Biology subjects

Norris, D.

Publications and source records attributed to Norris, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Optimal MR-ARFI encoding parameters for a range of contemporary magnetic field gradient systems

Purpose: To optimize motion encoding gradients in MR-Acoustic Radiation Force Imaging (ARFI) experiments under a range of experimental conditions, and to provide a general simulation tool. Methods: In MR-ARFI, Transcranial focused Ultrasound Stimulation (TUS) induced tissue displacement is encoded by motion encoding gradients as a phase change. We extended previously proposed equations for phase SNR to account for finite gradient switching times. We simulated the phase SNR while varying the strength and slew rate of motion encoding gradients for monopolar and bipolar encoding schemes in order to identify optimal configurations for various gradient hardware specifications. Phantom MR-ARFI experiments were performed to validate the simulations. Results: Optimized gradient durations are derived for a range of gradient strengths and slew rates. Gradient slew-rate is shown to influence the optimal parameters. Phantom MR-ARFI results showed good agreement with the simulations. Conclusion: The availability of modern gradient hardware is shown to dramatically improve the sensitivity of the ARFI experiment. Our openly available calculation tool allows ready calculation of optimal timings for any experimental conditions.

biophysics↗

bioRxiv2026

Demographic turnover undermines herd immunity in sympatric free-roaming dogs and cats: implications for zoonotic disease control in urban sentinel sites

Vaccination of free-roaming dogs (Canis lupus familiaris) and cats (Felis catus) remains a major public health challenge. Rapid urbanization forces these species into complex contact zones, where structural failure of pulsed vaccination under high demographic turnover undermines standard One Health interventions. In such cases species-specific intervention cycles are needed to reduce zoonotic disease risk. We integrated field-data within a simulated vaccination campaign to determine how species-specific turnover rates drive the erosion of herd immunity at an Amazonian urban sentinel site (university campus). We monitored free-roaming populations (72 dogs, 75 cats) using a non-invasive photographic mark-resight protocol from 2023 to 2025. We modelled time-to-disappearance using Cox Proportional Hazards and simulated the trajectory of effective vaccination coverage against a 40% herd immunity threshold, distinguishing between loss of vaccinated individuals and recruitment of susceptible individuals. The campus functioned as a high-turnover system, with 72% of dogs and 48% of cats classified as transients. Species significantly predicted persistence (Hazard Ratio = 0.56; 95% CI: 0.33-0.94; p=0.029), with cats exhibiting double the median residency of dogs (432 vs. 193 days). Consequently, the species experienced divergent epidemiological failure modes. For dogs, simulated vaccination coverage collapsed below a 40% herd immunity threshold in 160 days, driven by rapid immunity attrition (the loss of vaccinated individuals). Although cats persisted longer, their effective coverage was eroded by immunity dilution due to recruitment of naive juveniles, creating a 33% gap between cohort survival and population-level immunity by day 365. Annual vaccination campaigns are likely insufficient in this high-turnover urban dog population. Effective One Health zoonotic control strategies must transition from static abundance-based targets to dynamic, species-specific and turnover-adjusted intervention schedules.

ecology↗

bioRxiv2025

Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogenic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet to be expressed they must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA present in multiple copies (up to nine) in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes and is enriched in E. coli strains that carry the locus of enterocyte effacement (LEE). We show that HnrS directly base-pairs with the ribosome-binding site of the hha mRNA, repressing its translation and thereby reducing Hha-enhanced H-NS silencing. This counter-silencing de-represses the LEE type III secretion system and concomitantly represses motility. Transcriptomic profiling further revealed that HnrS indirectly activates genes involved in nitrate/nitrite respiration and nitric oxide resistance, metabolic pathways that contribute to survival in the inflamed gastrointestinal tract. Deletion of hnrS reduced expression of nitrate reductase genes and impaired actin pedestal formation on host epithelial cells. Our results indicate that prophage-encoded, multicopy hnrS provides a counter-silencing mechanism that reduces Hha-H-NS repression at specific virulence loci. This likely enables expression of horizontally acquired genes without broadly disrupting the core H-NS regulon. HnrS illustrates how mobile genetic elements deploy sRNAs to counteract xenogenic silencing and promote virulence gene expression, enhancing colonisation of the host. Importance statementHorizontally acquired genes are often silenced to protect bacterial genomes, but this defence also limits the expression of new traits. We identify a prophage-encoded small RNA, HnrS, that counteracts this restriction by repressing the xenogenic silencer Hha, lifting Hha-H-NS-mediated repression of virulence and metabolic genes. HnrS activates the locus of enterocyte effacement, nitrate/nitrite respiration, and nitric oxide resistance--pathways that help E. coli survive and colonise the inflamed gut. Our findings reveal an RNA-based counter-silencing mechanism encoded by mobile genetic elements, showing how phages can reprogram bacterial regulatory networks to promote adaptation and pathogenicity.

microbiology↗

bioRxiv2025

Spine-brain dynamics during human defensive threat-reactions

Synchrony between central and autonomic nervous system responses during threat rely on spine-brain interactions. Activation of the parasympathetic autonomic nervous system during acute threat has been linked to optimized action preparation and longer-term stress-resilience. However, it is unclear how this is orchestrated by spine-brain interactions during our widely used models of threat conditioning. Here we used a well-established threat conditioning procedure to test whether freezing-related bradycardia modulates the strength of motor- and sensory-relevant spinal-brain connectivity patterns. Conditioning elicited the expected autonomic and psychophysiological responses, with significant bradycardia and heightened differentiation between conditioned stimuli. Heart rate bradycardia modulated activity in the cingulate cortex and spinal cord, emphasizing their role in freezing. Notably, bradycardia-modulated spinal cord activity during threat was functionally coupled with motor cortex activity, suggesting a preparatory response for defensive actions. Establishing these effects for the first time in humans helps discovery of biomarkers for threat coping-relevant body-brain interactions, essential for clinical evaluations.

neuroscience↗

bioRxiv2025

Misleading monitoring: more hatchlings do not represent turtle population recovery

This article critiques a recent study by Lacava et al. (2024) that suggests the population of Podocnemis expansa has recovered in Brazil based on increased hatchling releases across 11 nesting areas. I present three main challenges to the study conclusions. Firstly, hatchling counts alone should not be used to assess population recovery. Secondly, the study failed to consider alternative hypotheses that could explain the observed increases, including changes in methods and effort over time. Lastly, the statistical analysis was flawed, specifically neglecting temporal autocorrelation and failing to distinguish between statistical significance and biological relevance. Reanalysis of the original data, accounting for temporal autocorrelation, revealed sustained increases in hatchlings released in only five of eleven areas, contradicting the original claim of increases in most areas. Furthermore, reanalysis suggests that methodological changes influenced results in at least one area. The study published by Lacava et al. (2024) requires correction to avoid ingenuous and potentially misleading conclusions and to more closely reflect the reality of 21st-century freshwater turtle conservation efforts.

zoology↗

bioRxiv2024

Characterizing BOLD activation patterns in the human hippocampus with laminar fMRI

The human hippocampus has been extensively studied at the macroscale using functional magnetic resonance imaging (fMRI) but the underlying microcircuits at the mesoscale (i.e., at the level of layers) are largely uninvestigated in humans. We target two questions fundamental to hippocampal laminar fMRI: How does the venous bias affect the interpretation of hippocampal laminar responses? And can we establish a benchmark laminar fMRI experiment which robustly elicits single-subject hippocampal activation utilizing the most widely applied GRE-BOLD contrast? We comprehensively characterized GRE-BOLD responses as well as T2*, tSNR and physiological noise as a function of cortical depth in individual subfields of the human hippocampus. Our results show that the vascular architecture differs between subfields leading to subfield-specific laminar biases of GRE-BOLD responses. Using an autobiographical memory paradigm, we robustly acquired depth-specific BOLD responses in hippocampal subfields. In the CA1 subregion, our results indicate a more pronounced trisynaptic path input rather than dominant direct inputs from entorhinal cortex during autobiographical memory retrival. Our study provides unique insights into the hippocampus at the mesoscale level, and will help interpreting hippocampal laminar fMRI responses and allow researchers to test mechanistic hypotheses of hippocampal function.

neuroscience↗

bioRxiv2021

Impacts of dams on freshwater turtles: a global review to identify conservation solutions

Background and Research AimsDams impact freshwater ecosystems and biodiversity. Freshwater turtles are at direct and indirect risk due to changes caused by damming including the loss of terrestrial and aquatic nesting habitats, changes to food availability and blocking movement. Effective management of these impacts requires robust evidence in order to gain an understanding of conservation solutions that work. MethodsWe reviewed the global scientific literature that evaluated the impact of dams on freshwater turtles, and carried out additional searches of literature published in seventeen languages for studies evaluating actions to mitigate dam impacts. ResultsThe search produced 47 published articles documenting dam impacts on 30 freshwater turtle species from seven families (Chelidae, Chelydridae, Emydidae, Geoemydidae, Kinosternidae, Podocnemididae and Trionychidae) in 13 countries. Few studies were found from Europe and Asia and none from Africa. Most studies were from temperate latitudes, where studies focused more on adults and less threatened species compared with tropical latitudes. More than half of the studies (57%, n = 27) suggested actions to help mitigate dam impacts. Yet, only five studies (three temperate and two tropical) documented the effect of interventions (dam removal, flow management, artificial pond maintenance and community-based action). ConclusionThese findings demonstrate a serious lack of documented evidence evaluating mitigation actions for dam impacts on freshwater turtles. Implications for Conservation: This lack of evidence reinforces the importance of strengthening and maintaining robust long-term studies needed to develop effective and adaptive conservation actions for this group of threatened vertebrates particularly in tropical regions.

zoology↗

bioRxiv2021

Amazonian run-of-river dam reservoir impacts underestimated: Evidence from a Before-After Control-Impact study of freshwater turtle nesting areas

O_LIConstruction of hydropower dams is associated with negative impacts on biodiversity, yet there remains a lack of robust scientific evidence documenting the magnitude of these impacts particularly across highly biodiverse tropical waterways. Hydropower expansion is an increasing threat to the Endangered yellow-spotted river turtle (Podocnemis unifilis) across its tropical South American range. C_LIO_LIYellow-spotted river turtle nesting areas were monitored as an indicator of dry season river level changes following run-of-river dam reservoir filling. A Before-After-Control-Impact (BACI) study design was used with multi-year field campaigns monitoring turtle nesting areas upstream of the dam. C_LIO_LIThe cause and extent of changes in nesting areas were established using Generalized Additive Models. Nesting area density was evaluated in relation to: time (before versus after), treatment (control versus impact), time treatment interaction (BACI), distance to the dam and precipitation. The extent of changes was examined by comparing the proportion of nesting areas remaining during four years after reservoir filling. C_LIO_LIDam construction generated an immediate and apparently permanent dry season river level rise that extended more than 20 km beyond impact assessment limits. On average the density of nesting areas declined 69% (from 0.48 to 0.15 per km) across 33 km of river directly impacted by the dam. This loss was reflected in a significant BACI interaction. Nesting area density was not explained by seasonal precipitation. C_LIO_LIStandardized monitoring of freshwater turtle nesting areas provided an effective means to quantify impacts of hydropower developments across biodiverse yet rapidly changing waterways. The negative impacts documented in this study should be preventable by mitigation actions including habitat creation and dry season flow regulation. Such measures would also likely benefit multiple species elsewhere in tropical rivers increasingly impacted by run-of-river dams. C_LI

zoology↗

bioRxiv2021

Understanding hydropower impacts on Amazonian wildlife is limited by a lack of robust evidence: results from a systematic review

Background and Research AimsAlthough hydropower provides energy to fuel economic development across Amazonia, strategies to minimize or mitigate impacts in highly biodiverse Amazonian environments remain unclear. The growing number of operational and planned hydroelectrics requires robust scientific evidence to evaluate impacts of these projects on Amazonian vertebrates. Here we investigated the existing scientific knowledge base documenting impacts of hydropower developments on vertebrates across Brazilian Amazonia. MethodsWe reviewed the scientific literature from 1945 to 2020 published in English, Spanish and Portuguese to assess the temporal and spatial patterns in publications and the types of study design adopted as well as scientific evidence presented. ResultsA total of 24 published articles documented impacts on fish (n = 20), mammals (n = 3) and freshwater turtles (n = 1). Most study designs (87.5%) lacked appropriate controls and only three studies adopted more robust Before-After-Control-Impact designs. The published evidence did not generally support causal inference with only two studies (8.3%) including appropriate controls and/or confounding variables. ConclusionDecades of published assessments (54.2% of which were funded by hydropower developers or their subsidiaries) do not appear to have established robust evidence of impacts of hydropower developments on Amazonian vertebrates. This lack of robust evidence could limit the development of effective minimization and mitigation actions for the diverse vertebrate groups impacted by hydroelectrics across Brazilian Amazonia. Implications for ConservationTo avoid misleading inferences there is a need to integrate more robust study designs into impact assessments of hydropower developments in the Brazilian Amazon.

scientific communication and education↗

bioRxiv2021

Investigation of layer specific BOLD in the human visual cortex during visual attention

Directing spatial attention towards a particular stimulus location enhances cortical responses at corresponding regions in cortex. How attention modulates the laminar response profile within the attended region, however, remains unclear. In this paper, we use high field (7T) fMRI to investigate the effects of attention on laminar activity profiles in areas V1-V3; both when a stimulus was presented to the observer, and in the absence of visual stimulation. Replicating previous findings, we find robust increases in the overall BOLD response for attended regions in cortex, both with and without visual stimulation. When analyzing the BOLD response across the individual layers in visual cortex, we observed no evidence for laminar-specific differentiation with attention. We offer several potential explanations for these results, including theoretical, methodological and technical reasons. Additionally, we provide all data and pipelines openly, in order to promote analytic consistency across layer-specific studies, improve reproducibility, and decrease the false positive rate as a result of analytical flexibility.

neuroscience↗

bioRxiv2020

An in-vivo study of BOLD laminar responses as a function of echo time and static magnetic field strength

Layer specific functional MRI requires high spatial resolution data. An approach often used for compensating for the poor signal to noise ratio (SNR) associated with small voxel sizes consists of integrating the signal from voxels at a given cortical depth over a patch of cortex. After this integration, physiological noise is expected to be the dominant noise source in the signal. In this context, the sensitivity gain in moving to higher static field strengths is expected to be lower than when thermal noise dominates. In this work, activation profiles in response to the same visual stimulus are compared at 1.5 T, 3 T and 7 T using a multi-echo, gradient echo (GE) FLASH sequence, with a 0.75 mm isotropic voxel size and the cortical integration approach. The results show that after integrating over a patch of cortex between 40 and 100 mm3(at 7 T and 1.5 T, respectively), the signal is in the physiological noise dominated regime, and that the obtained activation profiles are similar at the three different field strengths for equivalent echo times. The evolution of the resting-state signal over echo time indicates that BOLD-like noise is the dominant source of physiological noise. Consequently, the functional contrast to noise ratio is not strongly echo-time or field-strength dependent. The results show that compared to 7T, the gold standard, laminar GE-BOLD fMRI at lower field strengths is feasible at the cost of poorer spatial resolution (larger cortical integration extensions) and lower efficiency.

neuroscience↗

bioRxiv2020

Arterial blood contrast (ABC) enabled by magnetization transfer (MT): a novel MRI technique for enhancing the measurement of brain activation changes

Functional brain imaging in humans is almost exclusively performed using blood oxygenation level dependent (BOLD) contrast. This typically requires a period of tens of milliseconds after excitation of the spin system to achieve maximum contrast, leading to inefficient use of acquisition time, reduced image quality, and inhomogeneous sensitivity throughout the cortex. We utilise magnetisation transfer to suppress the signal differentially from grey matter relative to blood so that the local increase in blood volume associated with brain activation (mainly occurring in the arterioles and capillaries) will increase the measured signal. Arterial blood contrast (ABC) is additive to the residual BOLD effect, but will have its maximum value at the time of excitation. We measured brain activation using combined ABC and residual BOLD contrast at different times post-excitation and compared this to BOLD data acquired under otherwise identical conditions. We conclude that using ABC and measuring shortly after excitation gives comparable sensitivity to standard BOLD but will provide greater efficiency, spatial specificity, improved image quality, and lower inter-subject variability. ABC offers new perspectives for performing functional MRI.

neuroscience↗

bioRxiv2020

Big trees drive forest structure patterns across a lowland Amazon regrowth gradient

Degraded Amazonian forests can take decades to recover and the ecological results of natural regeneration are still uncertain. Here we use field data collected across 15 lowland Amazon smallholder properties to examine the relationships between forest structure, mammal diversity, regrowth type, regrowth age, topography and hydrography. Forest structure was quantified together with mammal diversity in 30 paired regrowth-control plots. Forest regrowth stage was classified into three groups: late second-regrowth, early second-regrowth and abandoned pasture. Basal area in regrowth plots remained less than half that recorded in control plots even after 20-25 years. Although basal area did increase in sequence from pasture, early to late-regrowth plots, there was a significant decline in basal area of late-regrowth control plots associated with a decline in the proportion of large trees. There was also contrasting support for different non-mutually exclusive hypotheses, with proportion of small trees (DBH <20cm) most strongly supported by topography (altitude and slope) whereas the proportion of large trees (DBH >60cm) supported by plot type and regrowth class. These findings support calls for increased efforts to actively conserve large trees to avoid retrogressive succession around edges of degraded Amazon forests.

ecology↗

bioRxiv2019

Population Dynamics and Biological Feasibility of Sustainable Harvesting as a Conservation Strategy for Tropical and Temperate Freshwater Turtles

BackgroundConservation strategies are urgently needed for tropical turtles. Studies conducted exclusively in the temperate zone have revealed that the suite of life history traits that characterizes turtles and includes delayed sexual maturity and high adult survivorship makes sustainable harvest programs an unviable strategy for turtle conservation. However, most turtles are tropical in distribution and the tropics have higher, more constant and more extended ambient temperature regimes that, in general, are more favorable for population growth. MethodsTo estimate the capacity of freshwater turtle species from temperate and tropical regions to sustain harvest we synthesized life history traits from 165 freshwater turtle species in 12 families (Carettochelydae, Chelidae, Chelydridae, Dermatemydidae, Emydidae, Geoemydidae, Kinosternidae, Pelomedusidae, Platysternidae, Podocnemididae, Staurotypidae and Trionychidae). The influence of climate variables and latitude on freshwater turtle life history traits (clutch size, clutch frequency, age at sexual maturity, and annual adult survival) were examined using Generalized Additive Models. The biological feasibility of sustainable harvest in temperate and tropical species was evaluated using a sensitivity analysis of population growth rates obtained from stage structured matrix population models. ResultsTurtles at low latitudes (tropical zones) exhibit smaller clutch sizes, higher clutch frequency, and earlier age at sexual maturity than those at high latitudes (temperate zone). Adult survival increased weakly with latitude and declined significantly with increasing bioclimatic temperature (mean temperature of warmest quarter). A modeling synthesis of these data indicates that the interplay of life history traits does not create higher harvest opportunity in adults of tropical species. Yet we found potential for sustainable exploitation of eggs in tropical species. ConclusionsSustainable harvest as a conservation strategy for tropical turtles appears to be as biologically problematic as in temperature zones and likely only possible if the focus is on limited harvest of eggs. Further studies are urgently needed to understand how the predicted population surplus in early life stages can be most effectively incorporated into conservation programs for tropical turtles increasingly threatened by unsustainable exploitation, climate change and deforestation.

zoology↗

bioRxiv2019

The time course of updating in running span

Running span can be performed by either passively listening to to-be-remembered items or actively updating the target set during presentation. This choice of strategy is influenced by the rate of presentation in the task. Previous research suggests that the active updating process is demanding and time-consuming. It is favored at relatively slow rates of presentation, while the passive strategy is more successful when applied at fast rates. In two experiments the time course of resource demand during task performance and its sensitivity to presentation rate was examined. We hypothesized that running span imposes a high cognitive load only when active updating is employed. Participants performed running span simultaneously with a spatial reaction time (RT) task, and RTs on the concurrent task were used to index the resource demands of the memory task. A slow-paced running span exhibited a large overall resource demand in comparison with the serial recall tasks (Experiment 1) and fast-paced running span (Experiment 2). This demand was observed from the position in the list from which participants are presumed to start updating, suggesting a cognitive shift to a demanding mode of updating. In addition, a demand burst was found approximately 1000ms following item onset at these later positions. These data establish that the process of active updating in running span task is slow and cognitively demanding and indicate that this limits its application during fast presentation rates.

neuroscience↗

bioRxiv2018

Human sequence learning involves creating new neural representations not strengthening old ones

We contrast two computational models of sequence learning. The associative learner posits that learning proceeds by strengthening existing association weights. Alternatively, recoding posits that learning creates new and more efficient representations of the learned sequences. Importantly, both models propose that humans act as optimal learners but capture different statistics of the stimuli in their internal model. Furthermore, these models make dissociable predictions as to how learning changes the neural representation of sequences. We tested these predictions by using fMRI to extract neural activity patters from the dorsal visual processing stream during a sequence recall task. We observed that only the recoding account can explain the similarity of neural activity patterns, suggesting that participants recode the learned sequences using chunks. We show that associative learning can theoretically store only very limited number of overlapping sequences, such as common in ecological working memory tasks, and hence an efficient learner should recode initial sequence representations.

neuroscience↗

bioRxiv2018

Is reading automatic? Are the ERP correlates of masked priming really lexical?

Humans have an almost unbounded ability to adapt their behaviour to perform different tasks. In the laboratory, this flexibility is sometimes viewed as a nuisance factor that prevents access to the underlying cognitive mechanisms of interest. For example, in order to study \"automatic\" lexical processing, psycholinguists have used masked priming or evoked potentials to measure \"automatic\" lexical processing. However, the pattern of masked priming can be radically altered by changing the task. In lexical decision, priming is observed for words but not for nonwords, yet in a same-different matching task, priming is observed for same responses but not for different responses, regardless of whether the target is a word or a nonword (Norris & Kinoshita, 2008). Here we show that evoked potentials are equally sensitive to the nature of required decision, with the neural activity normally associated with lexical processing being seen for both words and nonwords on same trials, and for neither on different trials. (150)

neuroscience↗

bioRxiv2017

Visual recency bias is explained by a mixture model of short term memory

Human bias towards more recent events is a common and well-studied phenomenon. Recent studies in visual perception have shown that this recency bias persists even when past events contain no information about the future. Reasons for this suboptimal behaviour are not well understood and the internal model that leads people to exhibit recency bias is unknown. Here we use a well-known orientation estimation task to frame the human recency bias in terms of incremental Bayesian inference. We show that the only Bayesian model capable of explaining the recency bias relies on a weighted mixture of past states. Furthermore, we suggest that this mixture model is a consequence of participants failure to infer a model for data in visual short term memory, and reflects the nature of the internal representations used in the task.

animal behavior and cognition↗