bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal contributions to sensory-based decision-making by cell-type specific circuits in the tail striatum
Authors: Cui Lele , Tang Shunhang , Zhao Kai , Pan Jingwei , Zhang Zhaoran , Si Bailu , Xu Ning-long 
Published: August 2022

AbstractThe striatum comprises distinct types of neurons giving rise to the direct and indirect basal ganglia pathways and local circuits. A large amount of work has been focusing on cell-type specific striatal circuits in the context of movement control, proposing several models on their functional roles. But it remains to be elucidated how the cell-type specific striatal circuits contribute to decision-making behavior and whether the existing models apply. Here, we investigate the causal roles of the cell-type specific circuits in the posterior tail of the dorsal striatum (TS) of mice in an auditory-guided decision-making behavior. Transient unilateral activation of the direct- or indirect-pathway striatal spiny projection neurons (dSPNs or iSPNs) both biased decisions in opposite directions. These effects, however, were not due to a direct influence on movement, but was specific to the decision period preceding action execution. Optogenetic inactivation of dSPNs and iSPNs revealed their opposing causal contributions to decisions. At the local circuit level, simutaneous optical recording and manipulation of dSPNs and iSPNs revealed their antagnizing interactions. Inactivation of PV interneurons, a common inhibitory input to both dSPNs and iSPNs, facilitated contraversive choices, supporting a causal contribution of coordinated striatal circuits. Using a neural circuit model, we further demonstrated the computational implemenation of the causal circuit mechanism. Our results indicate that while the causal roles of the cell-type specific striatal circuits in decision-making largely agree with classic models in movement control, they show decision task-related specificity involving local circuit coordination.
Tree and shrub richness modify subtropical tree productivity by modulating the diversity and community composition of soil bacteria and archaea
Authors: Tao Siqi , Veen G. F. (Ciska) , Yu Tianhe , Zhang Naili , Qu Laiye 
Published: August 2022

AbstractBackgroundDeclines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial community composition. These relationships have been well-established in grasslands, and few studies also indicate that fungi play a role in driving tree diversity-productivity relationships in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been largely overlooked. Here, we investigated how tree and shrub richness affects stand-level tree productivity via modulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2 or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.ResultsOur results showed that tree and shrub species richness affected bacterial diversity, community composition, and co-occurrence networks, but such effects were marginal for archaea. Both tree and shrub species richness increased stand-level tree productivity by modulating soil microbial community composition, with the effects being mediated via increases in soil C:N ratios.ConclusionsOur findings imply the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight that we may require better a understanding of prokaryotic communities in forest soils.
Catalyst: Fast and flexible modeling of reaction networks
Authors: Loman Torkel E. , Ma Yingbo , Ilin Vasily , Gowda Shashi , Korsbo Niklas , Yewale Nikhil , Rackauckas Chris , Isaacson Samuel A. 
Published: August 2022

AbstractWe introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equation (stochastic differential equation), and reaction rate equation (ordinary differential equation) representations for CRNs. Through comprehensive benchmarks, we demonstrate that Catalyst simulation runtimes are often one to two orders of magnitude faster than other popular tools. More broadly, Catalyst acts as both a domain-specific language and an intermediate representation for symbolically encoding CRN models as Julia-native objects. This enables a pipeline of symbolically specifying, analyzing, and modifying CRNs; converting Catalyst models to symbolic representations of concrete mathematical models; and generating compiled code for numerical solvers. Leveraging ModelingToolkit.jl and Symbolics.jl, Catalyst models can be analyzed, simplified, and compiled into optimized representations for use in numerical solvers. Finally, we demonstrate Catalyst’s broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.
Differential Analysis of Stromal-Epithelial Interactions between In Situ and Invasive Breast Cancer using Gene Expression Profiling
Authors: Officer Adam , Dempsey Andre M. , Murrow Lyndsay M. , Gartner Zev , Tamayo Pablo , Yau Christina , Harismendy Olivier 
Published: August 2022

AbstractBackgroundChanges in microenvironment cell-cell interactions (CCI) during the progression from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) are poorly understood. Gene expression studies are confounded by cellular heterogeneity and few separate stromal and epithelial contributions, resulting in a lack of reliable prognostic biomarker to guide treatment decisions.MethodsThe gene expression of 293 microdissected regions from DCIS (92 epithelial, 31 stromal) and IDC (78 epithelial, 30 stromal) cases was aggregated from 6 datasets. Expression signatures of 6 cell lineages extracted from normal breast single-cell profiling were used to correct for differences in cell abundance. Subtype-specific functional differences between DCIS and IDC were measured for each region type using Gene Set Enrichment Analysis (GSEA). DCIS-IDC stromal-epithelial interactions were compared using the expression product of 139 ligand-receptor (LR) pairs permuting the DCIS-IDC labels to assess significance.ResultsVariation in cell-lineage abundance separated epithelial regions into 4 clusters, including one enriched for DCIS (Myoepi-Enriched) and two for IDC (Infiltrated, Vascularized). GSEA on cell lineage normalized expression data identified subtype-independent changes in epithelial regions (induction of Extracellular Matrix maintenance genes, reduction of Tp53 signaling in IDC), as well as subtype-specific changes (proliferation in ER- and Her2-IDC, reduction in Nucleotide Excision Repair in ER+ IDC). In the stroma, Notch and Rho-GTPase signaling were induced in IDC irrespective of subtype. The stromal-epithelial interaction level of 6 and 4 LR pairs were significantly enriched in DCIS and IDC, respectively. Five of the 6 DCIS-enriched LR pairs involved ephrin interactions, with interaction level progressively decreasing from normal to DCIS to IDC. In contrast, 2 IDC-enriched LR pairs involved T-cell activity likely regulating Treg proliferation (CD28-CD86) or T and NK cells stimulation (CD226-PVR). Notably, the bulk expression product of one identified LR pair (EPHB4-EFNB1) was associated with poor survival in IDC (HR=1.47, p=0.04) suggesting that early remodeling of this stromal-epithelial interaction may have long-lasting impact on disease severity.ConclusionsThe observed changes in cell states and stromal-epithelial interactions, beyond those driven by difference in cell abundance, may lead to new biomarkers for prognosis and targets for secondary prevention.
Neural patterns differentiate traumatic from sad autobiographical memories in PTSD
Authors: Perl Ofer , Duek Or , Kulkarni Kaustubh R. , Kelmendi Ben , Amen Shelley , Gordon Charles , Krystal John H. , Levy Ifat , Harpaz-Rotem Ilan , Schiller Daniela 
Published: August 2022

AbstractFor people with post-traumatic stress disorder (PTSD), recalling traumatic memories often displays as intrusions that differ profoundly from processing of ‘regular’ negative memories. These mnemonic features fueled theories speculating a qualitative divergence in cognitive state linked with traumatic memories. Yet to date, little empirical evidence supports this view. Here, we examined neural activity of PTSD patients who were listening to narratives depicting their own memories. An inter-subject representational similarity analysis of cross-subject semantic content and neural patterns revealed a differentiation in hippocampal representation by narrative type: Semantically similar sad autobiographical memories elicited similar neural representations across participants. By contrast, within the same individuals, semantically thematically similar trauma memories were not represented similarly. Furthermore, we were able to decode memory type from hippocampal multivoxel patterns. Finally, individual symptom severity modulated semantic representation of the traumatic narratives in the posterior cingulate cortex. Taken together, these findings suggest that traumatic memories are a qualitatively divergent cognitive entity.
Functional morphological innovation corresponds to shifting lines of genetic least resistance
Authors: Parins-Fukuchi C. Tomomi , Saulsbury James G. 
Published: August 2022

AbstractPhenotypic traits are often constrained in their evolution by the genetic and developmental map underlying them. However, the extent to which these constraints themselves evolve has not been well-characterized. Traits that are integrated are generally thought to be constrained in their ability to evolve because their shared developmental and genetic architecture causes any change in one to be mirrored in the other. Nevertheless, it is not yet clear whether correlations can constrain major episodes of phenotypic diversification over longer timescales. We reconstruct patterns in integration within nine primate lineages and model the evolution of the resulting modules in a phylogenetic context. We find that patterns in integration are generally evolvable across lineages, with apes displaying particular lability in the composition of morphological modules. This increased turnover in module composition corresponds to both divergent evolution of skeletal shape and the formation of novel complexes of locomotor behaviors and postures. While integration may play a role in constraining evolutionary innovation, its effects are dynamic, shifting as the structure of integration itself evolves during episodes of exceptional ecomorphological diversification.
Known phyla dominate the RNA virome in Tara Oceans data, not new phyla as claimed
Authors: Edgar Robert C. 
Published: August 2022

ABSTRACTThe Tara Oceans project claimed to identify five new RNA virus phyla, two of which “are dominant in the oceans”. However, their own assignments classify 28,353 of their putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five claimed new phyla combined. I mapped their reads to their contigs, finding that known phyla also account for a large majority (93.8%) of reads. I show that 510 of their putative viral contigs contain cellular proteins and further that predicted polymerase structures for their claimed phyla have incomplete and malformed palm domains, contradicting viral polymerase function and calling into question whether their putative polymerase sequences are derived from viruses.
Decoding Subject’s Own Name in the Primary Auditory Cortex
Authors: Wu Hang , Wang Dong , Liu Yueyao , Xie Musi , Zhou Liwei , Wang Yiwen , Cao Jin , Huang Yujuan , Qiu Mincong , Qin Pengmin 
Published: August 2022

AbstractCurrent studies have shown that perception of subject’s own name (SON) involves multiple multimodal brain regions, while activities in unimodal sensory regions (i.e., primary auditory cortex) and their interaction with multimodal regions during the self-processing remain unclear. To answer this, we combined multivariate pattern analysis and dynamic causal modelling analysis to explore the regional activation pattern and inter-region effective connection during the perception of SON. We found that SON and other names could be decoded from the activation pattern in the primary auditory cortex. In addition, we found an excitatory effect of SON on connections from the anterior insula/inferior frontal gyrus to the primary auditory cortex, and to the temporal parietal junction. Our findings extended the current knowledge of self-processing by showing that primary auditory cortex could discriminate SON from other names. Furthermore, our findings highlighted the importance of influence of the insula on the primary auditory cortex during self-processing.
Exploring the role of abiotic factors on the seedling recruitment of three plant species in the Colombian Amazon
Authors: Palma Ana C , Stevenson Pablo R. 
Published: August 2022

AbstractOur work seeks to explore certain abiotic factors that could affect seedling recruitment in neotropical moist forest. We selected three plant species (Caraipa sp., Tachigali sp., and Dicranostyles sp.) and investigated the role of nutrients, proximity to the parent tree, competition (intra-and inter-specific) and light availability on seedling growth and survival. We planted seedlings in the forest understory and in a shade house and applied four different treatments to evaluate the role of abiotic factors on recruitment. Our results show that the studied species were not negatively influenced by distance-dependent processes or by competition during the study period (6-7 mo.). We found that light availability was the most important factor determining seedlings’ early performance. The studied species showed distinct responses to the different treatments; therefore, it is hard to draw general conclusions about which factors might be affecting seedling recruitment and promoting the high plant diversity of tropical moist forest.
Large vesicle extrusions fromC. elegansneurons are consumed and stimulated by glial-like phagocytosis activity of the neighboring cell
Authors: Wang Yu , Arnold Meghan Lee , Smart Anna Joelle , Wang Guoqiang , Androwski Rebecca J. , Morera Andres , Nguyen Ken C. , Schweinsberg Peter J. , Bai Ge , Cooper Jason , Hall David H. , Driscoll Monica , Grant Barth D. 
Published: August 2022

ABSTRACTC. elegansneurons under stress can produce giant vesicles, several microns in diameter, called exophers. Current models suggest that exophers are neuroprotective, providing a mechanism for stressed neurons to eject toxic protein aggregates and organelles. However, little is known of the fate of the exopher once it leaves the neuron. We found that exophers produced by mechanosensory neurons inC. elegansare engulfed by surrounding hypodermal skin cells and are then broken up into numerous smaller vesicles that acquire hypodermal phagosome maturation markers, with vesicular contents gradually degraded by hypodermal lysosomes. Consistent with the hypodermis acting as an exopher phagocyte, we found that exopher removal requires hypodermal actin and Arp2/3, and the hypodermal plasma membrane adjacent to newly formed exophers accumulates dynamic F-actin during budding. Efficient fission of engulfed exopher-phagosomes to produce smaller vesicles and degrade their contents requires phagosome maturation factors SAND-1/Mon1, GTPase RAB-35, the CNT-1 ARF-GAP, and microtubule motor associated GTPase ARL-8, suggesting a close coupling of phagosome fission and phagosome maturation. Lysosome activity was required to degrade exopher contents in the hypodermis but not for exopher-phagosome resolution into smaller vesicles. Importantly, we found that GTPase ARF-6 and effector SEC-10/Exocyst activity in the hypodermis, along with the CED-1 phagocytic receptor, is required for efficient production of exophers by the neuron. Our results indicate that the neuron requires specific interaction with the phagocyte for an efficient exopher response, a mechanistic feature potentially conserved with mammalian exophergenesis, and similar to neuronal pruning by phagocytic glia that influences neurodegenerative disease.
Transcranial electrical stimulation modulates emotional experience and metabolites in the prefrontal cortex in a donation task
Authors: Mugnol-Ugarte L , Bortolini T , Mikkelsen M , Monteiro M Carneiro , Andorinho AC , Bramatti Ivanei E. , Melo B , Hoefle S , Meireles F , Yao Bo , Moll J , Pobric G 
Published: August 2022

AbstractIn this study we investigated whether transcranial Direct Current Stimulation (tDCS) applied to two prefrontal cortex regions, the ventromedial prefrontal cortex (vmPFC, anode) and right dorsolateral prefrontal cortex (DLPFC, cathode) can be used to induce changes in self-reported emotions and modulate metabolite concentrations under both electrodes. We employed in vivo quantitative MR Spectroscopy (MRS) in healthy adult participants and quantified the changes in GABA and Glx complex (Glutamate and Glutamine) before and after five sessions of tDCS stimulation. tDCS was delivered at 2mA intensity for 20 minutes for the active group and 1 minute for the sham group. tDCS was applied over five days while participants were engaged in a charitable donation task, known to engage the reward network. We observed increased levels of GABA in vmPFC, but not in DLPFC. Glx levels were decreased in both vmPFC and DLPFC. We found that self-reported happiness increased significantly over time only in the active group. There was a decrease in self-reported guiltiness in both active and sham groups. Altogether, the results indicate that self-reported emotions can be modulated by prefrontal stimulation. This may be because the changes in GABA and Glx concentrations following repeated stimulation induce remote changes in the reward network through interactions with other metabolites, previously thought to be unreachable with noninvasive stimulation techniques.
Learning Optimal White Matter Tract Representations from Tractography using a Deep Generative Model for Population Analyses
Authors: Feng Yixue , Chandio Bramsh Q. , Chattopadhyay Tamoghna , Thomopoulos Sophia I. , Owens-Walton Conor , Jahanshad Neda , Garyfallidis Eleftherios , Thompson Paul M. 
Published: August 2022

ABSTRACTWhole brain tractography is commonly used to study the brain’s white matter fiber pathways, but the large number of streamlines generated - up to one million per brain - can be challenging for large-scale population studies. We propose a robust dimensionality reduction framework for tractography, using a Convolutional Variational Autoencoder (ConvVAE) to learn low-dimensional embeddings from white matter bundles. The resulting embeddings can be used to facilitate downstream tasks such as outlier and abnormality detection, and mapping of disease effects on white matter tracts in individuals or groups. We design experiments to evaluate how well embeddings of different dimensions preserve distances from the original high-dimensional dataset, using distance correlation methods. We find that streamline distances and inter-bundle distances are well preserved in the latent space, with a 6-dimensional optimal embedding space. The generative ConvVAE model allows fast inference on new data, and the smooth latent space enables meaningful decodings that can be used for downstream tasks. We demonstrate the use of a ConvVAE model trained on control subjects’ data to detect structural anomalies in white matter tracts in patients with Alzheimer’s disease (AD). Using ConvVAEs to facilitate population analyses, we identified 6 tracts with statistically significant differences between AD and controls after controlling for age and sex effect, visualizing specific locations along the tracts with high anomalies despite large inter-subject variations in fiber bundle geometry.
Spatial mapping of human lung tissue reveals granuloma diversity and histopathological superstructure in tuberculosis
Authors: Sawyer Andrew , Patrick Ellis , Edwards Jarem , Wilmott James S , Fielder Timothy , Yang Qianting , Barber Daniel L , Ernst Joel D , Britton Warwick J , Palendira Umaimainthan , Chen Xinchun , Feng Carl G 
Published: August 2022

SummaryThe histopathological hallmark of tuberculosis (TB) is the formation of immune cell enriched aggregates called granulomas, but the scope of granuloma heterogeneity in human TB is unknown. By spatially mapping individual immune cells across large regions of TB lung tissue, we report that in addition to necrotizing granulomas, the human TB lung contains abundant non-necrotizing leukocyte aggregates surrounding areas of necrotizing tissue. These cellular lesions were more diverse in composition than necrotizing lesions and could be stratified into four general classes based on cellular composition and spatial distribution of B cells and macrophages, indicating there are foci of distinct immune reactions adjacent to necrotizing granulomas. We further show that the specific cellular composition of non-necrotizing structures correlates with their proximity to necrotizing lesions. Together, our study shows that during tuberculosis diseased lung tissue develops a histopathological superstructure comprising at least four different types of non-necrotizing cellular aggregates organized as satellites of necrotizing granulomas.
Origin, Prospective Identification, and Function of Circulating Endothelial Colony Forming Cells in Mouse and Human
Authors: Lin Yang , Banno Kimihiko , Gil Chang-Hyun , Myslinski Jered , Hato Takashi , Shelley William C. , Gao Hongyu , Xuei Xiaoling , Liu Yunlong , Basile David P. , Yoshimoto Momoko , Prasain Nutan , Tarnawsky Stefan P. , Adams Ralf H. , Naruse Katsuhiko , Yoshida Junko , Murphy Michael P. , Horie Kyoji , Yoder Mervin C. 
Published: August 2022

SummaryMost circulating endothelial cells are apoptotic, but rare circulating endothelial colony forming cells (C-ECFCs) with proliferative and vasculogenic activity can be cultured; the origin and naïve function of these C-ECFCs remains obscure. Herein, detailed lineage tracing reveals murine C-ECFCs emerge in the early postnatal period, display high vasculogenic potential, with enriched frequency of clonal proliferative cells compared to tissue-resident ECFCs, and are not committed to or derived from the bone marrow hematopoietic system but from tissue-resident ECFCs. In human subjects, C-ECFCs are present in the CD34bright cord blood mononuclear subset, possess proliferative potential and in vivo vasculogenic function in a naïve or cultured state, and display a single cell transcriptome sharing some umbilical venous endothelial cell features like, higher Protein C Receptor and extracellular matrix gene expression. This study provides an advance for the field by identifying the origin, naïve function, and antigens to prospectively isolate C-ECFCs for translational studies.