VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells.

Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell RNA-sequencing, we develop VarID2 for the quantification of biological noise at single-cell resolution. VarID2 reveals enhanced nuclear versus cytoplasmic noise, and distinct regulatory modes stratified by correlation between noise, expression, and chromatin accessibility.

Data-Driven Pupil Response Profiles as Transdiagnostic Readouts for the Detection of Neurocognitive Functioning in Affective and Anxiety Disorders.

Background: Neurocognitive functioning is a relevant transdiagnostic dimension in psychiatry. As pupil size dynamics track cognitive load during a working memory task, we aimed to explore if this parameter allows identification of psychophysiological subtypes in healthy participants and patients with affective and anxiety disorders.

Methods: Our sample consisted of 226 participants who completed the n-back task during simultaneous functional magnetic resonance imaging and pupillometry measurements.

Structural and Functional Brain Patterns Predict Formal Thought Disorder's Severity and Its Persistence in Recent-Onset Psychosis: Results From the PRONIA Study.

Background: Formal thought disorder (FThD) is a core feature of psychosis, and its severity and long-term persistence relates to poor clinical outcomes. However, advances in developing early recognition and management tools for FThD are hindered by a lack of insight into the brain-level predictors of FThD states and progression at the individual level.

Methods: Two hundred thirty-three individuals with recent-onset psychosis were drawn from the multisite European Prognostic Tools for Early Psychosis Management study.

Diversity of Ganglion Cell Responses to Saccade-Like Image Shifts in the Primate Retina.

Saccades are a fundamental part of natural vision. They interrupt fixations of the visual gaze and rapidly shift the image that falls onto the retina. These stimulus dynamics can cause activation or suppression of different retinal ganglion cells, but how they affect the encoding of visual information in different types of ganglion cells is largely unknown.

Asymmetric distribution of color-opponent response types across mouse visual cortex supports superior color vision in the sky.

Color is an important visual feature that informs behavior, and the retinal basis for color vision has been studied across various vertebrate species. While many studies have investigated how color information is processed in visual brain areas of primate species, we have limited understanding of how it is organized beyond the retina in other species, including most dichromatic mammals. In this study, we systematically characterized how color is represented in the primary visual cortex (V1) of mice.

Visualizing incompatibilities in phylogenetic trees using consensus outlines.

Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis. A consensus tree is often used to summarize what the trees have in common. Consensus networks were introduced to also allow the visualization of the main incompatibilities among the trees.

Information theoretic measures of causal influences during transient neural events.

Transient phenomena play a key role in coordinating brain activity at multiple scales, however their underlying mechanisms remain largely unknown. A key challenge for neural data science is thus to characterize the network interactions at play during these events. Using the formalism of Structural Causal Models and their graphical representation, we investigate the theoretical and empirical properties of Information Theory based causal strength measures in the context of recurring spontaneous transient events.

Effects of urban living environments on mental health in adults.

Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms.

Rearing is critical for forming spatial representations in pre-weanling rats.

Rearing, i.e., standing on the hind limbs in an upright posture, is part of a rat's innate exploratory motor program.

Practice walking on a treadmill-mounted balance beam modifies beam walking sacral movement and alters performance in other balance tasks.

The goals of this study were to determine if a single 30-minute session of practice walking on a treadmill mounted balance beam: 1) altered sacral marker movement kinematics during beam walking, and 2) affected measures of balance during treadmill walking and standing balance. Two groups of young, healthy human subjects practiced walking on a treadmill mounted balance beam for thirty minutes. One group trained with intermittent visual occlusions and the other group trained with unperturbed vision.

Latent Transitions of Census-level Deprivation and Network Analysis of Conduct Problem Behaviours.

Conduct problems are more prevalent in neighbourhoods that have a vulnerable structure (e.g., high neighbourhood-level deprivation) and disarranged interpersonal characteristics (e.

Link updating strategies influence consensus decisions as a function of the direction of communication.

Consensus decision-making in social groups strongly depends on communication links that determine to whom individuals send, and from whom they receive, information. Here, we ask how consensus decisions are affected by strategic updating of links and how this effect varies with the direction of communication. We quantified the coevolution of link and opinion dynamics in a large population with binary opinions using mean-field numerical simulations of two voter-like models of opinion dynamics: an incoming model (IM) (where individuals choose who to receive opinions from) and an outgoing model (OM) (where individuals choose who to send opinions to).

An integrated cell atlas of the lung in health and disease.

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population.

Direct fluorescent labeling of NF186 and NaV1.6 in living primary neurons using bioorthogonal click chemistry.

The axon initial segment (AIS) is a highly specialized neuronal compartment that regulates the generation of action potentials and maintenance of neuronal polarity. Live imaging of the AIS is challenging due to the limited number of suitable labeling methods. To overcome this limitation, we established a novel approach for live labeling of the AIS using unnatural amino acids (UAAs) and click chemistry.

The effect of context congruency on fMRI repetition suppression for objects.

The recognition of objects is strongly facilitated when they are presented in the context of other objects (Biederman, 1972). Such contexts facilitate perception and induce expectations of context-congruent objects (Trapp and Bar, 2015). The neural mechanisms underlying these facilitatory effects of context on object processing, however, are not yet fully understood.

MAIRA: Protein-based Analysis of MinION Reads on a Laptop.

Third-generation sequencing technologies are being increasingly used in microbiome research and this has given rise to new challenges in computational microbiome analysis. Oxford Nanopore's MinION is a portable sequencer that streams data that can be basecalled on-the-fly. Here we give an introduction to the MAIRA software, which is designed to analyze MinION sequencing reads from a microbiome sample, as they are produced in real-time, on a laptop.

DIAMOND + MEGAN Microbiome Analysis.

Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments.

Neural representations of the content and production of human vocalization.

Speech, as the spoken form of language, is fundamental for human communication. The phenomenon of covert inner speech implies functional independence of speech content and motor production. However, it remains unclear how a flexible mapping between speech content and production is achieved on the neural level.

Sex-specific and opposed effects of FKBP51 in glutamatergic and GABAergic neurons: Implications for stress susceptibility and resilience.

Mental health disorders often arise as a combination of environmental and genetic factors. The gene, encoding the GR co-chaperone FKBP51, has been uncovered as a key genetic risk factor for stress-related illness. However, the exact cell type and region-specific mechanisms by which FKBP51 contributes to stress resilience or susceptibility processes remain to be unravelled.

Mutual repression between JNK/AP-1 and JAK/STAT stratifies senescent and proliferative cell behaviors during tissue regeneration.

Epithelial repair relies on the activation of stress signaling pathways to coordinate tissue repair. Their deregulation is implicated in chronic wound and cancer pathologies. Using TNF-α/Eiger-mediated inflammatory damage to Drosophila imaginal discs, we investigate how spatial patterns of signaling pathways and repair behaviors arise.

New in, old out: Does learning a new language make you forget previously learned foreign languages?

Anecdotal evidence suggests that learning a new foreign language (FL) makes you forget previously learned FLs. To seek empirical evidence for this claim, we tested whether learning words in a previously unknown L3 hampers subsequent retrieval of their L2 translation equivalents. In two experiments, Dutch native speakers with knowledge of English (L2), but not Spanish (L3), first completed an English vocabulary test, based on which 46 participant-specific, known English words were chosen.

The long-loop recycling (LLR) of synaptic components as a question of economics.

The pre- and post-synaptic compartments contain a variety of molecules that are known to recycle between the plasma membrane and intracellular organelles. The recycling steps have been amply described in functional terms, with, for example, synaptic vesicle recycling being essential for neurotransmitter release, and postsynaptic receptor recycling being a fundamental feature of synaptic plasticity. However, synaptic protein recycling may also serve a more prosaic role, simply ensuring the repeated use of specific components, thereby minimizing the energy expenditure on the synthesis of synaptic proteins.

Robust encoding of natural stimuli by neuronal response sequences in monkey visual cortex.

Parallel multisite recordings in the visual cortex of trained monkeys revealed that the responses of spatially distributed neurons to natural scenes are ordered in sequences. The rank order of these sequences is stimulus-specific and maintained even if the absolute timing of the responses is modified by manipulating stimulus parameters. The stimulus specificity of these sequences was highest when they were evoked by natural stimuli and deteriorated for stimulus versions in which certain statistical regularities were removed.