bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scaling of Protein Function Across the Tree of Life
Authors: Gondhalekar Riddhi , Kempes Christopher P. , McGlynn Shawn Erin 
Published: March 2023

ABSTRACTScaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal non-trivial generalities as genomes change in size. The abundance of functional categories in a given genome scales with genome size, suggesting that universal constraints shape category abundance. Here we look across the tree of life to understand how genome evolution may be related to functional scaling. We revisit previous observations of functional genome scaling with an expanded taxonomy by analyzing 3726 bacterial, 220 archaeal, and 79 unicellular eukaryotic genomes. We find that for some functional classes, scaling is best described by multiple exponents, revealing previously unobserved shifts in scaling as genomes grow or contract. Furthermore, scaling varies between phyletic groups and is less universal than previously thought, with scaling shifts varying uniquely between domains and scaling exponents varying uniquely between phyla. We also find that individual phyla frequently span scaling exponents of functional classes, revealing that individual clades can move across scaling exponents. Across the tree of life, variability in functional scaling is not accounted for by genome phylogeny, suggesting that physiological and/or cell plan outweighs phylogeny.
Assigning a social status from face adornments: an fMRI study
Authors: Salagnon M , d’Errico F , Rigaud S , Mellet E 
Published: March 2023

AbstractThe human face has been culturally modified for at least 150,000 years using practices like painting, tattooing and scarification to convey symbolic meanings and individual identity. The present study used functional magnetic resonance imaging to explore the brain networks involved in attributing social status from face decorations. Results showed the fusiform gyrus, orbitofrontal cortex, and salience network were involved in social encoding, categorization, and evaluation. The hippocampus and parahippocampus were activated due to the memory and associative skills required for the task, while the inferior frontal gyrus likely interpreted face ornaments as symbols. Resting-state functional connectivity analysis clarified the interaction between these regions. The study highlights the importance of these neural interactions in the symbolic interpretation of social markers on the human face, which were likely active in early Homo species and intensified with Homo sapiens populations as more complex technologies were developed to culturalize the human face.
Stimulus-evoked and resting-state alpha oscillations show a linked dependence on patterned visual experience for development
Authors: Pant Rashi , Ossandón José , Stange Liesa , Shareef Idris , Kekunnaya Ramesh , Röder Brigitte 
Published: March 2023

AbstractPersistent visual impairments after congenital blindness due to dense bilateral cataracts have been attributed to altered visual cortex development within a sensitive period. Occipital alpha (8-14 Hz) oscillations were found to be reduced after congenital cataract reversal during visual motion tasks. However, it has been unclear whether reduced alpha oscillations were task-specific, or linked to impaired visual behavior in cataract-reversed individuals. Here, we compared resting-state and stimulus-evoked alpha activity between individuals who had been treated for dense bilateral congenital cataracts (CC, n = 13, mean duration of blindness = 11.0 years) and age-matched, normally sighted individuals (SC, n = 13). We employed the visual impulse response function, adapted from VanRullen and MacDonald (2012), to test for the characteristic alpha response to visual white noise. Participants observed white noise stimuli changing in luminance with equal power at frequencies between 0-30 Hz. Compared to SC individuals, CC individuals demonstrated a reduced likelihood of exhibiting an evoked alpha response. Moreover, stimulus-evoked alpha power was reduced and correlated with a corresponding reduction of resting-state alpha power in the same CC individuals. Finally, CC individuals with an above-threshold evoked alpha peak had better visual acuity than CC individual without an evoked alpha peak. Since alpha oscillations have been linked to feedback communication, we suggest that the concurrent impairment in resting-state and stimulus-evoked alpha oscillations indicates an altered interaction of top-down and bottom-up processing in the visual hierarchy, which likely contributes to incomplete behavioral recovery in individuals who had experienced transient congenital blindness.
Graph theory analysis reveals an assortative pain network vulnerable to attacks
Authors: Chen Chong , Tassou Adrien , Morales Valentina , Scherrer Grégory 
Published: March 2023

AbstractThe neural substrate of pain experience has been described as a dense network of connected brain regions. However, the connectivity pattern of these brain regions remains elusive, precluding a deeper understanding of how pain emerges from the structural connectivity. Here, we use graph theory to systematically characterize the architecture of a comprehensive pain network, including both cortical and subcortical brain areas. This structural brain network consists of 49 nodes denoting pain-related brain areas, linked by edges representing their relative incoming and outgoing axonal projection strengths. Sixty-three percent of brain areas in this structural pain network share reciprocal connections, reflecting a dense network. The clustering coefficient, a measurement of the probability that adjacent nodes are connected, indicates that brain areas in the pain network tend to cluster together. Community detection, the process of discovering cohesive groups in complex networks, successfully reveals two known subnetworks that specifically mediate the sensory and affective components of pain, respectively. Assortativity analysis, which evaluates the tendency of nodes to connect with other nodes with similar features, indicates that the pain network is assortative. Finally, robustness, the resistance of a complex network to failures and perturbations, indicates that the pain network displays a high degree of error tolerance (local failure rarely affects the global information carried by the network) but is vulnerable to attacks (selective removal of hub nodes critically changes network connectivity). Taken together, graph theory analysis unveils an assortative structural pain network in the brain processing nociceptive information, and the vulnerability of this network to attack opens up the possibility of alleviating pain by targeting the most connected brain areas in the network.
The degree of T cell stemness differentially impacts the potency of adoptive cancer immunotherapy in a Lef-1 and Tcf-1 dependent manner
Authors: Rangel Rivera Guillermo O. , Dwyer Connor J. , Knochelmann Hannah M. , Smith Aubrey S. , Aksoy Arman , Cole Anna C. , Wyatt Megan M. , Thaxton Jessica E. , Lesinski Gregory B. , Paulos Chrystal M. 
Published: March 2023

AbstractGenerating stem memory T cells (TSCM) is a key goal for improving cancer immunotherapy. Yet, the optimal way to modulate signaling pathways that enrich TSCMproperties remains elusive. Here, we discovered that the degree to which the PI3Kδ pathway is blocked pharmaceutically can generate T cells with differential levels of stemness properties. This observation was based on the progressive enrichment of transcriptional factors of stemness (Tcf-1 and Lef-1). Additional investigation revealed that T cells with high stemness features had enhanced metabolic plasticity, marked by heightened mitochondrial function and glucose uptake. Conversely, T cells with low or medium features of stemness expressed more inhibitory checkpoint receptors (Tim-3, CD39) and were vulnerable to antigen-induced cell death. Only TCR-antigen specific T cells with high stemness persisted following adoptive transferin vivoand mounted protective immunity to melanoma tumors. Likewise, the strongest level of PI3Kδ blockadein vitrogenerated human tumor infiltrating lymphocytes (TILs) and CAR T cells with heightened stemness properties, in turn bolstering their capacity to regress human mesothelioma tumors. We find that the level of stemness T cells possessin vitrodifferentially impacts their potency upon transfer in three tumor models. Mechanistically, both Lef-1 and Tcf-1 sustain anti-tumor protection by high TSCM, as deletion of either one compromised cellular therapy. Collectively, these findings highlight the therapeutic potential of carefully modulating PI3Kδ signaling in T cells to confer high stemness and mediate protective responses to solid tumors.
Hippocampal sclerosis of aging at post-mortem is evident on MRI more than a decade prior
Authors: Ortega-Cruz Diana , Iglesias Juan Eugenio , Rabano Alberto , Strange Bryan 
Published: March 2023

AbstractINTRODUCTIONHippocampal sclerosis of aging (HS) is an important component of combined dementia neuropathology. However, the temporal evolution of its histologically-defined features is unknown. We investigated pre-mortem longitudinal hippocampal atrophy associated with HS, as well as with other dementia-associated pathologies.METHODSWe analyzed hippocampal volumes from MRI segmentations in 64 dementia patients with longitudinal MRI follow-up and post-mortem neuropathological evaluation, including HS assessment in the hippocampal head and body.RESULTSSignificant HS-associated hippocampal volume changes were observed thoughout the evaluated timespan, up to 11.75 years before death. These changes were independent of age and Alzheimer’s Disease (AD) burden, and specifically driven by CA1 and subiculum. AD burden, but not HS, significantly associated with the rate of hippocampal atrophy.DISCUSSIONHS-associated volume changes are detectable on MRI earlier than 10 years before death. These findings could contribute to the derivation of volumetric cut-offs forin vivodifferentiation between HS and AD.
Histone variants shape chromatin states in Arabidopsis
Authors: Jamge Bhagyshree , Lorković Zdravko J. , Axelsson Elin , Osakabe Akihisa , Shukla Vikas , Yelagandula Ramesh , Akimcheva Svetlana , Kuehn Annika Luisa , Berger Frédéric 
Published: March 2023

SummaryHow different intrinsic sequence variation or regulatory modifications of histones regulate nucleosome interactions with transcription remain unclear. By contrast with H3 and H2B variants, H2A variants occupy specific domains of chromatin inArabidopsis thaliana.Broad domains of chromatin are affected by the loss of remodelers that affect the deposition or the exchange of H2A variants. Notably, the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) is required to maintain enrichment in all markers of constitutive heterochromatin including DNA methylation, H3K9me1/2 and the variant H2A.W. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in theArabidopsis thalianagenome and showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
Causal Effects of Pupil Size on Visual Processing
Authors: Mathôt Sebastiaan , Berberyan Hermine , Büchel Philipp , Ruuskanen Veera , Vilotijević Ana , Kruijne Wouter 
Published: March 2023

AbstractThe size of the eyes’ pupils determines how much light enters the eye and also how well this light is focused. Through this route, pupil size shapes the earliest stages of visual processing. Yet causal effects of pupil size on vision are poorly understood and rarely studied. Here we report the effects of both experimentally induced and spontaneous changes in pupil size on visual processing as measured through EEG. We compare these to the effects of stimulus intensity and covert visual attention, because previous studies have shown that these factors all have comparable effects on some common measures of early visual processing, such as detection performance and steady-state visual evoked potentials; yet it is still unclear whether these are superficial similarities, or rather whether they reflect similar underlying processes. Using a mix of neural-network decoding, ERP analyses, and time-frequency analyses, we find that induced pupil size, spontaneous pupil size, stimulus intensity, and covert visual attention all affect EEG responses, mainly over occipital and parietal electrodes, but—crucially—that they do so in qualitatively different ways. Induced and spontaneous pupil-size changes mainly modulate activity patterns (but not overall power or intertrial coherence) in the high-frequency beta range; this may reflect a causal effect of pupil size on oculomotor activity and/ or visual processing. In addition, spontaneous (but not induced) pupil size tends to correlate positively with intertrial coherence in the alpha band; this may reflect a non-causal relationship, mediated by arousal. Taken together, our findings suggest that pupil size has qualitatively different effects on visual processing from stimulus intensity and covert visual attention. This shows that pupil size causally affects visual processing, and provides concrete starting points for further study of this important yet understudied earliest stage of visual processing.
“Anthropogenic Threats and Conservation Practices: Evaluating LULC Changes in Relocated Villages of Panna Tiger Reserve, Madhya Pradesh, India”
Authors: Khan Susmita 
Published: March 2023

AbstractProtected areas globally, including India, face anthropogenic threats despite environmental and forest protection laws. To reduce these pressures, conservation related settlement evacuation from protected areas has been a common conservation practice for decades in many countries. Controversies aside, studies have shown that evacuation of settlements from protected areas has a positive impact on forest cover change and biodiversity increase. Here in this study, we conducted this study for the 14 relocated village sites of Panna Tiger Reserve to see the changes in major Land use Land cover changes over 15 years (2004-2019). We observed a significant increase in forested areas in those regions over time, as well as prominent changes in different land cover classes. The increase in Grassland, Open Forest, and Dense Forest from 2004 to 2019 was significant, and settlements in relocated areas were mainly converted to different forest types. Additionally, fieldwork and camera trap data showed that the relocated sites with established woodlands and other forest classes supported higher animal diversity and species composition compared to other sites. This study provides a knowledge base for conservation and management practices by identifying significant changes in various land use and land cover classes.
Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation
Authors: Tiwari Anupama , Hashemiaghdam Arsalan , Laramie Marissa A. , Maschi Dario , Haddad Tristaan , Stunault Marion I. , Bergom Carmen , Javaheri Ali , Klyachko Vitaly , Ashrafi Ghazaleh 
Published: March 2023

AbstractNeurotransmission is an energetically expensive process that underlies cognition. During intense electrical activity or dietary restrictions, glucose levels in the brain plummet, forcing neurons to utilize alternative fuels. However, the molecular mechanisms of neuronal metabolic plasticity remain poorly understood. Here, we demonstrate that glucose-deprived neurons activate the CREB and PGC1α transcriptional program that induces the expression of the mitochondrial deacetylase Sirtuin 3 (Sirt3) bothin vitroandin vivo. We show that Sirt3 localizes to axonal mitochondria and stimulates mitochondrial oxidative capacity in hippocampal nerve terminals. Sirt3 plays an essential role in sustaining synaptic transmission in the absence of glucose by powering the retrieval of synaptic vesicles after release. These results demonstrate that the transcriptional induction of Sirt3 ensures the metabolic plasticity of synaptic transmission.HighlightsGlucose deprivation drives transcriptional reprogramming of neuronal metabolism via CREB and PGC1α.Glucose or food deprivation trigger the neuronal expression of mitochondrial deacetylase sirtuin 3 (Sirt3) bothin vitroandin vivo.Sirt3 stimulates oxidative ATP synthesis in nerve terminals.Sirt3 sustains the synaptic vesicle cycle in the absence of glucose.
Biodiversity shows unique responses to land-use change across regional biomes
Authors: Bevan Peggy , Ferreira Guilherme Braga , Ingram Daniel J , Rowcliffe Marcus , Young Lucy , Freeman Robin , Jones Kate E. 
Published: March 2023

AbstractBiogeography has a critical influence on how ecological communities respond to threats and how effective conservation interventions are designed. For example, the resilience of ecological communities is linked to environmental and climatic features, and the nature of threats impacting ecosystems also varies geographically. Understanding community-level threat responses may be most accurate at fine spatial scales, however collecting detailed ecological data at such a high resolution would be prohibitively resource intensive. In this study, we aim to find the spatial scale that could best capture variation in community-level threat responses whilst keeping data collection requirements feasible. Using a database of biodiversity records with extensive global coverage, we modelled species richness and total abundance (the responses) across land-use types (reflecting threats), considering three different spatial scales: biomes, biogeographical realms, andregional biomes(the interaction between realm and biome). We then modelled data from three highly sampled biomes separately to ask how responses to threat differ between regional biomes and taxonomic group. We found strong support for regional biomes in explaining variation in species richness and total abundance compared to biomes or realms alone. Our biome case studies demonstrate that there is a high variation in magnitude and direction of threat responses across both regional biomes and taxonomic group, but all groups in tropical forest showed a consistently negative response, whilst many taxon-regional biome groups showed no clear response to threat in temperate forest and tropical grassland. Our results suggest that the taxon-regional biome unit has potential as a reasonable spatial and ecological scale for understanding how ecological communities respond to threats and designing effective conservation interventions to bend the curve on biodiversity loss.
Endothelial Histone Deacetylase 1 Activity Impairs Kidney Microvascular NO Signaling in Rats fed a High Salt Diet
Authors: Dunaway Luke S. , Cook Anthony K. , Botta Davide , Molina Patrick A. , d’Uscio Livius V. , Katusic Zvonimir S. , Pollock David M. , Inscho Edward W. , Pollock Jennifer S. 
Published: March 2023

AbstractAimWe aimed to identify new mechanisms by which a high salt diet (HS) decreases NO production in kidney microvascular endothelial cells. Specifically, we hypothesized HS impairs NO signaling through a histone deacetylase 1 (HDAC1)-dependent mechanism.MethodsMale Sprague Dawley rats were fed normal salt diet (NS; 0.49% NaCl) or high salt diet (4% NaCl) for two weeks. NO signaling was assessed by measuring L-NAME induced vasoconstriction of the afferent arteriole using the blood perfused juxtamedullary nephron (JMN) preparation. In this preparation, kidneys were perfused with blood from a donor rat on a matching or different diet to that of the kidney donor. Kidney endothelial cells were isolated with magnetic activated cell sorting and HDAC1 activity was measured.ResultsWe found that HS impaired NO signaling in the afferent arteriole. This was restored by inhibition of HDAC1 with MS-275. Consistent with these findings, HDAC1 activity was increased in kidney endothelial cells. We further found the loss of NO to be dependent upon the diet of the blood donor rather than the diet of the kidney donor and the plasma from HS fed rats to be sufficient to induce dysfunction suggesting a humoral factor, we termedPlasmaDerivedEndothelial-dysfunctionMediator (PDEM), mediates the endothelial dysfunction. The antioxidants, PEG-SOD and PEG-catalase, as well as the NOS cofactor, tetrahydrobiopterin, restored NO signaling.ConclusionWe conclude that HS activates endothelial HDAC1 through PDEM leading to decreased NO signaling. This study provides novel insights into the molecular mechanisms by which a HS decreases renal microvascular endothelial NO signaling.
Class-imbalanced Unsupervised and Semi-Supervised Domain Adaptation for Histopathology Images
Authors: Hosseini S. Maryam , Shafique Abubakr , Babaie Morteza , Tizhoosh H.R. 
Published: March 2023

AbstractIn dealing with the lack of sufficient annotated data and in contrast to supervised learning, unsupervised, self-supervised, and semi-supervised domain adaptation methods are promising approaches, enabling us to transfer knowledge from rich labeled source domains to different (but related) unlabeled target domains, reducing distribution discrepancy between the source and target domains. However, most existing domain adaptation methods do not consider the imbalanced nature of the real-world data, affecting their performance in practice. We propose to overcome this limitation by proposing a novel domain adaptation approach that includes two modifications to the existing models. Firstly, we leverage the focal loss function in response to class-imbalanced labeled data in the source domain. Secondly, we introduce a novel co-training approach to involve pseudo-labeled target data points in the training process. Experiments show that the proposed model can be effective in transferring knowledge from source to target domain. As an example, we use the classification of prostate cancer images into low-cancerous and high-cancerous regions.