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Song, Y.

Publications and source records attributed to Song, Y..

At least 235 records · Page 13Linked to original sources

Reward-Bases: Dopaminergic Mechanisms for Adaptive Acquisition of Multiple Reward Types

Animals can adapt their preferences for different types for reward according to physiological state, such as hunger or thirst. To describe this ability, we propose a simple extension of temporal difference model that learns multiple values of each state according to different reward dimensions such as food or water. By weighting these learned values according to the current needs, behaviour may be flexibly adapted to present demands. Our model predicts that different dopamine neurons should be selective for different reward dimensions. We reanalysed data from primate dopamine neurons and observed that in addition to subjective value, dopamine neurons encode a gradient of reward dimensions; some neurons respond most to food rewards while the others respond more to fluids. Moreover, our model reproduces instant generalization to new physiological state seen in dopamine responses and in behaviour. Our results demonstrate how simple neural circuit can flexibly optimize behaviour according to animals needs.

neuroscience↗

Apposed networks of interacting TCRs and BCRs exhibiting mosaicked CDR3 sequences made of fixed junctional motifs

T and B cells are the two arms of the adaptive immune system that mediate cellular and humoral immunity, respectively, using highly diverse repertoires of antigen receptors. T cells recognize antigens using the T cell receptor (TCR), whereas B cells use the B cell receptor (BCR or surface immunoglobulin). Complementary determining regions (CDR3) of TCRs and BCRs are randomly generated through somatic VDJ recombination and nucleotide deletions and insertions at the V-D and D-J junctions. Contrary to this paradigm, here we describe two networks of millions of TCR{beta} and IGH clonotypes that are made from only two CDR3 sequences and associated with more 63 diseases. The TCR{beta} network members bore either the prototypic signature CDR3 sequence (CASSPGTEAFF), its N-terminal VD motif (CASSPGT) recombined with various J{beta} segments (CASSPGT-J{beta}x) or its DJ{beta} motif recombined with various V{beta} (V{beta}x-PGTEAFF). The BCR network members exhibit one signature CDR3 sequence (CARx1-4DTAMVYYFYDW) made from an invariant DJH motif (DTAMVYYFDYW) combined with various VH genes. The prototypes of the two networks are apparently teleogically related as they were dually expressed on the rare population of dual expresser (DE) lymphocytes and molecular dynamic simulations show that they were interacting partners. We conclude that members of the two networks represent a core set of evolutionary-conserved primordial antigen receptors that play fundamental roles in host defense and autoimmune diseases.

immunology↗

The AGNOSTIC MRS Benchmark Dataset: Deep Learning for Out-of-voxel Artifacts

Neural networks are potentially valuable for many of the challenges associated with MRS data. The purpose of this manuscript is to describe the AGNOSTIC dataset, which contains 259,200 synthetic 1H MRS examples for training and testing neural networks. AGNOSTIC was created using 270 basis sets that were simulated across 18 field strengths and 15 echo times. The synthetic examples were produced to resemble in vivo brain data with combinations of metabolite, macromolecule, residual water signals, and noise. To demonstrate the utility, we apply AGNOSTIC to train two Convolutional Neural Networks (CNNs) to address out-of-voxel (OOV) echoes. A Detection Network was trained to identify the point-wise presence of OOV echoes, providing proof of concept for real-time detection. A Prediction Network was trained to reconstruct OOV echoes, allowing subtraction during post-processing. Complex OOV signals were mixed into 85% of synthetic examples to train two separate CNNs for the detection and prediction of OOV signals. AGNOSTIC is available through Dryad and all Python 3 code is available through GitHub. The Detection network was shown to perform well, identifying 95% of OOV echoes. Traditional modeling of these detected OOV signals was evaluated and may prove to be an effective method during linear-combination modeling. The Prediction Network greatly reduces OOV echoes within FIDs and achieved a median log10 normed-MSE of -1.79, an improvement of almost two orders of magnitude.

neuroscience↗

Isolated loss of the AUTS2 long isoform, brain-wide or targeted to Calbindin-lineage cells, generates a specific suite of brain, behavioral and molecular pathologies

Rearrangements within the AUTS2 region are associated with a rare syndromic disorder with intellectual disability, developmental delay and behavioral abnormalities as core features. In addition, smaller regional variants are linked to wide range of neuropsychiatric disorders, underscoring the genes essential role in brain development. Like many essential neurodevelopmental genes, AUTS2 is large and complex, generating distinct long (AUTS2-l) and short (AUTS2-s) protein isoforms from alternative promoters. Although evidence suggests unique isoform functions, the contributions of each isoform to specific AUTS2-linked phenotypes have not been clearly resolved. Furthermore, Auts2 is widely expressed across the developing brain, but cell populations most central to disease presentation have not been determined. In this study, we focused on the specific roles of AUTS2-l in brain development, behavior, and postnatal brain gene expression, showing that brain-wide AUTS2-l ablation leads to specific subsets of the recessive pathologies associated with C-terminal mutations that disrupt both isoforms. We identify downstream genes that could explain expressed phenotypes including hundreds of putative direct AUTS2- l target genes. Furthermore, in contrast to C-terminal Auts2 mutations which lead to dominant hypoactivity, AUTS2-l loss-of-function is associated with dominant hyperactivity, a phenotype exhibited by many human patients. Finally, we show that AUTS2-l ablation in Calbindin 1-expressing cell lineages is sufficient to yield learning/memory deficits and hyperactivity with abnormal dentate gyrus granule cell maturation, but not other phenotypic effects. These data provide new clues to in vivo AUTS2-l functions and novel information relevant to genotype-phenotype correlations in the human AUTS2 region.

genetics↗

Selenium reduction of ubiquinone via SQOR suppresses ferroptosis

The canonical biological function of selenium is in the production of selenocysteine residues of selenoproteins, and this forms the basis for its role as an essential antioxidant and cytoprotective micronutrient. Here, we demonstrate that selenium, via its metabolic intermediate hydrogen selenide, efficiently donates its electrons to ubiquinone to form ubiquinol in the mitochondria through catalysis by sulfide quinone oxidoreductase (SQOR). Hydrogen selenide is superior to hydrogen sulfide as an electron donor owing to its larger valence shell. We show that this mechanism, independently of selenoprotein production, protects against ferroptosis via ubiquinol production in a manner that depends on xCT mediated selenide formation and SQOR activity. Our findings identify a regulatory mechanism against ferroptosis that implicates SQOR and expands our understanding of selenium in biology.

biochemistry↗

Social Behavior Atlas: A computational framework for tracking and mapping 3D close interactions of free-moving animals

The study of social behaviors in animals is essential for understanding their survival and reproductive strategies. However, accurately tracking and analyzing the social interactions of free-moving animals has remained a challenge. Existing multi-animal pose estimation techniques suffer from drawbacks such as the need for extensive manual annotation and difficulty in discriminating between similar-looking animals in close social interactions. In this paper, we present the Social Behavior Atlas (SBeA), a novel computational framework that solves these challenges by employing a deep learning-based video instance segmentation model, 3D pose reconstruction, and unsupervised dynamic behavioral clustering. SBeA framework also involves a multi-camera setup to prevent occlusion, and a novel approach to identify individual animals in close social interactions. We demonstrate the effectiveness of SBeA in tracking and mapping the 3D close interactions of free-moving animals using the example of genetic mutant mice, birds, and dogs. Our results show that SBeA is capable of identifying subtle social interaction abnormalities, and the models and frameworks developed can be applied to a wide range of animal species. SBeA is a powerful tool for researchers in the fields of neuroscience and ecology to study animal social behaviors with a high degree of accuracy and reliability.

neuroscience↗

OsNLP4-OsD3 module integrates nitrogen-iron nutrient signals to promote rice tillering by repressing strigolactone signaling

Rice tillers are a major yield component regulated by phytohormones and nutrients. How nutrients interact with phytohormones to control tillering remains largely elusive. Here, we report a novel mechanism by which the transcription factor NIN-like protein 4 (OsNLP4) integrates nitrogen (N)-iron (Fe) nutrient signals to promote tillering by repressing OsD3 in strigolactone (SL) signaling. We show that the N-Fe balance modulates OsNLP4 nuclear accumulation, which is increased by Fe through H2O2 reduction. Furthermore, OsNLP4 upregulates multiple H2O2 scavenging genes, providing a positive regulatory loop for OsNLP4 nuclear accumulation. Our findings uncover a fundamental mechanism by which the OsNLP4-OsD3 module integrates N-Fe nutrient signals to downregulate SL signaling and thereby promote rice tillering and yield, thus facilitating sustainable agriculture worldwide.

plant biology↗

Complete Workflow for High Throughput Human Single Skeletal Muscle Fiber Proteomics

Skeletal muscle is a major regulatory tissue of whole-body metabolism and is composed of a diverse mixture of cell (fiber) types. Aging and several diseases differentially affect the various fiber types, and therefore, investigating the changes in the proteome in a fiber-type specific manner is essential. Recent breakthroughs in isolated single muscle fiber proteomics have started to reveal heterogeneity among fibers. However, existing procedures are slow and laborious requiring two hours of mass spectrometry time per single muscle fiber; 50 fibers would take approximately four days to analyze. Thus, to capture the high variability in fibers both within and between individuals requires advancements in high throughput single muscle fiber proteomics. Here we use a single cell proteomics method to enable quantification of single muscle fiber proteomes in 15 minutes total instrument time. As proof of concept, we present data from 53 isolated skeletal muscle fibers obtained from two healthy individuals analyzed in 13.25 hours. Adapting single cell data analysis techniques to integrate the data, we can reliably separate type 1 and 2A fibers. Sixty-five proteins were statistically different between clusters indicating alteration of proteins involved in fatty acid oxidation, muscle structure and regulation. Our results indicate that this method is significantly faster than prior single fiber methods in both data collection and sample preparation while maintaining sufficient proteome depth. We anticipate this assay will enable future studies of single muscle fibers across hundreds of individuals, which has not been possible previously due to limitations in throughput.

biochemistry↗

Impact of Peripheral Auditory Structure on the Development of Auditory-Language Network in Children with Profound Sensorineural Hearing Loss

Profound congenital sensorineural hearing loss (SNHL) prevents children from developing spoken language. Cochlear implantation and auditory brainstem implantation can provide hearing sensation, but language development outcomes can vary, particularly for patients with inner ear malformations and/or cochlear nerve deficiency (IEM&CND). Currently, the peripheral auditory structure is evaluated through visual inspection of clinical imaging, but this method is insufficient for surgical planning and prognosis. The central auditory pathway is also challenging to examine in vivo due to its delicate subcortical structures. Previous attempts to locate subcortical auditory nuclei using fMRI responses to sounds are not applicable to deaf patients. In this study, we developed a new pipeline for mapping the auditory pathway using structural and diffusional MRI. We used a fixel-based approach to investigate the structural development of the auditory-language network for profound SNHL children with normal peripheral structure and those with IEM&CND under six years old. Our findings indicate that the language pathway is more sensitive to peripheral auditory condition than the central auditory pathway, highlighting the importance of early intervention for profound SNHL children to provide timely speech inputs. We also propose a comprehensive pre-surgical evaluation extending from the cochlea to the auditory-language network, which has promising clinical potential.

neuroscience↗

Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker

Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring. Statement of SignificanceLINE-1 ORF1p transposon protein is pervasively expressed in many cancers and a highly specific biomarker of multiple common, lethal carcinomas and their high-risk precursors in tissue and blood. Ultrasensitive ORF1p assays from as little as 25 L plasma are novel, rapid, cost-effective tools in cancer detection and monitoring.

cancer biology↗

Impact of acquisition and modeling parameters on test-retest reproducibility of edited GABA+

Literature values for within-subject test-retest reproducibility of gamma-aminobutyric acid (GABA), measured with edited magnetic resonance spectroscopy (MRS), vary widely. Reasons for this variation remain unclear. Here we tested whether sequence complexity (two-experiment MEGA-PRESS versus four-experiment HERMES), editing pulse duration (14 versus 20 ms), scanner frequency drift (interleaved water referencing (IWR) turned ON versus OFF), and linear combination modeling variations (three different co-edited macromolecule models and 0.55 versus 0.4 ppm spline baseline knot spacing) affected the within-subject coefficient of variation of GABA + macromolecules (GABA+). We collected edited MRS data from the dorsal anterior cingulate cortex from 20 participants (30.8 {+/-} 9.5 years; 10 males). Test and retest scans were separated by removing the participant from the scanner for 5-10 minutes. Each acquisition consisted of two MEGA-PRESS and two HERMES sequences with editing pulse durations of 14 and 20 ms (referred to here as: MEGA-14, MEGA-20, HERMES-14, and HERMES-20; all TE = 80 ms, 224 averages). Reproducibility did not consistently differ for MEGA-PRESS compared with HERMES or for 14 compared with 20 ms editing pulses. A composite model of the 0.9 and 3 ppm macromolecules (particularly for HERMES) and sparser (0.55 compared with 0.4 ppm) spline baseline knot spacing yielded generally better test-retest reproducibility for GABA+. Replicating our prior results, linear combination modeling in Osprey compared with simple peak fitting in Gannet resulted in substantially better test-retest reproducibility. These results highlight the importance of model selection for edited MRS studies of GABA+, particularly for clinical studies which focus on individual patient differences in GABA+ or changes following an intervention.

neuroscience↗

sLASER and PRESS Perform Similarly at Revealing Metabolite-Age Correlations

PurposeTo compare the respective ability of PRESS and sLASER to reveal biological relationships, using age as a validation covariate. MethodsMRS data were acquired from 102 healthy volunteers using PRESS and sLASER in centrum semiovale (CSO) and posterior cingulate cortex (PCC) regions. Acquisition parameters included TR/TE 2000/30 ms; 96 transients; 2048 datapoints sampled at 2 kHz. Spectra were analyzed using Osprey. Signal-to-noise ratio (SNR), full-width-half-maximum linewidth of tCr, and metabolite concentrations were extracted. A linear model was used to compare SNR and linewidth. Paired t-tests were used to assess differences in metabolite measurements between PRESS and sLASER. Correlations were used to evaluate the relationship between PRESS and sLASER metabolite estimates, as well as the strength of each metabolite-age relationship. Coefficients of variation were calculated to assess inter-subject variability in each metabolite measurement. ResultsSNR and linewidth were significantly higher (p<0.05) for sLASER than PRESS. Paired t-tests showed significant differences between PRESS and sLASER in most metabolite measurements. Metabolite measures were significantly correlated (p<0.05) for most metabolites between the two methods except GABA, Gln and Lac in CSO and GSH, Lac and NAAG in PCC. Metabolite-age relationships were consistently identified using both PRESS and sLASER. Similar CVs were observed for most metabolites. ConclusionThe study results suggest strong agreement between PRESS and sLASER in identifying relationships between brain metabolites and age in CSO and PCC data acquired at 3T. sLASER is technically desirable due to the reduced chemical shift displacement artifact; however, PRESS performed similarly in good brain regions at clinical field strength.

neuroscience↗

Assessing assay absorption artefacts in in vitro cell responses to particles

In this study, we assessed the issue of coal particles absorbing extracellular proteins and tested the effects of different culture conditions and processing strategies to address this issue. Our data show that there is no effective strategy to solve this problem. We agree with previous reports that cytokine binding experiments should be performed to implement appropriate correction factors in order to calculate the accurate production of secreted cytokines in the supernatant of cell culture experiments. This is an underappreciated issue in many published studies on the comparative potency of particles from different sources.

pharmacology and toxicology↗

Metabolite T1 relaxation times differ across the adult lifespan

PurposeTo investigate the age-dependence of metabolite T1 relaxation times at 3T in both gray- and white-matter-rich voxels. MethodsThis manuscript analyzes publicly available metabolite and metabolite-nulled (single inversion recovery TI = 600 ms) spectra acquired at 3T using PRESS localization. Voxels were placed in posterior cingulate cortex and centrum semiovale in 102 healthy volunteers across 5 decades of life (20s to 60s). All spectra were analyzed in Osprey v2.4.0. To estimate T1 relaxation times for tNAA2.0 and tCr3.0, the ratio of modeled metabolite residual amplitudes in the metabolite-nulled spectrum to the full metabolite signal was calculated using the single inversion recovery signal equation. Correlations between T1 and subject age were evaluated. ResultsSpearman correlations revealed that estimated T1 relaxation times of tNAA2.0 (rs = -0.43; p < 0.001) and tCr3.0 (rs = -0.23; p = 0.021) decreased significantly with age in white-matter-rich CSO, and less steeply (and not significantly) for tNAA2.0 (rs = -0.15; p = 0.136) and tCr3.0 (rs = -0.10; p = 0.319) in gray-matter-rich PCC. ConclusionThe analysis harnessed a large publicly available cross-sectional dataset to test an important hypothesis, that metabolite T1 relaxation times change with age. This preliminary study stresses the importance of further work to measure age-normed metabolite T1 relaxation times for accurate quantification of metabolite levels in studies of aging.

neuroscience↗

High Throughput Proteomic Analysis of Heterogeneous Cell Populations with NanoDTSC

Identification and proteomic characterization of rare cell types within complex organ derived cell mixtures is best accomplished by label-free quantitative mass spectrometry. High throughput is required to rapidly survey hundreds to thousands of individual cells to adequately represent rare populations. Here we present parallelized nanoflow dual-trap single-column liquid chromatography (nanoDTSC) operating at 15 minutes of total run time per cell with peptides quantified over 11.5 minutes using standard commercial components, thus offering an accessible and efficient LC solution to analyze 96 single-cells per day. At this throughput, nanoDTSC quantified over 1,000 proteins in individual cardiomyocytes and heterogenous populations of single cells from aorta. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/522908v4_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@352d49org.highwire.dtl.DTLVardef@1304d2corg.highwire.dtl.DTLVardef@1a9df5org.highwire.dtl.DTLVardef@1785464_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Novel mRNA vaccines encoding Monkeypox virus M1R and A35R protect mice from a lethal virus challenge

The outbreak of Monkeypox virus infection urgently need effective vaccines. However, the vaccines so far approved are all based on whole-virus, which raises safety concerns. MRNA vaccines has demonstrated its high efficacy and safety against SARS-Cov-2 infection. Here, we developed three mRNA vaccines encoding Monkeypox proteins M1R and A35R, including A35R-M1R fusions (VGPox1 and VGPox 2) and a combination of encapsulated full-length mRNAs for A35R and M1R (VGPox 3). All three vaccines induced anti-A35R total IgGs as early as day 7 following a single vaccination. However, only VGPox 1 and 2 produced anti-M1R total IgGs at early dates following vaccination while VGPox 3 did not show significant anti-M1R antibody till day 35. Similar results were also found in neutralizing antibodies and T cell immune response. However, all mRNA vaccine groups completely protected mice from a lethal dose virus challenge and effectively cleared virus in lungs. Collectively, our results indicate that the novel mRNA vaccines coding for a fusion protein of A35R and M1R had a better anti-virus immunity than co-expression of the two individual proteins. The mRNA vaccines are highly effective and can be an alternative to the current whole-virus vaccines to defend Monkeypox virus infection.

immunology↗

Somatic Loss of the Y Chromosome and Alzheimer's Disease Risk

Mosaic loss of the Y chromosome (LOY) is a somatic, age-related event that has been previously associated with a variety of diseases of aging. A prior study of European cohorts demonstrated an association between LOY and Alzheimers Disease and more recent molecular studies have shown that LOY can also occur within microglia, suggesting a potential functional role in AD pathogenesis. In this study, we further validate the association between LOY and AD via prospective analyses of 1,447 males, and perform Mendelian Randomization analysis on 10,013 males across 26 US cohorts. Significant results from these analyses provide further evidence for a role of LOY in the development of Alzheimers Disease.

genetics↗

Recurrent predictive coding models for associative memory employing covariance learning

The computational principles adopted by the hippocampus in associative memory (AM) tasks have been one of the mostly studied topics in computational and theoretical neuroscience. Classical models of the hippocampal network assume that AM is performed via a form of covariance learning, where associations between memorized items are represented by entries in the learned covariance matrix encoded in the recurrent connections in the hippocampal subfield CA3. On the other hand, it has been recently proposed that AM in the hippocampus is achieved through predictive coding. Hierarchical predictive coding models following this theory perform AM, but fail to capture the recurrent hippocampal structure that encodes the covariance in the classical models. Such a dichotomy pose potential difficulties for developing a unitary theory of how memory is formed and recalled in the hippocampus. Earlier predictive coding models that learn the covariance information of inputs explicitly seem to be a solution to this dichotomy. Here, we show that although these models can perform AM, they do it in an implausible and numerically unstable way. Instead, we propose alternatives to these earlier covariance-learning predictive coding networks, which learn the covariance information implicitly and plausibly, and can use dendritic structures to encode prediction errors. We show analytically that our proposed models are perfectly equivalent to the earlier predictive coding model learning covariance explicitly, and encounter no numerical issues when performing AM tasks in practice. We further show that our models can be combined with hierarchical predictive coding networks to model the hippocampo-neocortical interactions. Our models provide a biologically plausible approach to modelling the hippocampal network, pointing to a potential computational mechanism employed by the hippocampus during memory formation and recall, which unifies predictive coding and covariance learning based on the recurrent network structure. Author summaryThe hippocampus and adjacent cortical areas have long been considered essential for the formation of associative memories. Earlier theoretical works have assumed that the hippocampus stores in its recurrent connections statistical regularities embedded in the sensory inputs. On the other hand, it has been recently suggested that the hippocampus retrieves memory by generating predictions of ongoing sensory inputs. Computational models have thus been proposed to account for this predictive nature of the hippocampal network using predictive coding, a general theory of information processing in the cortex. However, these hierarchical predictive coding models of the hippocampus did not describe how it stores the statistical regularities that play a key role for associative memory in the classical hippocampal models, hindering a unified understanding of the underlying computational principles employed by the hippocampus. To address this dichotomy, here we present a family of predictive coding models that also learn the statistical information needed for associative memory. Our models can stably perform associative memory tasks in a biologically plausible manner, even with large structured data such as natural scenes. Our work provides a possible mechanism of how the recurrent hippocampal network may employ various computational principles concurrently to perform associative memory.

neuroscience↗