Biology subjects

Desrochers, A.

Publications and source records attributed to Desrochers, A..

10 recordsLinked to original sources

bioRxiv2026

Coordination-dynamics invariants from simultaneous vagus nerve electroneurogram and ECG: a Python pipeline applied to neonatal piglet endotoxaemia

HRV complexity metrics track the systemic cytokine response across mammalian inflammation models, but the dynamical mechanism translating molecular inflammation into HRV structure has remained unresolved, and no existing tool jointly extracts coordination-dynamics signatures from simultaneous vagus nerve electroneurogram (VENG) and ECG. We describe a modular open-source Python pipeline that (i) detects spectrally distinct latent states in 20 kHz whole-trunk VENG using a symmetric-Kullback-Leibler scan-statistic changepoint detector ported from earthquake seismology and verified against its R progenitor; (ii) places the inter-changepoint-interval series in the Haken-Kelso-Bunz coupled-oscillator framework, computes the Kuramoto order parameter R, fits the bistable potential V({varphi}) = -a cos{varphi} - b cos 2{varphi}, and maps each timepoint into the Arnold-tongue ({Omega}, K) plane; contrasts compound-action-potential band power between successive latent states; and (iii) couples the VENG analysis to a CIMVA HRV pipeline driven by a 5-algorithm Pro-MAC R-peak ensemble. Applied to a previously published two-animal neonatal piglet endotoxaemia cohort (Castel et al., 2020, 2024), the pipeline recovers known features of the (iv) preparation and surfaces three case-series observations that we frame as hypotheses for prospective replication: (1) a 6-8 s VENG state-switching period coincident with the HRV LF/HF spectral boundary; (2) qualitatively divergent coordination-dynamics trajectories under LPS versus LPS + VNS (Kuramoto R collapses from 0.69 to 0.12 without VNS, undergoes biphasic recovery to 0.99 with VNS, the two trajectories crossing at 60-75 min); (3) a regime-dependent empirical coupling between R and the HRV embedding scaling exponent eScalE (R {middle dot} eScalE {approx} 0.33 during moderate challenge, doubling to {approx}0.80 during VNS overshoot). Pre-specified null comparisons (Poisson and bootstrap surrogates) demonstrate that R and the critical-slowing-down indicators carry information beyond their most obvious null alternatives. With N = 2 animals no inferential statistics are possible, so these findings are reported as hypothesis-generating; the manuscript closes with a pre-registered prospective protocol designed specifically to falsify them. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/728499v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@5ad100org.highwire.dtl.DTLVardef@4f6bb2org.highwire.dtl.DTLVardef@27a58aorg.highwire.dtl.DTLVardef@e52e15_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIWe present an open-source Python pipeline that extracts coordination-dynamics invariants (Kuramoto phase coherence, Haken-Kelso-Bunz potential parameters, Arnold-tongue position, critical-slowing-down indicators) from simultaneously recorded vagus nerve electroneurogram (VENG) and ECG, starting from a spectral-KL scan-statistic changepoint detector ported from earthquake seismology. C_LIO_LIApplied to a previously published two-animal cohort (Castel et al., 2024), the pipeline reveals that VENG alternates between two spectrally distinct latent states at a baseline period of 6-8 s that coincides with the HRV low-frequency/high-frequency spectral boundary ([~]0.15 Hz). We propose the VENG latent-state oscillator as a candidate mechanistic generator of vagal LF HRV; this is a hypothesis motivated by the timescale match and is not established by the present data. C_LIO_LIIn this cohort, LPS endotoxaemia and vagus nerve stimulation drove qualitatively divergent trajectories in the coordination-dynamics phase space (Kuramoto R: 0.69 [->] 0.12 without VNS; biphasic to R [->] 0.99 with VNS at the IL-6/IL-8 cytokine peak). Because the design provides one animal per arm, these are case-series observations and not a between-arm statistical comparison. C_LIO_LIInter-changepoint-interval variance rose >100-fold roughly 15 min before overt state-switching collapse in the unmitigated animal. Bootstrap nulls drawn from the same animals pre-collapse ICI pool reject the same-distribution alternative ([§]2.6), motivating a critical-slowing-down early-warning hypothesis that requires prospective replication before any clinical use is warranted. C_LIO_LIThe pipeline surfaces a regime-dependent empirical coupling between VENG phase coherence (R) and HRV embedding scaling exponent (eScalE) in the VNS-treated animal: during moderate challenge R {middle dot} eScalE {approx} 0.33 (CV {approx} 0.20), during VNS-enhanced overshoot (45, 90, 105 min) the product doubles to {approx}0.80. The product is a post-hoc empirical construct, not a derived conservation law; we propose it as a falsification target for prospective cohorts ([§]6). C_LI

physiology↗

bioRxiv2025

Truncating RELA variants drive autoinflammation and autoimmunity by impairing the negative feedback control of NF-kB

The NF-{kappa}B signaling pathway coordinates inflammation, cell survival, and proliferation, while restraining excessive cell death to maintain immune homeostasis. Truncating mutations in RELA, encoding the NF-{kappa}B subunit p65, have been linked to autoinflammation and autoimmunity, but the underlying mechanisms remain incompletely defined. We investigated six patients from five unrelated families carrying novel heterozygous truncating RELA variants. Despite reduced p65 expression, patients exhibited a broad spectrum of inflammatory manifestations alongside elevated baseline and stimulus-induced pro-inflammatory cytokines. Functional analyses in patient-derived cells and mutant RELA knock-in models showed that upstream NF-{kappa}B signaling was intact, but induction of inhibitory regulators such as I{kappa}B and A20 was impaired. This defective feedback control shifted immune homeostasis toward amplified inflammatory responses that depended on the residual activity of the remaining functional RELA allele. Single-cell transcriptomics revealed distinct cell type-specific consequences: monocytes displayed constitutive type I interferon and NF-{kappa}B activation, B cells retained partial compensatory signaling, whereas T and NK cells exhibited transcriptional signatures of cell death pathways. Patient fibroblasts and mutant RELA knock-in cells further confirmed enhanced TNF-induced inflammatory gene expression and hypersensitivity to apoptosis and necroptosis. These findings establish RELA haploinsufficiency as a cause of systemic immune dysregulation, and link defective NF-{kappa}B feedback control to unchecked inflammation and inflammatory cell death. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/687461v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1f0bfe6org.highwire.dtl.DTLVardef@c6cb60org.highwire.dtl.DTLVardef@1522accorg.highwire.dtl.DTLVardef@177c724_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Conspecific attraction in songbirds during spring migration

AO_SCPLOWBSTRACTC_SCPLOWConspecific attraction has often been hypothesized as a mechanism that could facilitate migration and territory acquisition. We studied conspecific attraction by songbirds during spring migration between 2019 and 2025 at the Dunes of Tadoussac, Quebec, Canada. This location is known to produce spectacular migration events with thousands of passerine birds flying at close range from the observers. We recorded sequences of individual birds moving just over the ground in a [~]20 m wide corridor along the edge of the St. Lawrence estuary. We also conducted hourly counts to detect conspecific clusters at a coarser temporal scale. Birds were much more likely to be following conspecifics at close range than other species, as evidenced by randomization tests, after accounting for species composition and abundance during each specific migration event. Conspecific sequences were mostly of two individuals, but much larger sequences occurred, up to 103 consecutive individuals of the same species. We found no evidence of leading species, i.e. species that were more likely to lead, rather than follow, another species. Hourly species counts were often much more variable than expected from a random (Poisson) process, at least in the case of Tennessee and Magnolia Warblers, providing evidence for conspecific attraction at a coarser temporal scale. This study provides the first detailed evidence of conspecific attraction with passerine birds during migration.

zoology↗

bioRxiv2022

Factors determining success of the chronically instrumented unanesthetized fetal sheep model of human development: a retrospective cohort study

AimChronically instrumented non-anesthetized fetal sheep (CINAFS) have been the mainstay model of human fetal development for 60 years. As a large "two for one" animal model, with instrumentation of the ewe and her fetus, the model poses challenges to implement de novo and to maintain overtime at the highest standards of operating procedures to ensure its ongoing performance. A common, yet conventionally underreported issue researchers face is the rate of animal loss. Here, we investigate what determines the success of the pregnant sheep model. MethodsWe conducted a retrospective cohort study consisting of 82 experiments spanning the course of six years. Our team identified ten variables that we anticipated were likely to influence the experimental outcome, such as the time of year, animal size, and surgical complexity. ResultsThe single variable identified in this study as determining the successful outcome of the experiments is the experience level of the team. ConclusionThe CINAFS model offers enormous potential to further our understanding of human fetal development and to create interventional technologies. However, to improve the outcomes of CINAFS models, improved communication and training are needed. We discuss the implications of our findings for the successful implementation of this challenging yet scientifically advantageous animal model of human physiology. Key pointsO_LIThe fetal sheep model closely mirrors the physiology of human fetal development C_LIO_LIIn addition to its high translational potential, this model is known to have some generally not reported rate of experimental failure C_LIO_LIWe show that factors such as animal characteristics & surgical complexity do not influence the experimental outcomes C_LIO_LIInstead, the key factor in model experimental success is the level of the research teams experience C_LIO_LIThe key factors to improve the animal model outcomes are an intra- and inter-team communication C_LI

physiology↗

bioRxiv2021

Avian recolonization of unrestored and restored bogs in Eastern Canada

Over the last several decades, peat has been extracted from bogs of temperate, populated regions of Eastern Canada, leaving large areas devoid of vegetation if unrestored. For the last 25 years, projects have been conducted in these regions to re-establish vegetation and facilitate recolonization by wildlife. We tested whether vegetation structure and bird species assemblages 10 to 20 years post extraction differ among natural, unrestored and restored bogs at the scales of individual sites and entire bogs. We conducted bird counts and vegetation surveys between 1993 and 2019, using both point counts (309 sites) and Autonomous Recording Units (80 sites). According to our vegetation surveys, restoration of sites that were previously used for peat harvesting accelerated the establishment of Sphagnum and herbaceous strata, but ericaceous and tree strata were unaffected over a 17-year period. None of the bird species with large home ranges were associated specifically to natural, unrestored, or restored areas at the bog level. Bird species diversity was similar in restored and natural sites, but lower in unrestored sites. Alder Flycatcher and American Goldfinch occupied restored and unrestored sites more frequently than natural sites, independent of the number of years post extraction. Occupancy of restored sites by Palm and Yellow-rumped Warblers increased over the years, reaching levels similar to those in natural sites 20 years after restoration was implemented. Occupancy of restored sites by Song and Savannah sparrows increased from 1993-2019 and diverged from their declining occupancy of natural sites. Species assemblages of restored and unrestored sites differed significantly from those of natural sites soon after peat extraction ceased or post restoration. But assemblages from restored and unrestored sites became progressively similar to those of natural sites during the first 20 years, especially in restored sites. We conclude that bird species assemblages of restored bog sites are converging toward those of natural sites, and that restoration provides novel habitats for regionally declining species, e.g., Savannah Sparrows.

ecology↗

bioRxiv2021

No general shift in spring migration phenology by eastern North American birds since 1970

We studied the phenology of spring bird migration from eBird and EPOQ checklist programs South of 49{degrees}N in the province of Quebec, Canada, between 1970 and 2020. 152 species were grouped into Arctic, long-distance, and short-distance migrants. Among those species, 75 significantly changed their migration dates, after accounting for temporal variability in observation effort, species abundance, and latitude. But in contrast to most studies on the subject, we found no general advance in spring migration dates, with 36 species advancing and 39 species delaying their migration. Several early-migrant species associated to open water advanced their spring migration, possibly due to decreasing early-spring ice cover in the Great Lakes and the St-Lawrence river since 1970. Arctic breeders and short-distance migrants advanced their first arrival dates more than long-distance migrants not breeding in the arctic. However, there was no difference among migrant groups when median arrival dates were considered. We conclude that general claims about advances in spring migration dates in eastern North America are misleading due to large taxonomic variation.

ecology↗

bioRxiv2021

Out-of-sight or out-of-site? Forays and detection probabilities in single-season occupancy models

Occupancy models have become popular in wildlife survey analyses because they account for the frequent failure to detect individuals of targeted species. Those individuals sometimes move outside sampling sites, i.e. exhibit temporary emigration. In such cases, occupancy models may become difficult to interpret or even misleading either at the species or the individual level, because they confound presence at the site, availability for detection given presence, and actual detection by the observer. We quantified the probabilities of these three components with spruce grouse (Falcipennis canadensis) in southern Quebec, Canada. We conducted call-response surveys of 24 grouse monitored by radio-telemetry. We defined sites empirically as circular areas of 83 m radius centered on the observer, corresponding to the maximum detection distance obtained. Based on telemetry locations, grouse were present at the site during 42 % of the surveys. Six stationary grouse were present during surveys, but were never detected. Thus, only individuals that moved in the presence of the observer (89 %) were considered available for detection. Individuals available for detection were detected in 51 % of the cases. We simulated detection histories and built single-season occupancy models, based on the empirical relationship between detection probability and the distance measured between observers and grouse. When temporary emigration was ignored, site occupancy was{psi} = 0.89, and the associated probability of detection was p = 0.23. When instances of temporary emigration were dropped, estimates were{psi} = 0.88 and p = 0.41. Using only grouse available for detection, estimates were{psi} = 0.87 and p = 0.42. Disentangling the components of detection probabilities had little impact on occupancy estimates, but showed a major effect of temporary emigration on estimated detection probabilities.

ecology↗

bioRxiv2021

How much does habitat isolation drive forest bird morphology?

Rapid environmental change caused by humans has become a major concern for wildlife conservationists. But phenotypic and evolutionary responses of species to such change may often be swift enough to prevent their collapse. Several North American bird species living in boreal forests now have more pointed wings (a proxy for sustained ight efficiency), than they had a century ago. This remarkable pattern has been hypothesized as resulting from selective pressures favoring colonization of isolated habitat. Additionally, aerodynamics predict that heavier birds can achieve faster ight, a further advantage for exploring isolated habitats. We tested whether birds establishing territories in isolated areas have more pointed wings and are heavier than con-specifics found in more densely populated areas. Wing shapes of wild-caught adults from 21 passerine bird species did not generally support this prediction. However individuals with large body mass relative to their species were found more frequently in isolated habitats. Our results offer partial support for the isolation hypothesis at the landscape scale. We encourage further work at coarser, regional, scales to further examine whether wing shape and body mass evolutionarily respond to habitat isolation.

zoology↗

bioRxiv2018

Combined effects of migration distance, foraging method vegetation density, and population density on wing shapes of boreal songbirds

In birds, migration distance is known to influence morphological attributes that influence flight performance, especially wing shape. However, wing shape is under the likely influence of less documented factors such as foraging method, vegetation density and isolation of individuals and populations. To better understand factors leading to interspecific differences in wing shape, we measured the pointedness of wings (Kipps distance) of 1017 live birds of 22 species in an eastern Canadian boreal forest. We modeled wing pointedness as a function of migration distances from eBird records, foraging, habitat, and population density data from Birds of North America monographs. Long-distance migrants and species living in low-density vegetation had more pointed wings than shorter-distance migrants and dense-vegetation dwellers, in accordance to our predictions. After accounting for vegetation density and migration distance, we found no link between the extent of aerial foraging or mean breeding population density, an indicator of isolation, and wing pointedness. Those results are consistent with a tradeoff between sustained flight efficiency and maneuverability, but suggest that interspecific variation in wing shape due specifically to foraging method or habitat isolation is nonexistent or obscured by other factors.

zoology↗

bioRxiv2017

α7 nicotinic acetylcholine receptor signalling modulates the inflammatory and iron homeostasis in fetal brain microglia

Neuroinflammation in utero may result in life-long neurological disabilities. Microglia play a pivotal role, but the mechanisms are poorly understood. No early postnatal treatment strategies exist to enhance neuroprotective potential of microglia. We hypothesized that agonism on 7 nicotinic acetylcholine receptor (7nAChR) in fetal microglia will augment their neuroprotective transcriptome profile, while the antagonistic stimulation of 7nAChR will achieve the opposite. Using an in vivo - in vitro model of developmental programming of neuroinflammation induced by lipopolysaccharide (LPS), we validated this hypothesis in primary fetal sheep microglia cultures re-exposed to LPS in presence of a selective 7nAChR agonist or antagonist. Our RNAseq and protein level findings show that a pro-inflammatory microglial phenotype acquired in vitro by LPS stimulation is reversed with 7nAChR agonistic stimulation. Conversely, antagonistic 7nAChR stimulation potentiates the pro-inflammatory microglial phenotype. Surprisingly, under conditions of LPS double-hit an interference of a postulated 7nAChR - ferroportin signaling pathway may impede this mechanism. These results suggest a therapeutic potential of 7nAChR agonists in early re-programming of microglia in neonates exposed to in utero inflammation via an endogenous cerebral cholinergic anti-inflammatory pathway. Future studies will assess the role of interactions between inflammation-triggered microglial iron sequestering and 7nAChR signaling in neurodevelopment.

neuroscience↗