bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species -Shared and -Unique Gyral Peaks on Human and Macaque Brains
Authors: Zhang Songyao , Zhang Tuo , Cao Guannan , Zhou Jingchao , He Zhibin , Li Xiao , Ren Yudan , Liu Tao , Jiang Xi , Guo Lei , Han Junwei , Liu Tianming 
Published: July 2023

AbstractCortical folding is an important feature of primate brains that plays a crucial role in various cognitive and behavioral processes. Extensive research has revealed both similarities and differences in folding morphology and brain function among primates including macaque and human. The folding morphology is the basis of brain function, making cross-species studies on folding morphology important for understanding brain function and species evolution. However, prior studies on cross-species folding morphology mainly focused on partial regions of the cortex instead of the entire brain. Previously, we defined a whole-brain landmark based on folding morphology: the gyral peak. It was found to exist stably across individuals and ages in both human and macaque brains. In this study, we identified shared and unique gyral peaks in human and macaque, and investigated the similarities and differences in the spatial distribution, anatomical morphology, and functional connectivity of them.
Plasma Activated Water as a Pre-Treatment Strategy in the Context of Biofilm-Infected Chronic Wounds
Authors: Vyas Heema K. N. , Xia Binbin , Alam David , Gracie Nicholas P. , Rothwell Joanna G. , Rice Scott A. , Carter Dee , Cullen Patrick J. , Mai-Prochnow Anne 
Published: July 2023

AbstractHealing and treatment of chronic wounds are often complicated due to biofilm formation by pathogens. Here, the efficacy of Plasma Activated Water (PAW) as a pre-treatment strategy has been investigated prior to the application of topical antiseptics polyhexamethylene biguanide, povidone iodine, and MediHoney, which are routinely used to treat chronic wounds. The efficacy of this treatment strategy was determined against biofilms ofEscherichia coliformed on a plastic substratum and on a human keratinocyte monolayer substratum used as anin vitrobiofilm-skin epithelial cell model. PAW pre-treatment greatly increased the killing efficacy of all the three antiseptics to eradicate theE. colibiofilms formed on the plastic and keratinocyte substrates. However, the efficacy of the combined PAW-antiseptic treatment and single treatments using PAW or antiseptic alone was lower for biofilms formed in thein vitrobiofilm-skin epithelial cell model compared to the plastic substratum. Scavenging assays demonstrated that reactive species present within the PAW were largely responsible for its anti-biofilm activity. PAW treatment resulted in significant intracellular RONS accumulation within theE. colibiofilms, while also rapidly acting on the microbial membrane leading to outer membrane permeabilisation and depolarisation. Together, these factors contribute to significant cell death, potentiating the antibacterial effect of the assessed antiseptics.
Impaired value-based decision-making in Parkinson’s Disease Apathy
Authors: Gilmour William , Mackenzie Graeme , Feile Mathias , Tayler-Grint Louise , Suveges Szabolcs , Macfarlane Jennifer A , Macleod Angus D , Marshall Vicky , Grunwald Iris Q , Steele J Douglas , Gilbertson Tom 
Published: July 2023

AbstractApathy is a common and disabling complication of Parkinson’s disease characterised by reduced goal-directed behaviour. Several studies have reported dysfunction within pre-frontal cortical regions and projections from brainstem nuclei whose neuromodulators include dopamine, serotonin and noradrenaline. Work in animal and human neuroscience have confirmed contributions of these neuromodulators on aspects of motivated decision making. Specifically, non-dopaminergic neuromodulators, influence decisions to explore alternative courses of action or persist in an existing strategy to achieve a rewarding goal.Building upon this work, we hypothesised that Apathy in Parkinson’s disease should be associated with a failure to adequately monitor and make adaptive choices when the rewarding outcome of decisions are uncertain. Using a 4-armed restless bandit reinforcement learning task, we studied decision making in 75 volunteers; 53 patients with Parkinson’s disease, with and without clinical apathy, and 22 age matched healthy controls. Patients with Apathy exhibited impaired ability to choose the highest value bandit. Task performance predicted an individual patient’s apathy severity measured using the Lille Apathy Rating scale (R = -0.46, p<0.001). Computational modelling of the patient’s choices confirmed the apathy group made decisions that that were indifferent to the learnt value of the options, consistent with previous reports of reward insensitivity. Further analysis demonstrated a shift away from exploiting the highest value option and a reduction in perseveration which also correlated with apathy scores (R = -0.5, p<0.001).We went on to acquire fMRI in 59 volunteers; a group of 19 patients with and 20 without apathy and 20 age matched controls performing the restless bandit task. Analysis of the fMRI signal at the point of reward feedback confirmed diminished signal within ventromedial prefrontal cortex in Parkinson’s disease, which was more marked in Apathy, but not predictive of their individual Apathy severity. Using a model-based categorisation of choice type, decisions to explore lower value bandits in the apathy group activated pre-frontal cortex to a similar degree to the age-matched controls. In contrast, Parkinson’s patientswithoutapathy demonstrated significantly increased activation across a distributed thalamo-cortical network. Enhanced activity in the thalamus predicted individual apathy severity across both patient groups and exhibited functional connectivity with dorsal anterior cingulate cortex and anterior insula.Given that task performance in patients without apathy was no different to the age-matched controls, we interpret the recruitment of this network as a possible compensatory mechanism, which compensates against symptomatic manifestation of apathy in Parkinson’s disease.
Site-specific proximity labeling at single residue resolution for identification of protein partnersin vitroand on cells
Authors: Bartholow Thomas G. , Burroughs Paul , Elledge Susanna K. , Byrnes James R. , Kirkemo Lisa L. , Garda Virginia , Leung Kevin K. , Wells James A. 
Published: July 2023

AbstractThe cell surface proteome, or surfaceome, is encoded by more than 4000 genes, but we are only beginning to understand the complexes they form. Rapid proximity labeling around specific membrane targets allows for capturing weak and transient interactions expected in the crowded and dynamic environment of the surfaceome. Recently, a high-resolution approach called μMap has been described (Geri, J. B., Oakley, J. V., Reyes-Robles, T., Wang, T., McCarver, S. J., White, C. H., Rodriguez-Rivera, F. P., Parker, D. L., Hett, E. C., Fadeyi, O. O., Oslund, R. C., and MacMillan, D. W. C. (2020)Science 367, 1091–1097) in which an iridium (Ir)-based photocatalyst is attached to a specific antibody to target labeling of neighbors utilizing light-activated generation of carbenes from diazirine compounds via Dexter Energy Transfer (DET). Here we studied and optimized the spatial resolution for the method using an oncoprotein complex between the antibody drug, trastuzumab (Traz), and its target HER2. A set of eight single site-specific Ir-catalytic centers were engineered into Traz to study intra- and inter-molecular labelingin vitroand on cells by mass spectrometry. From this structurally well-characterized complex we observed a maximum distance of ∼110 Å for labeling. Labeling occurred almost uniformly over the full range of amino acids, unlike the residue specific labeling of other techniques. To examine on cell labeling that is specific to HER2 as opposed to simply being on the membrane, we compared the labeling patterns for the eight Traz-catalyst species to random labeling of membrane proteins using a metabolically integrated fatty acid catalyst. Our results identified 20 high confidence HER2 neighbors, many novel, that were more than 6-fold enriched compared to the non-specific membrane tethered catalyst. These studies define distance labeling parameters from single-site catalysts placed directly on the membrane target of interest, and more accurately compare to non-specific labeling to identify membrane complexes with higher confidence.
A REM-active basal ganglia circuit that regulates anxiety
Authors: Ba Wei , Nollet Mathieu , Yu Xiao , Wong Sara , Miao Andawei , Beckwith Esteban , Harding Edward C. , Ma Ying , Yustos Raquel , Vyssotski Alexei L. , Wisden William , Franks Nicholas P. 
Published: July 2023

SUMMARYREM sleep has been hypothesized to promote emotional resilience, but any neuronal circuits mediating this have not been identified. We find that in mice, somatostatin (Som) neurons in the entopeduncular nucleus (EPSom)/internal globus pallidus are predominantly active selectively during REM sleep. This unique REM activity is necessary and sufficient for maintaining normal REM sleep. Inhibiting or exciting EPSomneurons reduced or increased REM sleep duration, respectively. Activation of the sole downstream target of EPSomneurons, Vglut2 cells in the lateral habenula (LHb), increased sleep via the ventral tegmental area (VTA). A simple chemogenetic scheme to periodically inhibit the LHb over 4 days selectively removed a significant amount of cumulative REM sleep. Chronic REM reduction correlated with mice becoming anxious and more sensitive to aversive stimuli. Therefore, we suggest that REM sleep, in part generated by the EP→LHb→VTA circuit identified here, could contribute to stabilizing reactions to habitual aversive stimuli.
Representation of a Perceptual Bias in the Prefrontal Cortex
Authors: Serrano-Fernández Luis , Beirán Manuel , Romo Ranulfo , Parga Néstor 
Published: July 2023

AbstractPerception is influenced by sensory stimulation, prior knowledge, and contextual cues, which collectively contribute to the emergence of perceptual biases. However, the precise neural mechanisms underlying these biases remain poorly understood. This study aims to address this gap by analyzing neural recordings from the prefrontal cortex (PFC) of monkeys performing a vibrotactile frequency discrimination task. Our findings provide empirical evidence supporting the hypothesis that perceptual biases can be reflected in the neural activity of the PFC. We found that the state-space trajectories of PFC neuronal activity encoded a warped representation of the first frequency presented during the task. Remarkably, this distorted representation of the frequency aligned with the predictions of its Bayesian estimator. The identification of these neural correlates expands our understanding of the neural basis of perceptual biases and highlights the involvement of the PFC in shaping perceptual experiences. Similar analyses could be employed in other delayed comparison tasks and in various brain regions to explore where and how neural activity reflects perceptual biases during different stages of the trial.
The Mediterranean mussel,Mytilus galloprovincialis, a novel model for developmental studies of mollusks
Authors: Miglioli Angelica , Tredez Marion , Boosten Manon , Sant Camille , Carvalho João E. , Dru Philippe , Canesi Laura , Schubert Michael , Dumollard Rémi 
Published: July 2023

AbstractA model organism in developmental biology is defined by its experimental amenability as well as by resources created for the model system by the scientific community. For the most powerful models, the combination of both has already yielded a thorough understanding of development. However, the number of developmental model systems is still very limited, and their phylogenetic distribution is heavily biased. Members of one of the largest animal phyla, the mollusks, for example, have long been neglected as developmental model organisms. To remedy this shortcoming, we produced a detailed developmental transcriptome for the Mediterranean musselMytilus galloprovincialis, a bivalve mollusk, and expanded the list of experimental protocols available for this species. Our high-quality transcriptome allowed us to identify transcriptomic signatures of developmental transitions and to perform a first comparison with the Pacific oysterCrassostrea gigasthat can be used in future multi-species analyses. To allow co-labelling studies, we optimized protocols for immunohistochemistry and hybridization chain reaction and combined both techniques to create high-resolution co-expression maps of developmental genes. The resources and protocols we describe here thus represent an enormous boost for the establishment of the Mediterranean mussel as a laboratory model in developmental biology.Summary statementResources and techniques are described for the Mediterranean musselMytilus galloprovincialis, which, together, establish a novel model system for studying mollusk development and animal evolution.
Connexin 41.8 mediates the correct temporal induction of haematopoietic stem and progenitor cells
Authors: Petzold Tim , Watanabe Masakatsu , Bertrand Julien Y. 
Published: July 2023

AbstractHaematopoietic stem and progenitor cells (HSPCs) derive from a subset of endothelial cells (ECs), known as haemogenic ECs by the process of endothelial-to-haematopoietic transition (EHT). Although many factors involved in EHT have been elucidated, we still have a poor understanding of the temporal regulation of this process. Mitochondrial-derived reactive oxygen species (ROS) have been shown to stabilise hypoxia-inducible factors 1/2α (Hif1/2α), allowing them to positively regulate EHT. Here, we show a developmental delay in EHT and HSPC induction in a gap junction mutant,connexin (cx)41.8(orthologous to mammalianCX40), in zebrafish. In mammalian cells, CX40 has been shown to localise to the mitochondria. We demonstrate that Cx41.8 is important for the correct temporal generation of mitochondrial ROS, which stabilise the Hif pathway, allowing for the subsequent specification of the haemogenic endothelium. Taken together, our data indicate that Cx41.8 mediates the correct induction of HSPCs.
Tartrolon sensing and detoxification by theListeria monocytogenes timABRresistance operon
Authors: Engelgeh Tim , Herrmann Jennifer , Jansen Rolf , Müller Rolf , Halbedel Sven 
Published: July 2023

AbstractListeria monocytogenesis a foodborne bacterium that naturally occurs in the soil. Originating from there, it contaminates crops and infects farm animals and their consumption by humans may lead to listeriosis, a systemic life-threatening infectious disease. The adaptation ofL. monocytogenesto such contrastive habitats is reflected by the presence of virulence genes for host infection and other genes for survival under environmental conditions. Among the latter are ABC transporters for excretion of antibiotics produced by environmental competitors, however, most of these transporters have not been characterized. Here, we generated a collection of promoter-lacZfusions for genes encoding ABC-type drug transporters ofL. monocytogenesand screened this reporter strain collection for induction using a library of natural compounds produced by various environmental microorganisms. We found that thetimABRlocus (lmo1964-lmo1962) was induced by the macrodiolide antibiotic tartrolon B, which is synthesized by the soil myxobacteriumSorangium cellulosum. Tartrolon B resistance ofL. monocytogeneswas dependent ontimAB, encoding the ATPase and the permease component of a novel ABC transporter. Moreover, transplantation oftimABwas sufficient to confer tartrolon B resistance toBacillus subtilis. Expression of thetimABRlocus was found to be auto-repressed by the TimR repressor, whose repressing activity was lost in the presence of tartrolon B. We also demonstrate that tartrolon sensitivity was suppressed by high external potassium concentrations, suggesting that tartrolon acts as potassium ionophore. Our results help to map the ecological interactions of an important human pathogen with its co-residing species within their joint natural reservoir.ImportanceListeria monocytogenesis an environmental bacterium that can cause listeriosis in humans when ingested. The genome of this bacterium contains many genes encoding putative ATP binding cassette transporters with unknown function. Presumably, these transporters serve the excretion of antimicrobial compounds produced by co-residing species competing withL. monocytogenesfor nutrients and habitats. We here fused thelacZreporter gene to the promoters of these transporter genes and screened a natural compound library for activating substances. We discovered that tartrolon B activates expression of theL. monocytogenes timABRoperon, encoding the TimAB exporter and the TimR repressor. Tartrolon B is an antibiotic produced by the soil-dwelling myxobacteriumSorangium cellulosum. We elucidate how thetimABRgenes mediate sensing and detoxification of this antibiotic. This represents the first known mechanism of tartrolon resistance and may help to better define the natural reservoir ofL. monocytogenes.
The effective number of shared dimensions: A simple method for revealing shared structure between datasets
Authors: Giaffar Hamza , Buxó Camille Rullán , Aoi Mikio 
Published: July 2023

AbstractA number of recent studies have sought to understand the behavior of artificial and biological neural networks by comparing representations across layers, networks and brain areas. Simultaneously, there has been growing interest in using dimensionality of a dataset as a proxy for computational complexity. At the intersection of these topics, studies exploring the dimensionality of shared computational and representational subspaces have relied on model-based methods, but a standard, model-free measure is lacking. Here we present a candidate measure for shared dimensionality that we call the effective number of shared dimensions (ENSD). The ENSD can be applied to data matrices sharing at least one dimension, reduces to the well-known participation ratio when both data sets are equivalent and has a number of other robust and intuitive mathematical properties. Notably, the ENSD can be written as a similarity metric that is a re-scaled version of centered kernel alignment (CKA) but additionally describes the dimensionality of the aligned subspaces. Unlike methods like canonical correlation analysis (CCA), the ENSD is robust to cases where data is sparse or low rank. We demonstrate its utility and computational efficiency by a direct comparison of CKA and ENSD on across-layer similarities in convolutional neural networks as well as by recovering results from recent studies in neuroscience on communication subspaces between brain regions. Finally, we demonstrate how the ENSD and its constituent statistics allow us to perform a variety of multi-modal analyses of multivariate datasets. Specifically, we use connectomic data to probe the alignment of parallel pathways in the fly olfactory system, revealing novel results in the interaction between innate and learned olfactory representations. Altogether, we show that the ENSD is an interpretable and computationally efficient model-free measure of shared dimensionality and that it can be used to probe shared structure in a wide variety of data types.
Insights into Gastrointestinal Redox Dysregulation in a Rat Model of Alzheimer’s Disease and the Assessment of the Protective Potential of D-galactose
Authors: Homolak Jan , Varvaras Konstantinos , Sciacca Vittorio , Perhoc Ana Babic , Virag Davor , Knezovic Ana , Barilar Jelena Osmanovic , Salkovic-Petrisic Melita 
Published: July 2023

AbstractIntroductionRecent evidence suggests that the gut plays a vital role in the development and progression of Alzheimer’s disease (AD) by triggering systemic inflammation and oxidative stress. The well-established rat model of AD, induced by intracerebroventricular administration of streptozotocin (STZ-icv), provides valuable insights into the GI implications of neurodegeneration. Notably, this model leads to pathophysiological changes in the gut, including redox dyshomeostasis, resulting from central neuropathology. Our study aimed to investigate the mechanisms underlying gut redox dyshomeostasis and assess the effects of D-galactose, which is known to benefit gut redox homeostasis and alleviate cognitive deficits in this model.Materials and MethodsDuodenal rings isolated from STZ-icv animals and control groups were subjected to a prooxidative environment using AAPH or H2O2with or without D-galactose in oxygenated Krebs buffer ex vivo. Redox homeostasis was analyzed through protein microarrays and functional biochemical assays, alongside cell survival assessment. Structural equation modeling, univariate, and multivariate models were employed to evaluate the differential response of STZ-icv and control samples to the controlled prooxidative challenge.ResultsSTZ-icv samples showed suppressed expression of catalase and glutathione peroxidase 4 (GPX4) and increased baseline activity of enzymes involved in H2O2and superoxide homeostasis. The altered redox homeostasis status was associated with an inability to respond to oxidative challenges and D-galactose. Conversely, the presence of D-galactose increased antioxidant capacity, enhanced catalase and peroxidase activity, and upregulated superoxide dismutases in the control samples.ConclusionSTZ-icv-induced gut dysfunction is characterized by a diminished ability of the redox regulatory system to maintain long-term protection through the transcription of antioxidant response genes, as well as compromised activation of enzymes responsible for immediate antioxidant defense. D-galactose can exert beneficial effects on gut redox homeostasis under physiological conditions.
H2O2sulfenylates CHE linking local infection to establishment of systemic acquired resistance
Authors: Cao Lijun , Yoo Heejin , Chen Tianyuan , Mwimba Musoki , Zhang Xing , Dong Xinnian 
Published: July 2023

AbstractIn plants, a local infection can lead to systemic acquired resistance (SAR) through increased production of salicylic acid (SA). For 30 years, the identity of the mobile signal and its direct transduction mechanism for systemic SA synthesis in initiating SAR have been hotly debated. We found that, upon pathogen challenge, the cysteine residue of transcription factor CHE undergoes sulfenylation in systemic tissues, enhancing its binding to the promoter of SA-synthesis gene,ICS1, and increasing SA production. This occurs independently of previously reported pipecolic acid (Pip) signal. Instead, H2O2produced by NADPH oxidase, RBOHD, is the mobile signal that sulfenylates CHE in a concentration-dependent manner. This modification serves as a molecular switch that activates CHE-mediated SA-increase and subsequent Pip-accumulation in systemic tissues to synergistically induce SAR.One Sentence SummaryRBOHD-generated H2O2sulfenylates transcription factor CHE to establish systemic acquired resistance in plants.