Biology subjects

Hui, R.

Publications and source records attributed to Hui, R..

9 recordsLinked to original sources

bioRxiv2026

Causally validated phase-amplitude coupling enables high-fidelity motor decoding for next-generation brain-computer interfaces

Modern Brain-Computer Interfaces (BCIs) face a fundamental performance plateau due to their reliance on broad spectral power reduction (Event-Related Desynchronization, ERD) as the primary decoding feature. ERD acts as a coarse metabolic proxy for cortical activation, discarding the high-frequency temporal syntax necessary for high-dimensional motor control. Here, we demonstrate that Phase-Amplitude Coupling (PAC)--specifically, the phase-locking of high-gamma (70-150 Hz) firing to residual Beta oscillations--provides a high-fidelity temporal feature for decoding motor intent. Using high-density electrocorticography (HD-ECoG) during motor imagery, we show that incorporating Beta-PAC into machine-learning classifiers (LDA/SVM) significantly outperforms traditional power-based features. To definitively validate the causal robustness of this feature against mathematically-derived artifacts, we leveraged a rare in vivo human structural lesion model. In a patient with focal tumor infiltration of the motor tract, the metabolic gate (ERD) was preserved, yet structural uncoupling completely abolished Beta-PAC, collapsing network topology and reducing single-trial decoding accuracy to chance levels. Our findings causally validate Beta-PAC as a robust, independent control signal, establishing a physiological foundation for next-generation, phase-dependent neuroprostheses.

neuroscience↗

bioRxiv2026

Zhi-Shi-Huang-Wu slows Parkinson's disease progression in transgenic C. elegans models

Parkinsons disease (PD) is the second most progressive degenerative disorder of the brain due to dopaminergic (DA) neuron degenerations and alpha-synuclein (-Syn) accumulations. At present, the disease has no effective treatment. Therefore, the current study objective is to identify a novel anti-PD formula (Zhi-Shi-Huang-Wu Formula, F-2) computed at 8:4:2:1 ratio from HSP 70 promoter activators Valeriana jatamansi (V), Acori talarinowii (A), Scutellaria baicalensis (S), Fructus Schisandrae (F). Traditionally, V is used to cure memory impairments, A treats mental disorders, and chronic mild stress, S for neuroprotection, and F showed multiple therapeutic actions to treat insomnia. This study investigated the neuroprotective potential of the V, A, S, F, formula F-2 and its underlying molecular mechanisms in transgenic Caenorhabditis elegans models. A, S, F, and F-2 successfully restored 6-hydroxydopamine intoxicated DA neuron degenerations, reduced food-sensing behavior disabilities, and attenuated -Syn aggregations. Moreover, activates the lipid deposition and proteasome expressions to confirm -Syn degradations at the cellular level. Reactive oxygen species (ROS) cause oxidative stress, and A, S, F, and F-2 repressed ROS and raised SOD-3 expressions. Overall, these data indicate that V, A, S, F combined into F-2 (22.3%) are more effective against PD progression-like symptom than individual drugs V (0.7%), A (11.4%), S (9.6%), and F (12.6%). These improved neuroprotective actions of F-2 possibly due to following the antioxidative pathway. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/709540v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1a6f1f7org.highwire.dtl.DTLVardef@157a270org.highwire.dtl.DTLVardef@69a238org.highwire.dtl.DTLVardef@1194b5e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Zhi-Shi-Wu-Huang attenuates amyloid beta toxicity in Caenorhabditis elegans Alzheimer's disease models via modulating insulin DAF-16 signaling pathway

Alzheimers disease (AD) is a common neurodegenerative disorder primarily caused by Amyloid-beta (A{beta}) toxicity. Therefore, there is an urgent need to develop novel, effective, and safe drugs to treat AD. Traditional Chinese Medicine (TCM) has a long history of use in protecting against memory impairments. Recently, TCM has attracted growing attention from researchers as a source of potent neuroprotective compounds. In this study, we focus on four TCM herbs with multiple therapeutic properties: Valeriana jatamansi (V; 20 mg/mL), Acori tatarinowii (A; 10 mg/mL), Fructus Schisandrae (F; 5 mg/mL), and Scutellaria baicalensis (S; 2.5 mg/mL). The aim is to develop a neuroprotective anti-AD formulation, named "Zhi-Shi-Wu-Huang" derived from V, A, F, and S, and evaluate its efficacy in transgenic Caenorhabditis elegans models of AD. These four TCM herbs are among the most potent activators of the HSP-70 promoter, promoting the expression of heat shock protein 70 (HSP-70), which helps prevent protein misfolding and aggregation. Additionally, V, A, F, S, and the Zhi-Shi-Wu-Huang formula were found to reduce reactive oxygen species (ROS) production and enhance the expression of superoxide dismutase-3 (sod-3) and chymotrypsin-like proteasomes. Our findings demonstrate that both the individual extracts (V, A, F, S) and the Zhi-Shi-Wu-Huang formulation significantly reduce A{beta}-induced toxicity in transgenic worms by activating the insulin/DAF-16 signaling pathway.

neuroscience↗

bioRxiv2024

The Genomic portrait of the Picene culture: new insights into the Italic Iron Age and the legacy of the Roman expansion in Central Italy.

BackgroundThe Italic Iron Age was characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focused on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9th and the 3rd century BCE, until the Roman colonization. ResultsWe analyzed more than 50 samples, spanning more than 1,000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to genetic contacts between populations residing on the Italian and Balkan shores of the Adriatic Sea. Additionally, we found several individuals with ancestries deviating from their general population. Lastly, In the Late Antiquity period, the genetic landscape of the Middle Adriatic region drastically changed, indicating a relevant influx from the Near East. ConclusionsOur findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlighted the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impacted the Italian peninsula.

genomics↗

bioRxiv2023

Local population structure in Cambridgeshire during the Roman occupation

The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today the United Kingdom. While there is written evidence of high mobility into and out of Britain for administrators, traders and the military, the impact of imperialism on local population structure is invisible in the textual record. The extent of genetic change that occurred in Britain before the Early Medieval Period and how closely linked by genetic kinship the local populations were, remains underexplored. Here, using genome-wide data from 52 ancient individuals from Cambridgeshire, we show low levels of genetic ancestry differentiation between Romano-British sites and lower levels of runs of homozygosity over 4 centimorgans (cM than in the Bronze Age and Neolithic. We find fourteen cases of genetic relatedness within and one between sites without evidence of patrilineal dominance and one case of temporary mobility within a family unit during the Late Romano-British period. We also show that the modern patterns of genetic ancestry composition in Modern Britain emerged after the Roman period.

genetics↗

bioRxiv2023

Medieval social landscape through the genetic history of Cambridgeshire before and after the Black Death

The extent of the devastation of the Black Death pandemic (1346-53) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at local scale in the context of the social stratification of medieval communities. Here we study 275 newly reported ancient genomes from later medieval and post-medieval Cambridgeshire, from individuals buried before, during, and after the Black Death. The majority of individuals examined had local genetic ancestries. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. Accounting for the genetic component for height accentuates the disparities between social groups in stature estimated from long bones, as a proxy for health and the quality of life. While we detect long-term shifts in local genetic ancestry in Cambridgeshire that either pre- or postdate the Black Death, we find no evidence of major changes in genetic ancestry nor, in contrast to recent claims, higher differentiation of immune loci between cohorts living before and after the Black Death.

genetics↗

bioRxiv2022

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5x with paired human genomes up to 10.16x. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 x 10-7 - 1.13 x 10-6 for non-African diversity leading to an estimated age of sampled modern Eurasian diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of these rates indicate the age of sampled HSV-1 to 5.29 (4.60-6.12 kya, suggesting lineage replacement coinciding with late Neolithisation and implicating Bronze Age migrations6 in the distribution of HSV-1 through Eurasia.

genomics↗

bioRxiv2019

Insights into human genetic variation and population history from 929 diverse genomes

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

genomics↗

bioRxiv2018

Detecting archaic introgression without archaic reference genomes

Human populations out of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a small rate of false detection. Furthermore our approach is able to accurately infer admixture proportions and divergence time of human and archaic populations.\n\nWe apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and directly find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in West Eurasians, South East Asians and South Asians.

evolutionary biology↗