Biology subjects

Park, W. J.

Publications and source records attributed to Park, W. J..

8 recordsLinked to original sources

bioRxiv2026

Blindness reveals that Heschl's gyrus folding is not altered by auditory experience

Heschls gyrus (HG), which contains the primary auditory cortex, shows marked individual variability in its folding pattern, ranging from a single gyrus to partial or complete duplication. Greater HG duplication has been reported in expert musicians, often interpreted as evidence that auditory experience can shape cortical morphology. However, these structural differences might alternatively indicate a bias for musical careers in individuals whose anatomical predispositions facilitate expertise. Here, we examined HG morphology in blind individuals--a population with extensive auditory experience but without selection based on auditory ability. T1-weighted MRI data from 100 human participants (48 females, 42 males, 10 unknown) across blind and sighted groups were analyzed. HG was manually defined in each hemisphere, and folding was measured using both categorical morphology classification and continuous surface-based metrics. Across all analyses, blindness did not increase HG folding. These results suggest that the morphology of HG is largely predetermined. Significance statementIncreased anatomical folding in the auditory cortex has been reported in professional musicians. Is this structural variability due to experience-dependent plasticity, or is it that individuals with increased anatomical folding are more likely to become musicians? We examined Heschls gyrus (HG), which contains the primary auditory cortex, in blind individuals who rely heavily on auditory input. Despite extensive auditory experience, blindness did not alter HG folding. This finding suggests that the morphology of HG is not strongly influenced by auditory experience.

neuroscience↗

bioRxiv2025

Enhanced pitch perception in early blind individuals and musicians is due to reduced internal noise

Although it is commonly assumed that early blind individuals have enhanced pitch perception, the literature to date has been contradictory. We measured performance in two tasks known to recruit early vs. late stages of auditory frequency tuning in early blind and sighted individuals with matched levels of musical training. The two groups showed equivalent performance on a tone detection in a notched-noise task that assesses peripheral and subcortical frequency selectivity. In contrast, early blind individuals showed enhanced performance in a pitch discrimination task thought to be mediated by cortical mechanisms. Computational modeling revealed that this enhancement was best explained by reduced internal noise rather than narrower frequency tuning, with both blindness and musical training predicting a reduction in internal noise. These findings identify internal noise as a key factor in experience-driven auditory plasticity as a result of both musical experience and early blindness.

neuroscience↗

bioRxiv2025

Sensory Neural Noise as a Limiting Factor in Visual Working Memory Precision in Neurotypicals and Schizophrenia

The neural mechanisms that determine the capacity limits of working memory (WM) are not well understood, with traditional views identifying prefrontal circuitry as the main source of WM limits. Sensory noise, however, remains an underexplored explanation for WM limits despite its unavoidable influence on brain systems that encode and relay sensory information. Here, we show that individual differences in internal sensory noise during visual processing predict visual WM capacity. We further demonstrate that the well-documented WM deficits observed in schizophrenia can be associated with atypically high levels of visual sensory noise, offering a new explanatory framework for these deficits. By experimentally manipulating sensory noise via transcranial direct current stimulation applied to the visual cortex, we also show that changes in sensory noise led to corresponding changes in visual WM precision in individuals with schizophrenia. Finally, a computational model demonstrates that the same sensory noise measured during visual perception can limit WM precision during WM maintenance. These findings show that sensory noise may explain a significant amount of variance in WM function in both neurotypical adults and individuals with schizophrenia.

neuroscience↗

bioRxiv2022

The perception of auditory motion in sighted and early blind individuals

Motion detection is a fundamental property of the visual system that plays an important role across many of the human senses. In vision, motion processing is classically described using a motion energy model which assumes spatiotemporally selective (i.e., non-separable) filters that capture the smooth continuous change in spatial position over time afforded by moving objects. However, in the case of audition, it is still not clear whether or not the primary mechanisms underlying motion sensitivity are spatiotemporally selective. We used a psychophysical reverse correlation paradigm, where participants discriminated the direction of a motion signal in the presence of spatiotemporal noise, to determine whether the filters underlying auditory motion discrimination were spatiotemporally separable or non-separable. We then examined whether these auditory motion filters were altered as a result of early blindness. We found that both sighted and early blind individuals have separable filters. However, early blind individuals show increased sensitivity to auditory motion, with reduced susceptibility to noise, with filters that were more accurate in detecting motion onsets/offsets. An ideal observer model suggested that the reliance on separable filters may be more optimal given the limited spatial resolution in auditory input.

neuroscience↗

bioRxiv2021

A nuclear import pathway exploited by viroid RNAs

The prevailing view regarding intracellular RNA trafficking in eukaryotic cells describes that RNAs transcribed in the nucleus either stay in the nucleus or cross the nuclear envelope entering the cytoplasm for function. Interestingly, emerging evidence illustrates numerous functional RNAs trafficking in the reverse direction from the cytoplasm to the nucleus. However, the mechanism underlying the RNA nuclear import has not been well elucidated. Viroids are single-stranded circular noncoding RNAs that infect plants. Using nuclear-replicating viroids as a model, we showed that cellular Importin alpha-4 is likely involved in viroid RNA nuclear import, empirically supporting the involvement of Importin-based cellular pathway in RNA nuclear import. We also confirmed the involvement of a cellular protein (Virp1) that binds both Importin alpha-4 and viroids. Furthermore, a conserved C-loop in nuclear-replicating viroids is critical for Virp1 binding. Disrupting C-loop impairs Virp1 binding, viroid nuclear accumulation and infectivity. Further, C-loop exists in a subviral satellite noncoding RNA that relies on Virp1 for nuclear import. These results have significant implications for understanding the infection process of subviral agents. In addition, our data outline a cellular pathway responsible for the nuclear import of RNAs and uncover a 3-dimensional RNA motif-based regulation over RNA nuclear import.

plant biology↗

bioRxiv2020

Online Transcranial Random Noise stimulation improves perception at high levels of visual white noise

Transcranial random noise stimulation (tRNS), a relatively recent addition to the field of non-invasive, electrical brain stimulation, has been shown to improve perceptual and cognitive functions across a wide variety of tasks. However, the underlying mechanisms of visual improvements caused by tRNS remain unclear. To study this question, we employed a well-established, equivalent-noise approach, which measures perceptual performance at various levels of external noise and is formalized by the Perceptual Template Model (PTM). This approach has been used extensively to infer the underlying mechanisms behind changes in visual processing, including those from perceptual training, adaptation and attention. Here, we used tRNS during an orientation discrimination task in the presence of increasing quantities of external visual white noise and fit the PTM to gain insights into the effects of tRNS on visual processing. Our results show that tRNS improves visual processing when stimulation is applied during task performance, but only at high levels of external visual white noise--a signature of improved external noise filtering. There were no significant effects of tRNS on task performance after the stimulation period. Of interest, the reported effects of tRNS on visual processing mimic those previously reported for endogenous spatial attention, offering a potential area of investigation for future work.

neuroscience↗

bioRxiv2020

Hormone Receptor-status Prediction in Breast Cancer Using Gene Expression Profiles and Their Macroscopic Landscape

The cost of next-generation sequencing technologies is rapidly declining, making RNA-seq-based gene expression profiling (GEP) an affordable technique for predicting receptor expression status and intrinsic subtypes in breast cancer (BRCA) patients. Based on the expression levels of co-expressed genes, GEP-based receptor-status prediction can classify clinical subtypes more accurately than can immunohistochemistry (IHC). Using data from the cancer genome atlas TCGA BRCA and METABRIC datasets, we identified common predictor genes found in both datasets and performed receptor-status prediction based on these genes. By assessing the survival outcomes of patients classified using GEP- or IHC-based receptor status, we compared the prognostic value of the two methods. We found that GEP-based HR prediction provided higher concordance with the intrinsic subtypes and a stronger association with treatment outcomes than did IHC-based hormone receptor (HR) status. GEP-based prediction improved the identification of patients who could benefit from hormone therapy, even in patients with non-luminal BRCA. We also confirmed that non-matching subgroup classification affected the survival of BRCA patients and that this could be largely overcome by GEP-based receptor-status prediction. In conclusion, GEP-based prediction provides more reliable classification of HR status, improving therapeutic decision making for breast cancer patients.

cancer biology↗

bioRxiv2017

TraRECo: A Greedy Approach based de novo Transcriptome Assembler with Read Error Correction using Consensus Matrix

BackgroundChallenges in developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize de Bruijn graph, which has a complexity linearly growing with data size while suffers from errors and repeat. Although one can correct errors by inspecting topological structure of the graph, it is an uneasy task when there are too many branches. There are two research directions: improving either graph reliability or path search precision. We focused on improving the reliability.\n\nResultsWe present TraRECo, a greedy approach to de novo assembly employing error-aware graph construction. The idea is similar to overlap-layout-consensus approach used for genome assembly, but is different in that consensus is made through the entire graph construction step. Basically, we built contigs by direct read alignment within a distance margin and performed junction search to construct splicing graphs. While doing so, however, a contig of length l was represented by 4x1 matrix (called consensus matrix), of which each element was the base count of aligned reads so far. A representative sequence is obtained, by taking majority in each column of the consensus matrix, to be used for further read alignment. Once splicing graphs were obtained, we used IsoLasso to find paths with noticeable read depth. The experiments using real and simulated reads showed that the method provides considerable improvements in sensitivity and reasonably better performances when comparing both sensitivity and precision. This could be achieved by making more erroneous reads to be participated in graph construction, which, in turn, improved the depth information quality used for the subsequent path search step. The results for simulated reads showed also challenges are still remaining since non-negligible percentage of transcripts with high abundance were not recovered by the assemblers we considered.\n\nConclusionde novo assembly is mainly to explore not-yet-discovered isoforms and must be able to represent as much reads as possible in an efficient way. In this sense, TraRECo provides us a potential alternative to improve graph reliability, even though the computational burden can be much higher than single k-mer de Bruijn graph approach.

bioinformatics↗