Patient-reported symptomatic events do not adequately reflect atrial arrhythmia

BACKGROUND

Management of atrial fibrillation is frequently geared toward improving symptoms. Yet, the magnitude of symptom-rhythm discordance is not well known in the setting of monitoring by ambulatory electrocardiography (AECG).

OBJECTIVE

We aimed to quantify the symptom-rhythm correlation (SRC) for atrial arrhythmia (atrial tachycardia/atrial fibrillation [AT/AF]) events.

METHODS

This was a retrospective cohort analysis of AECG data at a tertiary care center. All AECGs of ≥7 days with at least 1 AT/AF were included. Patient-triggered symptoms included shortness of breath, tiredness, palpitations, dizziness, or passing out with or without concurrent AT/AF. SRC was calculated for each patient. In addition, AT/AF-symptom association was evaluated at the event level by multivariable mixed effects logistic regression.

RESULTS

We identified 742 patients with qualifying AECG data; mean age was 64 years, 50% were female, and 22% had heart failure. The mean CHA2DS2-VASc score was 2.5. There were 6289 symptomatic events and 6900 AT/AF episodes. Of symptomatic events, 1013 (16%) had shortness of breath, 839 (13%) tiredness, 2640 (42%) palpitations, 783 (12%) dizziness, and 93 (1%) passing out. Overall SRC was 0.39 (range, 0-1.0), but presence of AT/AF increased odds of symptoms by ∼8.3 times in adjusted analyses (P < .01). In multivariable analysis, prior AF rhythm control treatment and lower heart rate were associated with worse SRC (P < .01).

CONCLUSION

Whereas AT/AF events increase the chances of symptoms, there is poor overall correlation between symptomatic events and documented AT/AF. Patient factors and prior treatments influence SRC. An improved understanding of this relationship correlation is needed to optimize clinical outcomes and to improve the rigor of AF research.

A single-nuclei paired multiomic analysis of the human midbrain reveals age- and Parkinson's disease-associated glial changes

Age is the primary risk factor for Parkinson's disease (PD), but how aging changes the expression and regulatory landscape of the brain remains unclear. Here we present a single-nuclei multiomic study profiling shared gene expression and chromatin accessibility of young, aged and PD postmortem midbrain samples. Combined multiomic analysis along a pseudopathogenesis trajectory reveals that all glial cell types are affected by age, but microglia and oligodendrocytes are further altered in PD. We present evidence for a disease-associated oligodendrocyte subtype and identify genes lost over the aging and disease process, including CARNS1, that may predispose healthy cells to develop a disease-associated phenotype. Surprisingly, we found that chromatin accessibility changed little over aging or PD within the same cell types. Peak-gene association patterns, however, are substantially altered during aging and PD, identifying cell-type-specific chromosomal loci that contain PD-associated single-nucleotide polymorphisms. Our study suggests a previously undescribed role for oligodendrocytes in aging and PD.

Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures

BACKGROUND

Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science.

RESULTS

Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice.

CONCLUSIONS

C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.

Convergent evolutionary patterns of heterostyly across angiosperms support the pollination-precision hypothesis

Since the insights by Charles Darwin, heterostyly, a floral polymorphism with morphs bearing stigmas and anthers at reciprocal heights, has become a model system for the study of natural selection. Based on his archetypal heterostylous flower, including regular symmetry, few stamens and a tube, Darwin hypothesised that heterostyly evolved to promote outcrossing through efficient pollen transfer between morphs involving different areas of a pollinator's body, thus proposing his seminal pollination-precision hypothesis. Here we update the number of heterostylous and other style-length polymorphic taxa to 247 genera belonging to 34 families, notably expanding known cases by 20%. Using phylogenetic and comparative analyses across the angiosperms, we show numerous independent origins of style-length polymorphism associated with actinomorphic, tubular flowers with a low number of sex organs, stamens fused to the corolla, and pollination by long-tongued insects. These associations provide support for the Darwinian pollination-precision hypothesis as a basis for convergent evolution of heterostyly across angiosperms.

Unveiling functional linkages between habitats and organisms: Macroalgal habitats as influential factors of fish functional traits

Understanding the relationship between the characteristics of habitats and their associated community is essential to comprehend the functioning of ecological systems and prevent their degradation. This is particularly relevant for in decline, habitat-forming species, such as macroalgae, which support diverse communities of fish in temperate rocky reefs. To understand the link between the functional habitats of macroalgae and the functional dimension of their associated fish communities, we used a standardized underwater visual census to quantify the macroalgal functional diversity, as well as the functional diversity, redundancy, and richness of fish communities in 400 sites scattered in three southern temperate marine realms. Our findings reveal that functional macroalgal habitats can be classified into three groups that shape the functional diversity, redundancy, and richness of fish when considering trait commonness. These results enhance our comprehension of the functional connections between the habitat and coexisting fish within marine ecosystems, providing valuable insights for the preservation of these habitats.

Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains

The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.

Ancient insect vision tuned for flight among rocks and plants underpins natural flower colour diversity

Understanding the origins of flower colour signalling to pollinators is fundamental to evolutionary biology and ecology. Flower colour evolves under pressure from visual systems of pollinators, like birds and insects, to establish global signatures among flowers with similar pollinators. However, an understanding of the ancient origins of this relationship remains elusive. Here, we employ computer simulations to generate artificial flower backgrounds assembled from real material sample spectra of rocks, leaves and dead plant materials, against which to test flowers' visibility to birds and bees. Our results indicate how flower colours differ from their backgrounds in strength, and the distributions of salient reflectance features when perceived by these key pollinators, to reveal the possible origins of their colours. Since Hymenopteran visual perception evolved before flowers, the terrestrial chromatic context for its evolution to facilitate flight and orientation consisted of rocks, leaves, sticks and bark. Flowers exploited these pre-evolved visual capacities of their visitors, in response evolving chromatic features to signal to bees, and differently to birds, against a backdrop of other natural materials. Consequently, it appears that today's flower colours may be an evolutionary response to the vision of diurnal pollinators navigating their world millennia prior to the first flowers.

Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity

Advances in single-cell technology have enabled molecular dissection of heterogeneous biospecimens at unprecedented scales and resolutions. Cluster-centric approaches are widely applied in analyzing single-cell data, however they have limited power in dissecting and interpreting highly heterogenous, dynamically evolving data. Here, we present GSDensity, a graph-modeling approach that allows users to obtain pathway-centric interpretation and dissection of single-cell and spatial transcriptomics (ST) data without performing clustering. Using pathway gene sets, we show that GSDensity can accurately detect biologically distinct cells and reveal novel cell-pathway associations ignored by existing methods. Moreover, GSDensity, combined with trajectory analysis can identify curated pathways that are active at various stages of mouse brain development. Finally, GSDensity can identify spatially relevant pathways in mouse brains and human tumors including those following high-order organizational patterns in the ST data. Particularly, we create a pan-cancer ST map revealing spatially relevant and recurrently active pathways across six different tumor types.

Evaluating the interplay between estrous cyclicity and flurothyl-induced seizure susceptibility in Scn2a K1422E mice

Recently, we demonstrated that Scn2a K1422E female mice showed a distinct distribution of flurothyl-induced seizure thresholds. To evaluate whether the estrous cycle contributes to this effect, estrous cycle monitoring was performed in mice that had undergone ovariectomy, sham surgery, or no treatment prior to seizure induction. Ovariectomy did not affect the non-unimodal distribution of flurothyl seizure thresholds observed in Scn2a K1422E females. Additionally, seizure thresholds were not associated with estrous cycle stage in mice that underwent sham surgery or in non-surgerized (intact) mice. Interestingly, intact Scn2a K1422E females showed evidence of disrupted estrous cyclicity, an effect not previously described in a genetic epilepsy model.

Detection and annotation of transposable element insertions and deletions on the human genome using nanopore sequencing

Repetitive sequences represent about 45% of the human genome. Some are transposable elements (TEs) with the ability to change their position in the genome, creating genetic variability both as insertions or deletions, with potential pathogenic consequences. We used long-read nanopore sequencing to identify TE variants in the genomes of 24 patients with antithrombin deficiency. We identified 7 344 TE insertions and 3 056 TE deletions, 2 926 were not previously described in publicly available databases. The insertions affected 3 955 genes, with 6 insertions located in exons, 3 929 in introns, and 147 in promoters. Potential functional impact was evaluated with gene annotation and enrichment analysis, which suggested a strong relationship with neuron-related functions and autism. We conclude that this study encourages the generation of a complete map of TEs in the human genome, which will be useful for identifying new TEs involved in genetic disorders.

Effects of Cognitive Load on Vocal Fold Vibratory Patterns in Bilingual Speakers of Low and High German

OBJECTIVES

Increased cognitive load has been observed to correlate with decreased vocal fold perturbation, reduced additive noise, increased periodicity, and a higher rate of vocal fold vibration. The aim of this study was to explore whether vocal fold vibratory patterns can serve as indicators of increased cognitive load in nonbalanced bilingual speakers when they use their weaker language.

STUDY DESIGN

This is a comparative experimental study with a within-speaker design.

METHODS

We recorded a total of 95 bilingual speakers of Low German (LG), which is an endangered language spoken in Northern Germany, and Standard High German (HG). Participants completed four tasks in both languages: engaging in free narration, describing a picture story, giving directions, and reading a narrative passage. For the last three tasks, the difficulty levels were varied. Measurements included jitter, shimmer, harmonics-to-noise ratio (HNR), cepstral peak prominence (CPP), the proportion of creak, pitch level, and pitch span. Changes in voice characteristics were examined both in terms of the participants' age and their language dominance. For the latter, we calculated a dominance score derived from age of acquisition, frequency of use, and self-perceived linguistic competence in the two languages.

RESULTS

Younger speakers showed a higher dominance of HG over LG, which decreased with age. Younger and more HG-dominant speakers exhibited lower jitter and shimmer, along with a higher HNR and a lower creak proportion in LG compared to HG. CPP and pitch level were higher in LG but showed little variation with age or language dominance. No clear effects on pitch span were observed. Overall, age was a slightly more reliable predictor than language dominance. Acoustic differences in voice quality were about equally detectable across the different speech tasks while varying difficulty levels had minimal impact.

CONCLUSIONS

The variation in vocal fold vibratory patterns suggests that younger and more HG-dominant speakers experienced greater cognitive load when speaking LG. Given that increased cognitive load may negatively impact language usage, voice analysis opens up new possibilities for evaluating the future prospects of endangered languages.

ERBB2 Amplification and HER2 Expression in Salivary Duct Carcinoma: Evaluation of Scoring Guidelines and Potential for Expanded Anti-HER2 Therapy

Salivary duct carcinoma (SDC) is aggressive with limited therapeutic options. A subset of SDC display human epidermal growth factor receptor 2 (HER2) protein overexpression by immunohistochemistry, and some show ERBB2 gene amplification. Guidelines for HER2 scoring are not firmly established. Recent advances in breast carcinoma have established a role for anti-HER2 therapies in lesions with low HER2 expression lacking ERBB2 amplification. Delineating HER2 staining patterns in SDC is critical for evaluating anti-HER2 treatments. In total, 53 cases of SDC resected at our institution between 2004 and 2020 were identified. Androgen receptor (AR) and HER2 immunohistochemistry and ERBB2 fluorescence in situ hybridization were performed in all cases. AR expression was scored for percentage positive cells and categorized as positive (>10% of cells), low positive (1%-10%), or negative (<1%). HER2 staining levels and patterns were recorded, scored using 2018 ASCO/CAP guidelines, and categorized into HER2-positive (3+ or 2+ with ERBB2 amplification), HER2-low (1+ or 2+ without ERBB2 amplification), HER2-very low (faint staining in <10% of cells), or HER2-absent types. Clinical parameters and vital status were recorded. Median age was 70 years, with a male predominance. ERBB2-amplified tumors (11/53; 20.8%) presented at lower pT stages (pTis/pT1/pT2; P = .005, Fisher exact test) and more frequently had perineural invasion (P = .007, Fisher exact test) compared with ERBB2 nonamplified tumors; no other pathologic features differed significantly by gene amplification status. In addition, 2+ HER2 staining by 2018 ASCO/CAP criteria was most common (26/53; 49%); only 4 cases (8%) were HER2-absent status; 3+ HER2 staining was found in 9 tumors, and all were ERBB2 amplified. Six patients with HER2-expressing tumors received trastuzumab therapy, including 2 with ERBB2-amplified tumors. Overall survival and recurrence-free survival did not differ significantly based on ERBB2 status. This work suggests that 2018 ASCO/CAP guidelines for HER2 evaluation in breast carcinoma could be applied to SDC. Our findings also show broad overexpression of HER2 in SDC raising the possibility that more patients may benefit from anti-HER2-directed therapies.

Differentiated, rather than shared, strategies for time-coordinated action in social and non-social domains in autistic individuals

Autism spectrum disorder (ASD) is a neurodevelopmental condition with a highly heterogeneous adult phenotype that includes social and non-social behavioral characteristics. The link between the characteristics assignable to the different domains remains unresolved. One possibility is that social and non-social behaviors in autism are modulated by a common underlying deficit. However, here we report evidence supporting an alternative concept that is individual-centered rather than deficit-centered. Individuals are assumed to have a distinctive style in the strategies they adopt to perform social and non-social tasks with these styles presumably being structured differently between autistic individuals and typically-developed (TD) individuals. We tested this hypothesis for the execution of time-coordinated (synchronized) actions. Participants performed (i) a social task that required synchronized gaze and pointing actions to interact with another person, and (ii) a non-social task that required finger-tapping actions synchronized to periodic stimuli at different time-scales and sensory modalities. In both tasks, synchronization behavior differed between ASD and TD groups. However, a principal component analysis of individual behaviors across tasks revealed associations between social and non-social features for the TD persons but such cross-domain associations were strikingly absent for autistic individuals. The highly differentiated strategies between domains in ASD are inconsistent with a general synchronization deficit and instead highlight the individualized developmental heterogeneity in the acquisition of domain-specific behaviors. We propose a cognitive model to help disentangle individual-centered from deficit-centered effects in other domains. Our findings reinforce the importance to identify individually differentiated phenotypes to personalize autism therapies.

Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex

Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than 2-fold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.

Analysis of convolutional neural networks reveals the computational properties essential for subcortical processing of facial expression

Perception of facial expression is crucial for primate social interactions. This visual information is processed through the ventral cortical pathway and the subcortical pathway. However, the subcortical pathway exhibits inaccurate processing, and the responsible architectural and physiological properties remain unclear. To investigate this, we constructed and examined convolutional neural networks with three key properties of the subcortical pathway: a shallow layer architecture, concentric receptive fields at the initial processing stage, and a greater degree of spatial pooling. These neural networks achieved modest accuracy in classifying facial expressions. By replacing these properties, individually or in combination, with corresponding cortical features, performance gradually improved. Similar to amygdala neurons, some units in the final processing layer exhibited sensitivity to retina-based spatial frequencies (SFs), while others were sensitive to object-based SFs. Replacement of any of these properties affected the coordinates of the SF encoding. Therefore, all three properties limit the accuracy of facial expression information and are essential for determining the SF representation coordinate. These findings characterize the role of the subcortical computational processes in facial expression recognition.

Morphological analysis of neck muscle nerves and neurons in cats

Previous studies have failed to show morphological differences between neck muscle alpha and gamma motor fibers or alpha and gamma motoneurons. The present study aimed to investigate the morphological features of neck muscle motor nerves and motoneurons in cats. To determine the morphological features of peripheral motor fibers, the value of the outer contours of each fiber was converted into a perfect circle after ganglionectomy to remove sensory fibers, and the fiber diameters were calculated based on their circumferences. The sizes of neck motor fibers in the peripheral nerves had an evident bimodal distribution into small and large fiber groups, as depicted in histograms. The sizes of small and large motor fibers ranged from 2 to 12 µm and from 12 to 40 µm, respectively. The small fiber group is likely to correspond to gamma motor fibers and the large fiber group to alpha motor fibers. The morphological features of neck muscle motoneurons sectioned in the horizontal plane were examined using the horseradish peroxidase (HRP) retrograde labeling technique. The diameters of the biventer cervicis and complexus motoneurons had bimodal distributions. The inflection point between the small and large diameter population was 28 µm for the biventer cervicis and 26 µm for the complexus. We also observed that larger neurons displayed more dendrites. In conclusion, we could identify morphological differences likely to correlate with alpha and gamma motoneurons in both neck muscle peripheral nerves and neck motoneurons.

Evaluating the interplay between estrous cyclicity and induced seizure susceptibility in Scn2aK1422E mice

Pathogenic variants in SCN2A are associated with a range of neurodevelopmental disorders (NDD). SCN2A-related NDD show wide phenotypic heterogeneity, suggesting that modifying factors must be considered in order to properly elucidate the mechanisms of pathogenic variants. Recently, we characterized neurological phenotypes in a mouse model of the variant SCN2A-p.K1422E. We demonstrated that heterozygous Scn2aK1422E female mice showed a distinct, reproducible distribution of flurothyl-induced seizure thresholds. Women with epilepsy often show a cyclical pattern of altered seizure susceptibility during specific phases of the menstrual cycle which can be attributed to fluctuations in hormones and corresponding changes in neurosteroid levels. Rodent models have been used extensively to examine the relationship between the estrous (menstrual) cycle, steroid hormones, and seizure susceptibility. However, the effects of the estrous cycle on seizure susceptibility have not been evaluated in the context of an epilepsy-associated genetic variant. To determine whether the estrous cycle affects susceptibility to flurothyl-induced seizures in Scn2aK1422E female mice, estrous cycle monitoring was performed in mice that had undergone ovariectomy (OVX), sham surgery, or no treatment prior to seizure induction. Removing the influence of circulating sex hormones via OVX did not affect the non-unimodal distribution of flurothyl seizure thresholds observed in Scn2aK1422E females. Additionally, flurothyl seizure thresholds were not associated with estrous cycle stage in mice that underwent sham surgery or were untreated. These data suggest that variation in Scn2aK1422E flurothyl seizure threshold is not significantly influenced by the estrous cycle and, by extension, fluctuations in ovarian hormones. Interestingly, untreated Scn2aK1422E females showed evidence of disrupted estrous cyclicity, an effect not previously described in a genetic epilepsy model. This unexpected result highlights the importance of considering sex specific effects and the estrous cycle in support of more inclusive biomedical research.

Evidence for top-down suppression of negative features in the target feature dimension

While searching for a goal-relevant object, an internal representation of the features necessary to identify the to-be-searched-for object (i.e., target) guides attention towards visual stimuli with matching properties. Recent evidence suggests that features that negatively define a target (i.e., negative features) also bias attentional allocation through top-down suppression. Since humans usually know what to look for, it will rarely, if ever, be the case that a negative feature defines a goal-relevant object alone. Thus, to better understand the relevance of top-down suppression, our participants searched for a target conjunctively defined by a positive (e.g., a blue bar) and a negative feature (e.g., a nonred bar) with both features realized within the same dimension (color in Experiments 1, 3 and 4, orientation in Experiment 2). Experiments 1 and 2 showed that reaction times were slower if cues with a negative feature preceded the target at the same versus a different position (i.e., validly vs. invalidly cued targets), indicating suppression. In contrast, cues with a task-irrelevant different-dimension feature elicited no significant reaction time difference between validly cued and invalidly cued trials. In addition, Experiment 3 showed that while negative cues were top-down suppressed, cues with a positive feature captured attention. This finding indicated that both positive and negative features guide visual attention through capture and suppression, respectively, during the search for a target defined by the presence of one and the absence of another feature from the same dimension. However, suppression seems to apply to the negative and all nontarget features in the task-relevant dimension. This was shown in Experiment 4, in which participants suppressed cues with a task-irrelevant color similarly to cues with a negative color.

Terpene chemotypes in Gossypium hirsutum (wild cotton) from the Yucatan Peninsula, Mexico

Cultivated plants of Gossypium hirsutum Cav. (cotton) consistently emit low levels of volatile organic compounds, primarily mono- and sesquiterpenoids, which are produced and stored in pigment glands. In this study, we provide a comprehensive evaluation of the terpene profiles of wild G. hirsutum plants sourced from sites located throughout natural distribution of this species, thus providing the first in-depth assessment of the scope of its intraspecific chemotypic diversity. Chemotypic variation can potentially influence resistance to herbivory and diseases, or interact with abiotic stress such as extreme temperatures. Under controlled environmental conditions, plants were grown from seeds of sixteen G. hirsutum populations collected along the coastline of the Yucatan Peninsula, which is its likely centre of origin. We found high levels of intraspecific diversity in the terpene profiles of the plants. Two distinct chemotypes were identified: one chemotype contained higher levels of the monoterpenes γ-terpinene, limonene, α-thujene, α-terpinene, terpinolene, and p-cymene, while the other chemotype was distinguished by higher levels of α- and β-pinene. The distribution of chemotypes followed a geographic gradient from west to east, with an increasing frequency of the former chemotype. Concurrent analysis of maternal plants revealed that chemotypes in wild G. hirsutum are highly heritable.

Time-resolved characterization of the innate immune response in the respiratory epithelium of human, porcine, and bovine during influenza virus infection

Viral cross-species transmission is recognized to be a major threat to both human and animal health, however detailed information on determinants underlying virus host tropism and susceptibility is missing. Influenza C and D viruses (ICV, IDV) are two respiratory viruses that share up to 50% genetic similarity, and both employ 9-O-acetylated sialic acids to enter a host cell. While ICV infections are mainly restricted to humans, IDV possesses a much broader host tropism and has shown to have a zoonotic potential. This suggests that additional virus–host interactions play an important role in the distinct host spectrum of ICV and IDV. In this study, we aimed to characterize the innate immune response of the respiratory epithelium of biologically relevant host species during influenza virus infection to identify possible determinants involved in viral cross-species transmission. To this end, we performed a detailed characterization of ICV and IDV infection in primary airway epithelial cell (AEC) cultures from human, porcine, and bovine origin. We monitored virus replication kinetics, cellular and host tropism, as well as the host transcriptional response over time at distinct ambient temperatures. We observed that both ICV and IDV predominantly infect ciliated cells, independently from host and temperature. Interestingly, temperature had a profound influence on ICV replication in both porcine and bovine AEC cultures, while IDV replicated efficiently irrespective of temperature and host. Detailed time-resolved transcriptome analysis revealed both species-specific and species uniform host responses and highlighted 34 innate immune-related genes with clear virus-specific and temperature-dependent profiles. These data provide the first comprehensive insights into important common and species-specific virus-host dynamics underlying the distinct host tropism of ICV and IDV, as well as possible determinants involved in viral cross-species transmission.

Regional income convergence in Colombia: population, space, and long-run dynamics

We examine the trajectory of regional income dynamics in Colombia. Using data on all 33 Colombian departments from 2000 to 2016, we employ extensions of (spatial) Markov chains, space-time mobility measures, along with a fully weighted version of the distribution analysis approach. By considering these extensions, our analysis enables us to answer questions such as whether the role of spatial context influences the distributional dynamics of Colombian departments, or the magnitude of the moderating effect of department's population. The inclusion of additional measures such as the asymptotic half-life of convergence provides additional results, informing on how long it would take to reach the hypothetical long-run distribution of per capita income. Results, which are reported for both pre- and post-2008 trends, complement previous literature on regional economic convergence in a relevant South American context, showing stronger convergence patterns when controlling for the population living in each department. The patterns do not particularly intensify when controlling for spatial spillovers, since the role of spatial context was already playing a relevant role from the beginning of the period analyzed. Therefore, although the ergodic distributions show a conditional-convergence pattern, addressing the problems of spatial exclusion fully, persistent polarization among geographical departments and populations, along with the relevant core-periphery gaps, still requires the design and implementation of specific policies.

The French Early Breast Cancer Cohort (FRESH): A Resource for Breast Cancer Research and Evaluations of Oncology Practices Based on the French National Healthcare System Database (SNDS)

Simple Summary

Because of an important disparity of care pathways and quality of care among women diagnosed with an early-stage breast cancer, we aimed to create a unique cohort of patients including all French women aged 18 years or over, treated by surgery and registered in the general health insurance coverage plan. After aggregating and annotating medico-administrative data on 235,368 early breast cancer patients, we open up perspectives for research on adverse effects, morbidity, mortality, the monitoring of care consumption, or medical-economic studies. We describe data sources, inclusion, and exclusion criteria, basic descriptive analyses, and longitudinal trends over time.

Abstract

Background: Breast cancer (BC) is the most frequent cancer and the leading cause of cancer-related death in women. The French National Cancer Institute has created a national cancer cohort to promote cancer research and improve our understanding of cancer using the National Health Data System (SNDS) and amalgamating all cancer sites. So far, no detailed separate data are available for early BC. Objectives: To describe the creation of the French Early Breast Cancer Cohort (FRESH). Methods: All French women aged 18 years or over, with early-stage BC newly diagnosed between 1 January 2011 and 31 December 2017, treated by surgery, and registered in the general health insurance coverage plan were included in the cohort. Patients with suspected locoregional or distant metastases at diagnosis were excluded. BC treatments (surgery, chemotherapy, targeted therapy, radiotherapy, and endocrine therapy), and diagnostic procedures (biopsy, cytology, and imaging) were extracted from hospital discharge reports, outpatient care notes, or pharmacy drug delivery data. The BC subtype was inferred from the treatments received. Results: We included 235,368 patients with early BC in the cohort (median age: 60 years). The BC subtype distribution was as follows: luminal (80.2%), triple-negative (TNBC, 9.5%); HER2⁺ (10.3%), or unidentifiable (n = 44,388, 18.9% of the cohort). Most patients underwent radiotherapy (n = 200,685, 85.3%) and endocrine therapy (n = 165,655, 70.4%), and 38.3% (n = 90,252) received chemotherapy. Treatments and care pathways are described. Conclusions: The FRESH Cohort is an unprecedented population-based resource facilitating future large-scale real-life studies aiming to improve care pathways and quality of care for BC patients.

Epigenetic, genetic and maternal effects enable stable centromere inheritance

Centromeres are defined epigenetically by the histone H3 variant, CENP-A. The propagation cycle by which preexisting CENP-A nucleosomes serve as templates for nascent assembly predicts epigenetic memory of weakened centromeres. Using a mouse model with reduced levels of CENP-A nucleosomes, we find that an embryonic plastic phase precedes epigenetic memory through development. During this phase, nascent CENP-A nucleosome assembly depends on the maternal Cenpa genotype rather than the preexisting template. Weakened centromeres are thus limited to a single generation, and parental epigenetic differences are eliminated by equal assembly on maternal and paternal centromeres. These differences persist, however, when the underlying DNA of parental centromeres differs in repeat abundance, as assembly during the plastic phase also depends on sufficient repetitive centromere DNA. With contributions of centromere DNA and Cenpa maternal effect, we propose that centromere inheritance naturally minimizes fitness costs associated with weakened centromeres or epigenetic differences between parents.

Limitation by vapour pressure deficit shapes different intra-annual growth patterns of diffuse- and ring-porous temperate broadleaves

Understanding the effects of temperature and moisture on radial growth is vital for assessing the impacts of climate change on carbon and water cycles. However, studies observing growth at sub-daily temporal scales remain scarce. We analysed sub-daily growth dynamics and its climatic drivers recorded by point dendrometers for 35 trees of three temperate broadleaved species during the years 2015-2020. We isolated irreversible growth driven by cambial activity from the dendrometer records. Next, we compared the intra-annual growth patterns among species and delimited their climatic optima. The growth of all species peaked at air temperatures between 12 and 16°C and vapour pressure deficit (VPD) below 0.1 kPa. Acer pseudoplatanus and Fagus sylvatica, both diffuse-porous, sustained growth under suboptimal VPD. Ring-porous Quercus robur experienced a steep decline of growth rates with reduced air humidity. This resulted in multiple irregular growth peaks of Q. robur during the year. By contrast, the growth patterns of the diffuse-porous species were always right-skewed unimodal with a peak in June between day of the year 150-170. Intra-annual growth patterns are shaped more by VPD than temperature. The different sensitivity of radial growth to VPD is responsible for unimodal growth patterns in both diffuse-porous species and multimodal growth pattern in Q. robur.

Seasonal Changes in Locomotor Activity Patterns of Wild Social Natal Mole-Rats (Cryptomys hottentotus natalensis)

Differences in individual locomotor activity patterns may be linked to a number of ecological factors, such as changes in ambient temperature or photoperiod. Observations on subterranean mammals suggest that they exhibit diel rhythms despite the lack of visual cues in their underground burrows, but it is unknown how seasonality and individual characteristics affect their activity. In this study we use RFID technology to monitor daily activity patterns of wild, social Natal mole-rats (Cryptomys hottentotus natalensis) during the summer and winter to investigate how their activity varies with season and whether their activity depends on individual characteristics such as body mass, sex and reproductive status. We found that in winter, individuals were more active during the time with the highest soil temperatures, whereas in summer, they showed a bimodal activity pattern during early morning and late afternoon coinciding with cooler soil temperatures. Individual characteristics, including reproductive status, did not affect general activity indicating that reproductive and non-reproductive individuals contribute equally to cooperative behaviors. We suggest that the activity patterns may be a behavioral adaptation to avoid extreme burrow temperatures and a mechanism to maintain a stable core body temperature. We highlight the advantages of RFID technology to study wild small mammal movements.

Molecular Insight into Genetic Structure and Diversity of Putative Hybrid Swarms of Pinus sylvestris × P. mugo in Slovakia

The genetic structures of the four putative hybrid swarms of Pinus sylvestris × P. mugo in Slovakia were analyzed in terms of individual admixture proportions calculated via inter-primer binding site (iPBS) marker loci. This work aimed to reevaluate the hybrid swarms’ differentiation status as postulated in the previous studies at both population and genomic levels. The study confirmed intermediate divergence of each of the swarms examined. Based on 80-loci hybrid index scores, we have revealed the presence of introgressive and intermediate hybrids with frequencies corresponding to differentiation estimates. Surprisingly, irrespective of individual phenotypes, the most frequent intermediates were found in Sucha Hora (29.5%) and Obsivanka (28.6%) populations, which resemble rather pure P. mugo and were previously considered as bimodal hybrid zones with a negligible amount of hybrids. The remaining hybrid zone population Zuberec seems to be highly introgressed to P. sylvestris, while Tisovnica is clearly inclined to P. mugo. The results and different methodologies are discussed.

Evidence for ecological processes driving speciation among endemic lizards of Madagascar

Although genetic patterns produced by population isolation during speciation are well documented, the biogeographic and ecological processes that trigger speciation remain poorly understood. Alternative hypotheses for the biogeography and ecology of speciation include geographic isolation combined with niche conservation (soft allopatry) or parapatric distribution on an environmental gradient with niche divergence (ecological speciation). Here, we use species' distributions, environmental data, and two null models (the Random Translation and Rotation and the Background Similarity Test) to test these alternative hypotheses among 28 sister pairs of microendemic lizards in Madagascar. Our results demonstrate strong bimodal peaks along a niche divergence-conservation spectrum, with at least 25 out of 28 sister pairs exhibiting either niche conservation or divergence, and the remaining pairs showing weak ecological signals. Yet despite these significant results, we do not find strong associations of niche conservation with allopatric distributions or niche divergence with parapatric distributions. Our findings thus provide strong evidence of a role for ecological processes driving speciation, rather than the classic expectation of speciation through geographic isolation, but demonstrate that the link between ecological speciation and parapatry is complex and requires further analysis of a broader taxonomic sample to fully resolve.

Consensus driven by a minority in heterogenous groups of the cockroach Periplaneta american a

Many social species are able to perform collective decisions and reach consensus. However, how the interplay between social interactions, the diversity of preferences among the group members and the group size affects these dynamics is usually overlooked. The collective choice between odourous and odorless shelters is tested for the following three groups of social cockroaches (Periplaneta americana) which are solitary foragers: naive (individuals preferring the odorous shelter), conditioned (individuals without preference), and mixed (combining, unevenly, conditioned, and naive individuals). The robustness of the consensus is not affected by the naive individuals' proportion, but the rate and the frequency of selection of the odorous shelter are correlated to this proportion. In mixed groups, the naive individuals act as influencers. Simulations based on the mechanisms highlighted in our experiments predict that the consensus emerges only for intermediate group sizes. The universality of these mechanisms suggests that such phenomena are widely present in social systems.