascorbate). While the associations between specific molecular pathways and sensitivity to ascorbate are interesting, a major limitation is that the study is largely descriptive and incomplete, lacking evidence on the molecular underpinnings of cancer cells' sensitivity to high-dose vitamin C.

eLife Assessment

This computational study integrates detailed electrophysiology and mechanical contraction predictions, which are often modeled separately. The findings of this important work are that abnormal ECGs that are associated with higher risk of sudden cardiac death are predicted to have almost no relationship with left ventricular ejection fraction, which is conventionally used as a risk factor for arrhythmia. The conclusions are based on compelling evidence for the need of incorporating additional risk factors for assessing post-myocardial infarction patients.

eLife Assessment

This study reports differences in proteomic profiles of embryonic versus induced pluripotent stem cells. This important finding cautions against the interchangeable use of both types of cells in biomedical research, although the mechanisms responsible for these differences remains unknown. The proteomic evidence is convincing, even though there is limited validation with other methods.

eLife Assessment

This study reports important findings on identifying sequence motifs that predict substrate specificity in a class of lipid synthesis enzymes. It sheds light on a mechanism used by bacteria to modify the lipids in their membrane to develop antibiotic resistance. The evidence is compelling, with a careful application of machine learning methods, validated by mass spectrometry-based lipid analysis experiments. This interdisciplinary study will be of interest to computational biologists and to the community working on lipids and on enzymes involved in lipid synthesis or modification.

eLife Assessment

The authors analyses describe a novel mechanism by which a retrotransposon-derived LTR may be involved in genomic imprinting and demonstrate imprinting of the ZDBF2 locus in rabbits and Rhesus macaques using allele-specific expression analysis. This imprinting of the ZDBF2 locus correlates with transcription of GPR1-AS orthologs. The accompanying genomic analysis is very well executed allowing for the conclusions reached in the manuscript. The revisions made at the request of the reviewers in this important manuscript strengthen the evidence from the genomic analyses, and as a result, the evidence is now convincing and will be informative to the genomics and developmental biology communities.

eLife Assessment

This valuable study addresses a central question in systems neuroscience (validation of active inference models of exploration) using a combination of behaviour, neuroimaging, and modelling. The data provided offers solid evidence that humans do perceive, choose and learn in a manner consistent with the essential ingredients of active inference, and that quantities that correlate with relevant parameters of this active inference scheme are encoded in different regions of the brain.

eLife assessment

This article reports an important bioluminescence-based reporter system to evaluate kinase conformations. This assay is applied to four different kinases that have unique, very special regulatory features, thereby indicating that the assay can be used to provide convincing evidence on the conformational state of a large number of kinases. This paper will be of interest to researchers working on kinases and their conformational states.

eLife Assessment

This important study reports on PI3KR mutations and a paradoxical mechanism of PI3KR signaling. The strength of evidence for the study is mostly convincing, as conclusions are supported by a variety of mutational strategies and cellular systems to look at interactions among signaling pathways.

eLife assessment

The authors address the function of keratin 17 (K17), a marker of the most aggressive pancreatic ductal adenocarcinomas (PDACs). While this potentially useful study addresses a significant area of pancreatic cancer research, the lack of evidence demonstrating nuclear localization of K17 in human PDAC and the excessive reliance on a single cell line reduce the significance of the work. Moreover, the weak phenotypes of K17 phosphosite mutants provide incomplete support for the authors' mechanistic model.

eLife assessment

This important work suggests that the observed cosine-like activity in the head direction circuit of insects not only subserves vector addition but also minimizes noise in the representation. The authors provide solid evidence using the locust and fruit fly connectomes. The work raises important theoretical questions about the organization of the navigation system and will be of interest to theoretical and experimental researchers studying navigation.

eLife assessment

This study provides a fundamental advance in palaeontology by reporting the fossils of a new invertebrate, Beretella spinosa, and inferring its relationship with already described species. The analysis placed the newly described species in the earliest branch of moulting invertebrates. The study, supported by convincing fossil observation, hypothesizes that early moulting invertebrate animals were not vermiform.

eLife Assessment

This is a saturation mutagenesis screening of CDKN2A gene, successfully assessing the functionality of the missense variants. The work is solid and well-prosecuted. The manuscript was improved during the revision process and this work will serve as a valuable resource for diagnostic labs as well as cancer geneticists.

eLife assessment

The work by Lewis and co-workers presents important findings on the role of myosin structure/energetics on the molecular mechanisms of hibernation by comparing muscle samples from small and large hibernating mammals. The solid methodological approaches have revealed insights into the mechanisms of non-shivering thermogenesis and energy expenditure.