bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asticcacaulis aquaticus sp. nov., Asticcacaulis currens sp. nov. and Asticcacaulis machinosus sp. nov., isolated from streams in PR China
Authors: Lu Huibin , Chen Li , Kong Lingyang , Huang Linpei , Chen Guangjie 
Published: July 2023

Three Gram-stain-negative, aerobic, rod-shaped, stalked and motile strains with a polar flagellum (BYS171WT, DXS10WT and LKC15WT) were isolated from streams in PR China. Comparisons based on 16S rRNA gene sequences showed that strains BYS171WT and DXS10WT had the highest 16S rRNA gene sequence similarities (98.1 and 98.6 %, respectively) to

Asticcacaulis excentricus

CB 48T, and strain LKC15WT showed 99.6 % similarity to

Asticcacaulis endophyticus

ZFGT-14T. These three strains showed 16S rRNA gene sequence similarities of less than 96.9 % to other species of the genus

Asticcacaulis

. A phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains BYS171WT and DXS10WT took

A. excentricus

CB 48T as their closest neighbour, and strain LKC15WT formed a tight cluster with

A. endophyticus

ZFGT-14T. The phylogenomic tree also showed that these three strains belong to the genus

Asticcacaulis

and form a distinct clade with the species of the genus

Asticcacaulis

. The major cellular fatty acids of these three strains were summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C16 : 0 and 11-methyl C18 : 1
ω7c. Their polar lipids mainly consisted of phosphatidylglycerol, unidentified glycolipids and nitrogen-containing phosphoglycolipids. The calculated OrthoANIu and digital DNA–DNA hybridization values among strains BYS171WT, DXS10WT, LKC15WT and other related strains were less than 87.2 % and 34.0 %, respectively, indicating that these three strains should represent three independent novel species of the genus

Asticcacaulis

, for which the names Asticcacaulis aquaticus sp. nov. (type strain BYS171WT=GDMCC 1.3226T=KCTC 92612T), Asticcacaulis currens sp. nov. (type strain DXS10WT=GDMCC 1.3224T=KCTC 92543T) and Asticcacaulis machinosus sp. nov. (type strain LKC15WT=GDMCC 1.3225T=KCTC 92544T) are proposed.
Interactions between the representations of pain and reward suggest dynamic shifts in reference point
Authors: Hoskin R , Pernet C , Talmi D 
Published: July 2023

AbstractWith an aim to understand how brains compute the expected utility of mixed prospects, namely those associated with both negative and positive attributes, we designed a task which equated the opportunity to learn about these attributes and their hedonic value. Participants underwent fMRI scanning while they experienced a classical conditioning paradigm where emotionally-neutral faces predicted a probability of pain and reward conforming to a 2 (Electric Pain: high, low) x 2 (Monetary Reward: high, low) factorial design. We found a robust interaction between the anticipation of pain and reward in the BOLD signal. Analysis of simple effects revealed that sensitivity to each attribute increased under high levels of the other attribute. In the bilateral insula and mid-cingulate gyrus sensitivity to pain was greater under high reward, and in the OFC, caudate, ventral striatum and VTA sensitivity to reward was greater under high pain. We speculate that this pattern is due to dynamic shifts in the reference point participants considered to evaluate each attribute.
Cortical Responses Time-Locked to Continuous Speech in the High-Gamma Band Depend on Selective Attention
Authors: Commuri Vrishab , Kulasingham Joshua P. , Simon Jonathan Z. 
Published: July 2023

ABSTRACTAuditory cortical responses to speech obtained by magnetoencephalography (MEG) show robust speech tracking to the speaker’s fundamental frequency in the high-gamma band (70-200 Hz), but little is currently known about whether such responses depend on the focus of selective attention. In this study 22 human subjects listened to concurrent, fixed-rate, speech from male and female speakers, and were asked to selectively attend to one speaker at a time, while their neural responses were recorded with MEG. The male speaker’s pitch range coincided with the lower range of the high-gamma band, whereas the female speaker’s higher pitch range had much less overlap, and only at the upper end of the high-gamma band. Neural responses were analyzed using the temporal response function (TRF) framework. As expected, the responses demonstrate robust speech tracking of the fundamental frequency in the high-gamma band, but only to the male’s speech, with a peak latency of approximately 40 ms. Critically, the response magnitude depends on selective attention: the response to the male speech is significantly greater when male speech is attended than when it is not attended, under acoustically identical conditions. This is a clear demonstration that even very early cortical auditory responses are influenced by top-down, cognitive, neural processing mechanisms.
Higher general intelligence is linked to stable, efficient, and typical dynamic functional brain connectivity patterns
Authors: Ng Justin , Yu Ju-Chi , Feusner Jamie D. , Hawco Colin 
Published: July 2023

AbstractGeneral intelligence, referred to as g, is hypothesized to emerge from the capacity to dynamically and adaptively reorganize macroscale brain connectivity. Temporal reconfiguration can be assessed using dynamic functional connectivity (dFC), which captures the propensity of brain connectivity to transition between a recurring repertoire of distinct states. Conventional dFC metrics commonly focus on categorical state switching frequencies which do not fully assess individual variation in continuous connectivity reconfiguration. Here, we supplement frequency measures by quantifying within-state connectivity consistency, dissimilarity between connectivity across states, and conformity of individual connectivity to group-average state connectivity. We utilized resting-state fMRI data from the large-scale Human Connectome Project and applied data-driven multivariate Partial Least Squares Correlation to explore emergent associations between dynamic network properties and cognitive ability. Our findings reveal a positive association between g and the stable maintenance of states characterized by distinct connectivity between higher-order networks, efficient reconfiguration (i.e., minimal connectivity changes during transitions between similar states, large connectivity changes between dissimilar states), and ability to sustain connectivity close to group-average state connectivity. This hints at fundamental properties of brain-behavior organization, suggesting that general cognitive processing capacity is supported by the ability to efficiently reconfigure between stable and population-typical connectivity patterns.Impact StatementNovel evidence for an association between the stability, efficiency, and typicality of macro-scale dynamic functional connectivity patterns of the brain and higher general intelligence.
Interhemispheric inhibition between dorsal premotor and primary motor cortices is released during preparation of unimanual but not bimanual movements
Authors: Denyer Ronan , Greeley Brian , Greenhouse Ian , Boyd Lara A. 
Published: July 2023

ABSTRACTPrevious research applying transcranial magnetic stimulation during unimanual reaction time tasks indicates a transient change in the inhibitory influence of dorsal premotor cortex over contralateral primary motor cortex shortly after the presentation of an imperative stimulus. Interhemispheric inhibition from the dorsal premotor cortex to the contralateral primary motor cortex shifts depending on whether the targeted effector representation in the primary motor cortex is selected for movement. Further, the timing of changes in inhibition covaries with the selection demands of the reaction time task. Less is known about modulation of dorsal premotor to primary motor cortex interhemispheric inhibition during the preparation of bimanual movements. In this study, we used a dual coil transcranial magnetic stimulation to measure dorsal premotor to primary motor cortex interhemispheric inhibition between both hemispheres during unimanual and bimanual simple reaction time trials. Interhemispheric inhibition was measured early and late in the “pre-movement period” (defined as the period immediately after the onset of the imperative stimulus and before the beginning of voluntary muscle activity). We discovered that interhemispheric inhibition was more facilitatory early in the pre-movement period compared to late in the pre-movement period during unimanual reaction time trials. In contrast, interhemispheric inhibition was unchanged throughout the pre-movement period during symmetrical bimanual reaction time trials. These results suggest that there is greater interaction between the dorsal premotor cortex and contralateral primary motor cortex during preparation of unimanual actions compared to bimanual actions.
Human and chimpanzee-similar primates have distinct language gene polymorphism patterns
Authors: Xia Wei , Zhang Zhizhou 
Published: July 2023

AbstractThe difference in language gene polymorphism pattern (LGPP) between human and other primates may help to provide novel useful knowledge for language learning. One of important findings from many years’ worldwide research is that the primates like chimpanzee cannot easily recognize language grammars (even words). In this study, 189 SNPs (Single Nucleotide Polymorphism) in 13 language genes were scanned in 29 whole genomes from different human and primates populations. The 19 distinct SNPs in primates genomes were pointed out in several language genes including TPK1 that correlates with human’s syntactic and lexical ability. PCA analysis found that LGPPs for primates were highly aggregated together but they are distant from human’s LGPPs; representative human samples displayed high dispersion levels from each other in the context of LGPP. The above results may highlight a possibility that the LGPP should have more intermediate forms between human and chimpanzee-like primates.
Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication
Authors: Patel Dipak , Amiji Hatim , Shropshire William , Condic Natalia , Lermi Nejla Ozirmak , Sabha Youssef , John Beryl , Hanson Blake , Karras Georgios Ioannis 
Published: July 2023

AbstractProtein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.
Evaluation of gliovascular functions of Aqp4 readthrough isoforms
Authors: Mueller Shayna M. , White Kelli McFarland , Fass Stuart B. , Chen Siyu , Shi Zhan , Ge Xia , Engelbach John A. , Gaines Seana H , Bice Annie R , Vasek Michael J. , Garbow Joel R. , Culver Joseph P. , Martinez-Lozada Zila , Cohen-Salmon Martine , Dougherty Joseph D. , Sapkota Darshan 
Published: July 2023

AbstractAquaporin-4 (AQP4) is a water channel protein that links astrocytic endfeet to the blood-brain barrier (BBB) and regulates water and potassium homeostasis in the brain, as well as the glymphatic clearance of waste products that would otherwise potentiate neurological diseases. Recently, translational readthrough was shown to generate a C-terminally extended variant of AQP4, known as AQP4x, that preferentially localizes around the BBB through interaction with the scaffolding protein α-syntrophin, and loss of AQP4x disrupts waste clearance from the brain. To investigate the function of AQP4x, we generated a novel mouse AQP4 line (AllX) to increase relative levels of the readthrough variant above the ∼15% of AQP4 in the brain of wildtype (WT) mice. We validated the line and assessed characteristics that are affected by the presence of AQP4x, including AQP4 and α-syntrophin localization, integrity of the BBB, and neurovascular coupling. We compared AllXHomand AllXHetmice to wildtype, and to previously characterized AQP4 NoXHetand NoXHommice, which cannot produce AQP4x. Increased dose of AQP4x enhanced perivascular localization of α- syntrophin and AQP4, while total protein expression of the two were unchanged. However, at 100% readthrough, AQP4x localization and formation of higher-order complexes was disrupted. Electron microscopy showed that overall blood vessel morphology was unchanged except for increased endothelial cell vesicles in NoXHommice, which may correspond to a leakier BBB or altered efflux that was identified in NoX mice using MRI. These data demonstrate that AQP4x plays a small but measurable role in maintaining BBB integrity as well as recruiting structural and functional support proteins to the blood vessel. This also establishes a new set of genetic tools for quantitatively modulating AQP4x levels.Graphical Abstract
Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Authors: Islam Md Zohorul , Zimmerman Sam , Weidanz Jon , Ordovas-Montanes Jose , Robben Michael , Luber Jacob M. , Kostic Aleksandar D 
Published: July 2023

AbstractT cells primarily drive the autoimmune destruction of pancreatic beta cells in Type 1 diabetes (T1D). However, the profound yet uncharacterized diversity of the T cell populations in vivo has hindered obtaining a clear picture of the T cell changes that occur longitudinally during T1D onset. This study aimed to identify T cell clonal expansion and distinct transcriptomic signatures associated with T1D progression in Non-Obese Diabetic (NOD) mice. Here we profiled the transcriptome and T cell receptor (TCR) repertoire of T cells at single-cell resolution from longitudinally collected peripheral blood and pancreatic islets of NOD mice using single-cell RNA sequencing technology. Surprisingly, we detected a considerable high frequency of islet-matching T cell clones in the peripheral circulation and blood-matching T cell clones in the islets. Our analysis showed that transcriptional signatures of the T cells are associated with the matching status of the T cells, suggesting potential future applications as a marker for early prediction of diabetes onset using peripheral T cells. In addition, we discovered a high frequency of transcriptionally distinct double negative (DN) T cells that might arise from naïve and effector backgrounds through the loss of CD4 or CD8 in a yet unknown biological pathway. This study provides a single-cell level transcriptome and TCR repertoire atlas of T cells in NOD mice and opens the door for more research into the causes of type 1 diabetes and inflammatory autoimmune disease using mouse models.
Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing
Authors: Liu Fang , Patt Andrew , Chen Chloe , Huang Ruili , Xu Yanji , Mathé Ewy A. , Zhu Qian 
Published: July 2023

AbstractDrug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.
Dopamine challenge reduces mental state attribution accuracy
Authors: Schuster Bianca A. , Sowden Sophie , Rybicki Alicia J. , Fraser Dagmar S. , Press Clare , Hickman Lydia , Holland Peter , Cook Jennifer L. 
Published: July 2023

AbstractDifficulties in reasoning about others’ mental states (i.e., mentalising / Theory of Mind) are highly prevalent among disorders featuring dopamine dysfunctions (e.g., Parkinson’s disease) and significantly affect individuals’ quality of life. However, due to multiple confounding factors inherent to existing patient studies, currently little is known about whether these socio-cognitive symptoms originate from aberrant dopamine signalling or from psychosocial changes unrelated to dopamine. The present study therefore investigated the role of dopamine in modulating mentalising in a sample of healthy volunteers. We used a double-blind, placebo-controlled procedure to test the effect of the D2 antagonist haloperidol on mental state attribution, using an adaptation of the Heider & Simmel (1944) animations task. On two separate days, once after receiving 2.5mg haloperidol and once after receiving placebo, 33 healthy adult participants viewed and labelled short videos of two triangles depicting mental state (e.g., surprising) and non-mental state (e.g., following) interactions. Using Bayesian mixed effects models we observed that haloperidol decreased accuracy in labelling both mental- and non-mental state animations. Our secondary analyses suggest that dopamine modulates inference from mental- and non-mental state animations via independent mechanisms, pointing towards two putative pathways underlying the dopaminergic modulation ofmentalstate attribution: Action representation and a shared mechanism supporting mentalising and emotion recognition. We conclude that dopamine is causally implicated in Theory of Mind. Our results have implications for the neurochemical basis of socio-cognitive difficulties in patients with dopamine dysfunctions and generate new hypotheses about the specific dopamine-mediated mechanisms underlying social cognition.
FiPhA: An Open-Source Platform for Fiber Photometry Analysis
Authors: Bridge Matthew F. , Wilson Leslie R. , Panda Sambit , Stevanovic Korey D. , Letsinger Ayland C. , McBride Sandra , Cushman Jesse D. 
Published: July 2023

AbstractSignificanceFiber photometry is a widely used technique in modern behavioral neuroscience, employing genetically encoded fluorescent sensors to monitor neural activity and neurotransmitter release in awake-behaving animals, However, analyzing photometry data can be both laborious and time-consuming.AimWe propose the FiPhA (Fiber Photometry Analysis) app, which is a general-purpose fiber photometry analysis application. The goal is to develop a pipeline suitable for a wide range of photometry approaches, including spectrally resolved, camera-based, and lock-in demodulation.ApproachFiPhA was developed using the R Shiny framework and offers interactive visualization, quality control, and batch processing functionalities in a user-friendly interface.ResultsThis application simplifies and streamlines the analysis process, thereby reducing labor and time requirements. It offers interactive visualizations, event-triggered average processing, powerful tools for filtering behavioral events and quality control features.ConclusionsFiPhA is a valuable tool for behavioral neuroscientists working with discrete, event-based fiber photometry data. It addresses the challenges associated with analyzing and investigating such data, offering a robust and user-friendly solution without the complexity of having to hand-design custom analysis pipelines. This application thus helps standardize an approach to fiber photometry analysis.
Fast Connectivity Gradient Approximation: Maintaining spatially fine-grained connectivity gradients while reducing computational costs
Authors: Nenning Karl-Heinz , Xu Ting , Tambini Arielle , Franco Alexandre R. , Margulies Daniel S. , Colcombe Stanley J. , Milham Michael P. 
Published: July 2023

AbstractBrain connectome analysis suffers from the high dimensionality of connectivity data, often forcing a reduced representation of the brain at a lower spatial resolution or parcellation. However, maintaining high spatial resolution can both allow fine-grained topographical analysis and preserve subtle individual differences otherwise lost. This work presents a computationally efficient approach to estimate spatially fine-grained connectivity gradients and demonstrates its application in improving brain-behavior predictions.
Robust memory of face moral values is encoded in the human caudate tail: A simultaneous EEG-fMRI study
Authors: Ataei Ali , Amini Arash , Ghazizadeh Ali 
Published: July 2023

AbstractMoral judgements about people based on their actions is a key component that guides social decision making. It is currently unknown how positive or negative moral judgments associated with a person’s face are processed and stored in the brain. Here, we investigate the long-term memory of moral values associated with human faces using simultaneous EEG-fMRI data acquisition. Results show that only a few exposures to morally charged stories of people, are enough to form long-term memories a day later for a relatively large number of new faces. Event related potentials (ERPs) showed a significant differentiation of remembered good vs bad faces over centerofrontal electrode sites (value ERP). EEG-informed fMRI analysis revealed a subcortical cluster centered on the left caudate tail (CDt) as a correlate of the face value ERP. Importantly neither this analysis nor a conventional whole brain analysis revealed any significant activation in cortical areas in particular the fusiform face area (FFA). Conversely an fMRI-informed EEG source localization using accurate subject-specific EEG head models also revealed activation in the caudate tail. Nevertheless, the detected caudate tail region was found to be functionally connected to the FFA, suggesting FFA to be the source of face-specific information to CDt. These results identify CDt as the main site for encoding the long-term value memories of faces in humans suggesting that moral value of faces activates the same subcortical basal ganglia circuitry involved in processing reward value memory for objects in primates.