Biology subjects

Simons, J.

Publications and source records attributed to Simons, J..

12 recordsLinked to original sources

bioRxiv2026

Dissociable episodic memory performance and subjective experience across the aphantasia imagery spectrum

Mental imagery is often assumed to support episodic memory, yet whether this relationship depends on conscious access to imagery, and how reduced imagery differs from total aphantasia, remains unclear. The present study compared objective episodic memory performance, subjective trial-by-trial vividness, confidence, and response times in people reporting normal imagery, reduced imagery, or total aphantasia, across younger and older age groups. Participants completed an incidental-encoding episodic memory task requiring identification of visual or spatial changes in targets within scenes, alongside trial-by-trial vividness and confidence ratings. Across the full imagery spectrum, trial-level fluctuations in vividness were related to memory performance, whereas trait-level and averaged vividness measures were not. Moreover, reduced imagery and total aphantasia showed dissociable patterns of episodic memory performance and subjective experience. In the reduced-imagery group, vividness was a stronger predictor of accuracy and response times, vividness judgements were slower, and confidence was lower, suggesting greater metacognitive uncertainty when imagery is weak and inconsistent. Controls outperformed reduced and aphantasic groups on visual but not spatial changes, and both groups responded more slowly than controls; confidence did not differ between control and aphantasic groups. Age-related memory decline was observed in the control and reduced groups but not in the aphantasic group. Exit questionnaire data highlighted limited awareness of aphantasia among typical imagers and a persistent belief among aphantasic participants that their memory was inferior. Together, these findings show that reduced imagery should be distinguished from total aphantasia rather than treating both as a single population, and that trial-level fluctuations in vividness reveal relationships with episodic memory that trait-level and averaged measures do not capture.

neuroscience↗

bioRxiv2025

Informational Complexity as a Neural Marker of Cognitive Reserve

In Alzheimers disease (AD), a mismatch between neurological damage and cognitive functioning often is attributed to individual differences in cognitive reserve. Understanding the neural mechanism of cognitive reserve could help assessing the therapeutic effectiveness of interventions in AD. To address this, here, 38 elderly participants performed a sustained attention task during high-density EEG while awake and during drowsiness. Operationally, the degree to which performance was impaired under drowsiness signalled the extent of cognitive reserve, with less impairment indicating a higher level of cognitive reserve. Investigating performance variations during the active management of neural challenges offers a novel approach to studying cognitive reserve, capturing dynamics that mirror everyday cognitive demand. We related cognitive reserve to various measures, including informational complexity using the Lempel-Ziv (LZSUM) algorithm. We found a significant interaction effect between arousal and performance, where LZSUM values increased in high performers when drowsy but decreased in low performers. This effect was most pronounced in the frontal and central areas. Our findings suggest LZSUM to be indicative of a compensatory mechanism and thus show potential for LZSUM as a neural marker in assessing cognitive reserve. However, we found no consistent relationship between performance and structural brain measures, and proxies of cognitive reserve. Critically, our findings present a counterexample to the prevailing view that informational complexity purely reflects conscious level. Further research, such as a study with the same paradigm in patients with mild cognitive impairment (MCI) and AD, may lead to additional insights of whether we are truly measuring cognitive reserve.

neuroscience↗

bioRxiv2024

Sparse neural networks enable low-power, implantable neural interfaces

Recent advances in brain-machine interfaces (BMIs) using neural network decoders and increased channel count have improved the restoration of speech and motor function, but at the cost of higher power consumption. For wireless, implantable BMIs to be clinically viable, power consumption must be limited to prevent thermal tissue damage and enable long use without frequent charging. Here, we show how neural network "pruning" creates sparse decoders that require fewer computations and active channels for reduced power consumption. Across multiple movement decoding tasks using brain and muscle signals, recurrent neural network decoders can be compressed by over 100x while maintaining strong performance, enabling decoding on the implant with <1% power increase compared to decoding externally. Pruning also allows for deactivating up to 89% of channels, reducing BMI power by up to 5x. Counterintuitively, our findings suggest that BMIs employing a subset of a larger number of channels may achieve lower power consumption than BMIs with fewer channels, for a given performance level. These results suggest a path toward power-efficient, implantable BMIs suitable for long-term clinical use.

bioengineering↗

bioRxiv2021

A High-Resolution Method for the Systematic Detection of EMS-Induced Mutations in a Sequenced Population

The precise detection of causal DNA mutations is very crucial for forward genetic studies. Several sources of errors contribute to false-positive detections by current variant-calling algorithms, and these impact associating phenotypes with genotypes. To improve the accuracy of mutation detection we propose and implemented a high-resolution binning method for the accurate detection of likely EMS-induced mutations in a sequenced mutant population. The approach also incorporates a novel clustering algorithm for detecting likely false negatives with high accuracy. Sorghum bicolor is a very valuable crop species with tremendous potential for uncovering novel gene functions associated with highly desirable agronomical traits. We demonstrate the precision of the proposed method in the detection of likely EMS-induced mutations in the publicly available low-cost sequencing of the M3 generation from 600 sorghum BTx623 mutants. The method detected 3,274,606 single nucleotide polymorphisms (SNPs) of which 96% (3,141,908) were G/C to A/T DNA substitutions, as expected by EMS-mutagenesis action. We demonstrated the general applicability of the method, and showed a high concordance, 94% (3,074,759) SNPs overlap between SAMtools-based and GATK-based variant-calling algorithms. We also implemented a novel clustering algorithm which uncovered evidence for an additional 223,048 likely false-negative shared EMS-induced mutations. The final 3,497,654 SNPs represents an 87% increase in SNPs detected in the previous analysis of the sorghum mutant population. Annotation of the final SNPs revealed 10,263 high impact and 136,639 moderate impact SNPs, including 7,217 stop-gained mutations, and an average of 12 stop-gained mutations per mutant. We have implemented a public search database for this new genetic resource of 30,285 distinct sorghum genes containing medium or high impact EMS-induced mutations. Seedstock for a select 486 of the 600 described mutants are publicly available in the Germplasm Resources Information Network (GRIN) database.

bioinformatics↗

bioRxiv2020

Feasibility of Integrating Canine Olfaction with Chemical and Microbial Profiling of Urine to Detect Lethal Prostate Cancer

Prostate cancer is the second leading cause of cancer death in men in the developed world. A more sensitive and specific detection strategy for lethal prostate cancer beyond serum prostate specific antigen (PSA) population screening is urgently needed. Diagnosis by canine olfaction, using dogs trained to detect cancer by smell, has been shown to be both specific and sensitive. While dogs themselves are impractical as scalable diagnostic sensors, machine olfaction for cancer detection is testable. However, studies bridging the divide between clinical diagnostic techniques, artificial intelligence, and molecular analysis remains difficult due to the significant divide between these disciplines. We tested the clinical feasibility of a cross-disciplinary, integrative approach to early prostate cancer biosensing in urine using trained canine olfaction, volatile organic compound (VOC) analysis by gas chromatography-mass spectroscopy (GC-MS) artificial neural network (ANN)-assisted examination, and microbial profiling in a double-blinded pilot study. Two dogs were trained to detect Gleason 9 prostate cancer in urine collected from biopsy-confirmed patients. Biopsy-negative controls were used to assess canine specificity as prostate cancer biodetectors. Urine samples were simultaneously analyzed for their VOC content in headspace via GC-MS and urinary microbiota content via 16S rDNA Illumina sequencing. In addition, the dogs diagnoses were used to train an ANN to detect significant peaks in the GC-MS data. The canine olfaction system was 71% sensitive and between 70-76% specific at detecting Gleason 9 prostate cancer. We have also confirmed VOC differences by GC-MS and microbiota differences by 16S rDNA sequencing between cancer positive and biopsy-negative controls. Furthermore, the trained ANN identified regions of interest in the GC-MS data, informed by the canine diagnoses. Methodology and feasibility are established to inform larger-scale studies using canine olfaction, urinary VOCs, and urinary microbiota profiling to develop machine olfaction diagnostic tools. Scalable multi-disciplinary tools may then be compared to PSA screening for earlier, non-invasive, more specific and sensitive detection of clinically aggressive prostate cancers in urine samples.

cancer biology↗

bioRxiv2020

Did I imagine that? The functional role of paracingulate cortex in reality monitoring

Reality monitoring describes our ability to distinguish between internally and externally generated experiences. Individuals show significant variation in this ability and impaired reality monitoring has been linked to the experience of hallucinations. We undertook two studies to investigate the association between reality monitoring and morphology of the paracingulate region of medial prefrontal cortex. In Study 1 we compared reality monitoring accuracy and functional connectivity within paracingulate cortex in groups of healthy controls (N=20) and patients with schizophrenia and hallucinations (N=19). Controls showed greater reality monitoring accuracy that was associated with resting-state functional connectivity between paracingulate, precuneus and occipital cortices, while reality monitoring in patients was associated with more lateral functional connectivity. In Study 2 we used real-time fMRI neurofeedback to obtain causal evidence for the role of the paracingulate cortex in reality monitoring. Healthy individuals received Active feedback from paracingulate cortex (N=21) or Sham feedback based on randomised signal (N=18). Active-group participants showed a specific behavioural effect of improved reality monitoring for Imagined items, as well as increases in both activity within the paracingulate region, and its posterior functional connectivity with precuneus and lateral parietal cortices, and occipital cortex. Our findings suggest reality monitoring in healthy individuals is causally supported by a paracingulate mediated flexible network including the precuneus. Network connectivity can be enhanced using neurofeedback and tracks with improved reality monitoring ability. In contrast, patients with schizophrenia may utilise a distinct and more lateral network which may explain observed sub-optimal reality monitoring accuracy, contributing to the experience of hallucinations. Significance StatementReality monitoring refers to our ability to distinguish imagination from our experiences in the outside world, and is linked both to hallucinations in schizophrenia as well as to the morphology of paracingulate cortex area of the brain. Here, we revealed less paracingulate involvement in the functional reality monitoring networks in patients with schizophrenia compared to healthy individuals. Thereafter, we used real-time fMRI neurofeedback to show that healthy individuals can learn to upregulate brain activity within the paracingulate cortex, with this resulting in both improved reality monitoring ability and changes in paracingulate functional connectivity. This suggests that paracingulate cortex activity and connectivity play a causal role in reality monitoring, with implications for both the understanding and treatment of hallucinations.

neuroscience↗

bioRxiv2018

Healthy ageing reduces the precision of episodic memory retrieval

Episodic memory declines with older age, but it is unresolved whether this decline reflects reduced probability of successfully retrieving information from memory, or decreased precision of the retrieved information. Here, we used continuous measures of episodic memory retrieval in combination with computational modelling of participants retrieval errors to distinguish between these two potential accounts of age-related memory deficits. In three experiments, young and older participants encoded stimuli displays consisting of everyday objects varying along different perceptual features (e.g., location, colour and orientation) in a circular space. At test, participants recreated the features of studied objects using a continuous response dial. Across all three experiments, we observed age-related declines in the precision of episodic memory retrieval, whereas age differences in retrieval success were limited to the most challenging task condition. Reductions in mnemonic precision were evident for retrieval of both item-based and contextual information, and persisted after controlling for age-related decreases in the fidelity of perception and working memory. The findings highlight impoverished precision of memory representations as one factor contributing to age-related episodic memory loss, and suggest that the cognitive and neural changes associated with older age can differentially affect distinct aspects of episodic retrieval.

neuroscience↗

bioRxiv2018

Multimodal integration and vividness in the angular gyrus during episodic encoding and retrieval

Much evidence suggests that the angular gyrus (AnG) is involved in episodic memory, but its precise role is yet to be determined. We examined two possible accounts, within the same experimental paradigm: the CoBRA account (Shimamura, 2011), which suggests that the AnG acts as a convergence zone that binds multimodal episodic features; and the Subjectivity account (Yazar et al., 2012), which implicates AnG involvement in subjective mnemonic experience (such as vividness or confidence). fMRI was employed during both encoding and retrieval of paired-associates. During study, female and male human participants memorised picture-pairs of common objects (in the unimodal task) or of an object-picture and an environmental sound (in the crossmodal task). At test, they performed a cued-recall task, and further indicated the vividness of their memory. During retrieval, BOLD activation in the AnG was greatest for vividly remembered associates, consistent with the Subjectivity account. During encoding, the same effect of vividness was found, but this was further modulated by task: Greater activations were associated with subsequent recall in the crossmodal than the unimodal task. Thus, encoding data suggests an additional role to the AnG in cross-modal integration, consistent with its role at retrieval proposed by CoBRA. These results resolve some of the puzzles in the literature and indicate that the AnG can play different roles during encoding and retrieval, determined by the cognitive demands posed by different mnemonic tasks.\n\nSignificance StatementWe offer new insights into the multiplicity of processes that are associated with angular gyrus (AnG) activation during encoding and retrieval of newly formed memories. We used fMRI while human participants learned and subsequently recalled pairs of objects presented to the same sensory modality or to different modalities. We were able to show that the AnG is involved when vivid memories are created and retrieved, as well as when encoded information is integrated across different sensory modalities. These findings provide novel evidence for the contribution of the AnG to our subjective experience of remembering, alongside its role in integrative processes that promote subsequent memory.

neuroscience↗

bioRxiv2018

Neural evidence for age differences in representational quality and strategic retrieval processes

Mounting behavioral evidence suggests that declines in both representational quality and controlled retrieval processes contribute to episodic memory decline with age. The present study sought neural evidence for age-related change in these factors by measuring neural differentiation during encoding of paired associates, and changes in regional BOLD activity and functional connectivity during retrieval conditions that placed low (intact pairs) and high (recombined pairs) demands on controlled retrieval processes. Pattern similarity analysis revealed age-related declines in the differentiation of stimulus representations at encoding, manifesting as both reduced pattern similarity between closely related events, and increased pattern similarity between distinct events. During retrieval, both groups exhibited increased recruitment of areas within the core recollection network, including the hippocampus and angular gyrus, when endorsing studied pairs, whereas younger adults exhibited increased recruitment of, and hippocampal connectivity with, lateral prefrontal regions during correct rejections of recombined pairs. These results provide evidence for age-related changes in representational quality and in the neural mechanisms supporting memory retrieval under conditions of high, but not low, control demand.

neuroscience↗

bioRxiv2018

Specifying a causal role for angular gyrus in autobiographical memory

Considerable recent evidence indicates that angular gyrus dysfunction does not result in amnesia, but does impair a number of aspects of episodic memory. Patients with parietal lobe lesions have been reported to exhibit a deficit when freely recalling autobiographical events from their pasts, but can remember details of the events when recall is cued by specific questions. In apparent contradiction, inhibitory brain stimulation targeting angular gyrus in healthy volunteers has been found to have no effect on free recall or cued recall of word pairs. The present study sought to resolve this inconsistency by testing free and cued recall of both autobiographical memories and word pair memories in the same healthy participants following continuous theta burst stimulation (cTBS) of angular gyrus and a vertex control location. Angular gyrus cTBS resulted in a selective reduction in the free recall but not cued recall of autobiographical memories, whereas free and cued recall of word pair memories were unaffected. Additionally, participants reported fewer autobiographical episodes as being experienced from a first-person perspective following angular gyrus cTBS. The findings add to a growing body of evidence that a function of angular gyrus within the network of brain regions responsible for episodic recollection is to integrate memory features within an egocentric framework into the kind of first-person perspective representation that enables the subjective experience of remembering events from our personal pasts.

neuroscience↗

bioRxiv2018

Paracingulate sulcus morphology and hallucinations in clinical and non-clinical groups

Hallucinations are a characteristic symptom of psychotic mental health conditions that are also experienced by many individuals without a clinical diagnosis. Research has linked the experience of hallucinations in schizophrenia to differences in the length of the paracingulate sulcus (PCS), a structure in the medial prefrontal cortex of the brain which has previously been associated with the ability to differentiate perceived and imagined information. We investigated whether this notion of a specific morphological basis for hallucinations in the paracingulate cortex extends to individuals without a clinical diagnosis by testing the hypothesis that non-clinical individuals with hallucinations have shorter PCS than non-clinical individuals without hallucinations. Structural MRI scans were examined from three demographically matched groups of individuals: 50 patients with psychotic diagnoses who experienced auditory verbal hallucinations, 50 non-clinical individuals with auditory verbal hallucinations, and 50 healthy control subjects with no life-time history of hallucinations. Measurements of paracingulate sulcal length were compared between the groups and the results verified using automated data-driven gyrification analyses. Patients with hallucinations had shorter PCS than both healthy controls and non-clinical individuals with hallucinations, with no difference between non-clinical individuals with hallucinations and healthy controls. These findings suggest that the association of shorter PCS length with hallucinations is specific to patients with a psychotic disorder. This presents challenges for continuum models of psychosis and suggests possible differences in the mechanisms underlying hallucinations in clinical and non-clinical groups.

neuroscience↗

bioRxiv2017

No effect of hippocampal lesions on stimulus-response bindings

The hippocampus is believed to be important for rapid learning of arbitrary stimulus-response contingencies, or S-R bindings. In support of this, Schnyer et al., 2006 (Experiment 2) measured priming of reaction times (RTs) to categorise visual objects, and found that patients with medial temporal lobe damage, unlike healthy controls, failed to show evidence of reduced priming when response contingencies were reversed between initial and repeated categorisation of objects (a signature of S-R bindings). We ran a similar though extended object classification task on 6 patients who appear to have selective hippocampal lesions, together with 24 age-matched controls. Unlike Schnyer et al., 2006, we found that reversing response contingencies abolished priming in both controls and patients. Bayes Factors provided no reason to believe that response reversal had less effect on patients than controls. We therefore conclude that it is unlikely that the hippocampus is needed for S-R bindings.

neuroscience↗