bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-resolved functional connectivity during visuomotor graph learning
Authors: Loman Sophie , Caciagli Lorenzo , Kahn Ari E. , Szymula Karol P. , Nyema Nathaniel , Bassett Dani S. 
Published: July 2024

1AbstractHumans naturally attend to patterns that emerge in our perceptual environments, building mental models that allow for future experiences to be processed more effectively and efficiently. Perceptual events and statistical relations can be represented as nodes and edges in a graph, respectively. Recent work in the field of graph learning has shown that human behavior is sensitive to graph topology, but less is known about how that topology might elicit distinct neural responses during learning. Here, we address this gap in knowledge by applying time-resolved network analyses to fMRI data collected during a visuomotor graph learning task to assess neural signatures of learning modular graphs and non-modular lattice graphs. We found that performance on this task was supported by a highly flexible visual system and otherwise relatively stable brain-wide community structure, cohesiveness within the dorsal attention, limbic, default mode, and subcortical systems, and an increasing degree of integration between the visual and ventral attention systems. Additionally, we found that the time-resolved connectivity of the limbic, default mode, temporoparietal, and subcortical systems was associated with enhanced performance for the modular group but not the lattice group. These findings provide evidence for the differential neural processing of statistical structures with distinct topologies and highlight similarities between the neural correlates of graph learning and statistical learning more broadly.
Functional traits explain growth resistance to successive hotter droughts across a wide set of common and future tree species in Europe
Authors: Kretz Lena , Schnabel Florian , Richter Ronny , Raabgrund Anika , Kattge Jens , Andraczek Karl , Kahl Anja , Künne Tom , Wirth Christian 
Published: July 2024

AbstractIn many regions worldwide, forests suffer from climate change-induced droughts. The ‘hotter drought’ in Europe in 2018 with the consecutive drought years 2019 and 2020 caused large-scale growth declines and forest dieback. We investigated if tree growth responses to the 2018–2020 drought can be explained by tree functional traits related to drought tolerance, growth, and resource acquisition.We assessed growth resistance, that is, growth during drought compared to pre-drought-conditions, in 71 planted tree species using branch shoot increments. We leveraged gap-filled trait data related to drought tolerance (P50, stomata density and conductivity), growth and resource acquisition (SLA, LNC, C:N, Amax) and wood density from the TRY database to explain growth resistance for gymnosperms and angiosperms.We found significantly reduced growth during drought across all species. Legacy effects further decreased growth resistance in 2019 and 2020. Gymnosperms showed decreasing growth resistance with increasing P50 and acquisitiveness, such as high SLA, LNC, and Amax. Similar results were found for angiosperms, however, with less clear pattern. Four distinct response types emerged: ‘Sufferer’, ‘Late sufferer’, ‘Recoverer’ and ‘Resisters’, with gymnosperms predominately falling into the ‘Sufferer’ and ‘Late sufferer’ categories.Our study provides evidence for significant growth reductions and legacy effects in response to consecutive hotter droughts, which can be explained by functional traits across a wide set of tree species. The a posteriori classification into response types revealed the diversity of temporal responses to a prolonged drought. We conclude that high drought tolerance bolsters growth resistance, while acquisitive species suffer stronger under drought.
Microglial low-affinity FcγR mediates the phagocytic elimination of dopaminergic neurons in Parkinson’s disease degeneration
Authors: Casanova P.V. , Saavedra-López E. , Freitag-Berenguel I. , Usandizaga M. , Martínez-Remedios P. , Giménez-Montes C. , Clinton E. , Roig-Martínez M. , Cribaro G.P. , Barcia C 
Published: July 2024

AbstractMicroglia-mediated neuroinflammation contributes to dopaminergic (DA) neurodegeneration in Parkinson’s disease (PD). It is thought that microglial cells interact with DA neurons of the substantia nigra pars compacta (SNpc), the most vulnerable region in parkinsonian neuropathology, playing a critical role through the process of neuronal loss. However, the specific mechanisms by which microglial reactivity is triggered and exerts such a deleterious effect remains unclear. Experimental models of PD in mice have shown that phagocytosis plays an essential role in the elimination of degenerating neurons, suggesting that blocking this microglial function could be beneficial to preserve remaining DA neurons. In the present work, we pinpoint the role of the Fcγ receptor (FcγR) as a potential trigger of microglial phagocytosis in PD. We found that the FcγR is overexpressed in the degenerating SNpc in postmortem samples of PD patients, alongside histological indications of phagocytic microglia. Likewise, experimental models of PD also show increased FcγR expression, together with evidence of similar phagocytosis events. Most importantly, blocking FcγRin vitro, by using neutralizing antibodies, reduced the microglial-mediated elimination of DA cells. High resolution imaging revealed that the FcγR is involved in phagocytic synapse formation, and appeared polarized, and segregated to actin-rich protruding cups, when interacting one-on-one towards single target DA cells. Additionally, by inhibiting FcγR downstream actin-polymerizing signaling Cdc42, microglia were unable to eliminate DA cells. Finally, experimentsin vivo, using an experimental model of PD in mouse, revealed that passive immunotherapy with FcγR neutralizing monoclonal antibodies, as well as inhibiting its downstream signaling Cdc42, protect DA neurons from elimination. These results indicate that the FcγR may be a critical factor inducing DA neuron phagocytosis in PD and suggest a novel immunotherapeutic strategy targeting microglia to preserve neuronal loss.
A pilot study for deciphering post-translational modifications and proteoforms of tau protein by capillary electrophoresis-mass spectrometry
Authors: Fang Fei , Xu Tian , Hagar Hsiao-Tien Chien , Hovde Stacy , Kuo Min-Hao , Sun Liangliang 
Published: July 2024

AbstractAbnormal accumulation of tau proteins is one pathological hallmark of Alzheimer□s disease (AD). Many tau protein post-translational modifications (PTMs) are associated with the development of AD, such as phosphorylation, acetylation, and methylation. Therefore, a complete picture of PTM landscape of tau is critical for understanding the molecular mechanisms of AD progression. Here, we offered a pilot study of combining two complementary analytical techniques, capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) and reversed-phase liquid chromatography (RPLC)-MS/MS, for bottom-up proteomics of recombinant human tau-0N3R. We identified 53 phosphorylation sites of tau-0N3R in total, which is about 30% higher than that from RPLC-MS/MS alone. CZE-MS/MS provided more PTM sites (i.e., phosphorylation) and modified peptides of tau-0N3R than RPLC-MS/MS, and its predicted electrophoretic mobility helped improve the confidence of the identified modified peptides. We developed a highly efficient capillary isoelectric focusing (cIEF)-MS technique to offer a bird’s-eye view of tau-0N3R proteoforms, with 11 putative tau-0N3R proteoforms carrying up to nine phosphorylation sites and lower pI values from more phosphorylated proteoforms detected. Interestingly, under a native-like cIEF-MS condition, we observed three putative tau-0N3R dimers carrying phosphate groups. The findings demonstrate that CE-MS is a valuable analytical technique for the characterization of tau PTMs, proteoforms, and even oligomerization.
Assessing nutritional pigment content and plant health status of green and red leafy vegetables by image analysis: Catching the “red herring” of plant digital color processing
Authors: Agarwal Avinash , Colwell Filipe de Jesus , Galvis Viviana Andrea Correa , Hill Tom , Boonham Neil , Prashar Ankush 
Published: July 2024

AbstractEstimating pigment content in leafy vegetables via digital image analysis is a reliable method for real-time assessment of plant health status and nutritive value. However, the present leaf color analysis models developed using green-leafed plants do not perform reliably while analyzing images of anthocyanin-rich leaves, often giving misleading or “red herring” trends. Hence, the present study investigates variations in different digital color features for six types of leafy vegetables with varying levels of laminar anthocyanin to identify holistic digital color analysis models that could be implemented for real-time assessment of health status as well as nutritional pigment contents of leafy vegetables irrespective of laminar anthocyanin status. For this, datasets from three digital color spaces, viz., RGB (red, green, blue), HSI (hue, saturation, intensity), andL*a*b*(lightness, redness-greenness, yellowness-blueness), were compared with pigment contents ofn= 320 leaf samples, and were analyzed via linear and non-linear regression using single variables, multiple linear regression, Support Vector regression, and Random Forest regression to predict chlorophyll and anthocyanin contents. While most digital color features presented abrupt shifts between anthocyanin-rich and low-anthocyanin samples, the R digital color feature did not show any deviation due to leaf anthocyanin content and was found to have the best correlation with SPAD chlorophyll meter readings (R2= 0.83). Concomitantly, H (R2= 0.82) anda*(R2= 0.79) features correlated most strongly with leaf anthocyanin content. In general, prediction of pigment contents was more accurate when data from all channels within a color space was analyzed simultaneously. Further, most reliable estimates of pigment content were provided by Support Vector and Random Forest regression models (0.7 <R2< 0.85). Thus, the present findings demonstrate how digital color analysis of green as well as anthocyanin-rich leafy vegetables could be implemented for assessing plant health status and nutritional pigment content non-invasively.
Astroglial atrophy associates with loss of nuclear S100A10 in the hippocampus of aged male tree shrews
Authors: Rodriguez-Callejas Juan D. , Irene-Fierro Mariangel , Aguilar-Navarro Sara , Fuchs Eberhard , Perez-Cruz Claudia 
Published: July 2024

AbstractAstrocytes are glial cells that participate in multiple physiological functions, such as protecting neurons against all types of damage. However, astrocytes develop morphological alterations during aging, such as decreased length, volume, and branch points of their processes, also known as astrocytic atrophy. Until now, the exact mechanism associated with the onset of atrophy is unknown. Tree shrew (Tupaia belangeri) is a long-lived animal from the Scadentia order that develops several age-dependent brain alterations. In this study, we analyzed the morphology of GFAP+ astrocytes in the hippocampal region of adult, old, and aged male tree shrews. Aged animals presented more GFAP+ astrocytes in the proximal subiculum, CA3, and CA2-CA1 subregions than younger animals, being significantly higher only in CA3. However, in aged subjects, the number of atrophic astrocytes was significantly higher in the dentate gyrus and CA2 subregion compared to old animals. Interestingly, in the proximal subiculum, astrocytes had a reduced arborization at all ages evaluated. S100A10, a protein overexpressed by neuroprotective-type astrocytes, was mainly found in the nucleus of astrocytes of adult and old subjects. However, in old and aged animals, S100A10 was located in the cytoplasmic compartment of atrophic astrocytes. Furthermore, in astrocytes of aged tree shrews, cytoplasmic inclusions of S100A10 colocalized with the nuclear export protein, Crm-1. These results suggest that the transport of S100A10 from the nucleus to the cytoplasmic compartment of astrocytes could be a process related to astroglial atrophy during the aging process in the hippocampus of three shrews.
Enhancing Perceptual, Attentional, and Working Memory Demands through Variable Practice Schedules: Insights from High-Density EEG Multi-Scale Analyses
Authors: Cretton Alexandre , Schipper Kate , Hassan Mahmoud , Ruggeri Paolo , Barral Jérôme 
Published: July 2024

AbstractContextual interference (CI) enhances learning by practicing motor tasks in a random order rather than a blocked order. One hypothesis suggests that the benefits arise from enhanced early perceptual/attentional processes, while another posits that better learning is due to highly activated mnemonic processes. We propose to harness high-density electroencephalography in a multi-scale analysis approach, including topographic analyses, source estimations, and functional connectivity, to examine the intertwined dynamics of attentional and mnemonic processes within short time windows. We recorded scalp activity from 35 participants as they performed an aiming task at three different distances, under both random and blocked conditions using a crossover design. Our results showed that topographies associated with processes related to perception/attention (N1, P3a) and working memory (P3b) were more pronounced in the random condition. Source estimation analyses supported these findings, revealing greater involvement of the perceptual ventral pathway and the anterior cingulate and parietal cortices, along with increased functional connectivity in ventral alpha and frontoparietal theta band networks during random practice. Our results suggest that CI is driven, in the random compared to the blocked condition, by enhanced specific processes such as perceptual, attentional, and mnemonic, as well as large-scale general processes.
Delayed accumulation of inhibitory input explains gamma frequency variation with changing contrast in an Inhibition Stabilized Network
Authors: Krishnakumaran R , Pavuluri Abhimanyu , Ray Supratim 
Published: July 2024

AbstractGamma rhythm (30-70 Hz), thought to represent the push-pull activity of excitatory and inhibitory population, can be induced by presenting achromatic gratings in the primary visual cortex (V1) and is sensitive to stimulus properties such as size and contrast. In addition, gamma occurs in short bursts, and shows a “frequency-falloff” effect where its peak frequency is high after stimulus onset and slowly decreases to a steady state. Recently, these size-contrast properties and temporal characteristics were replicated in a self-oscillating Wilson-Cowan (WC) model operating as an Inhibition stabilized network (ISN), stimulated by Ornstein-Uhlenbeck (OU)-type inputs. In particular, frequency-falloff was explained by delayed and slowly accumulated inputs arriving at local inhibitory populations. We hypothesized that if the stimulus is preceded by another higher contrast stimulus, frequency-falloff could be abolished or reversed, since the excessive inhibition will now take more time to dissipate. We presented gratings at different contrasts consecutively to two female monkeys while recording gamma using microelectrode arrays in V1 and confirmed this prediction. Further, this model also replicated a characteristic pattern of gamma frequency modulation to counter-phasing stimuli as reported previously. Thus, the ISN model with delayed surround input replicates gamma frequency responses to time-varying contrasts.Significance statementGamma rhythms represent sustained push-pull dynamics between excitatory and inhibitory populations during visual stimulation. Gamma power and centre frequency varies depending on stimulus features, and onset of stimulus produces a “frequency-fall” trend where onset frequency is higher and subsequently plateaus to a lower value. In an earlier work, we argued, using a noisy rate-model of V1, that a delayed onset of inhibition-drive from the surround populations produced the gamma ‘frequency-falloff’. We tested a key prediction of this hypothesis that the frequency-falloff can be abolished or reversed if the stimulus is preceded by a higher contrast stimulus, and confirmed the same by recording from primate primary visual cortex while presenting multiple stimuli consecutively at varying contrasts.
Exploring Effector Protein Dynamics and Natural Fungicidal Potential in Rice Blast PathogenMagnaporthe oryzae
Authors: Ferdausi Jannatul , Robin Tanjin Barketullah , Nasrin Sanjida , Ahmed Istiak , Hossain Tawsif , Hasan Md Mehedi , Soaeb Mehrab Hassan , Tamim Md. Ahsanul , Yeasmin Nusrat Jahan , Habiba Ummay , Ahmed Nadim , Rani Nurul Amin , Bhuyian Md Shishir , Vakare Suvarna N. , Moin Abu Tayab , Patil Rajesh B. , Hossain Mohammad Shahadat 
Published: July 2024

AbstractRice blast, caused byMagnaporthe oryzae, is a severe agricultural disease leading to significant global economic losses. Genetic and genomic investigations have identified crucial genes and pathways involved in its pathogenesis, particularly highlighting effector proteins like AvrPik variants and MAX proteins. These proteins interact with specific Pik alleles on rice chromosome 11, influencing host immune responses. This study focused on 35 plant-derived metabolites known for their antifungal properties, evaluating their potential as fungicidal agents against M. oryzae. Molecular docking analyses identified Hecogenin and Cucurbitacin E as highly effective binders to MAX40 and APIKL2A proteins, respectively, which are pivotal for fungal virulence and immune evasion. Molecular dynamics simulations further validated strong and stable interactions, affirming the therapeutic potential of these compounds. Additional assessments including Lipinski’s rule of five criteria and toxicity predictions indicated their suitability for agricultural use. These findings underscore the promise of Hecogenin and Cucurbitacin E as lead candidates in developing novel fungicidal strategies against rice blast, offering prospects for enhanced crop protection and agricultural sustainability.
Effectiveness of CRISPR-Cas in Sensitizing Bacterial Populations with Plasmid-Encoded Antimicrobial Resistance
Authors: Kippnich Johannes , Benz Fabienne , Uecker Hildegard , Baumdicker Franz 
Published: July 2024

The spread of bacteria resistant to antibiotics poses a serious threat to human health. Genes that encode antibiotic resistance are often harbored by plasmids, extra-chromosomal DNA molecules found in bacteria. The ability of plasmids to spread horizontally among bacteria facilitates the emergence and spread of multiresistant strains, outpacing the development of new antibiotics. CRISPR-Cas derived tools with their sequence specificity offer a promising new approach to combating antibiotic resistance. By introducing CRISPR-encoding plasmids that specifically target antibiotic resistance genes encoded on plasmids, the susceptibility of bacteria to conventional antibiotics can be restored. However, genetic variation within bacterial populations can hinder the effectiveness of such CRISPR-Cas tools by allowing some mutant strains to evade CRISPR-mediated cleaving or gene silencing.In this study, we model the effectiveness of CRISPR-Cas in sensitizing bacterial populations and assess the success probability of a subsequent treatment with conventional antibiotics. We evaluate this probability according to the target interference mechanism, the copy number of the resistance-encoding plasmid and its compatibility with the CRISPR-encoding plasmid.Our results identify promising approaches to revert antibiotic resistance with CRISPR-encoding plasmids: Cleaving by CRISPR systems onincompatibleplasmids is most effective against AMR plasmids with a low copy number, while for higher copy numbers, gene silencing by CRISPR systems encoded oncompatibleplasmids offers the superior solution.
Selective promotion of oligonucleotides in the course of evolution
Authors: Mathew Bernadette , Halder Abhishek , Jaiswal Nancy , Panda Smruti , Pramanik Debjit , Peela Sreeram Chandra Murthy , Garg Abhishek , Tripathi Sadhana , Gupta Prashant , Malhotra Vandana , Ahuja Gaurav , Sengupta Debarka 
Published: July 2024

AbstractDNA is essentially a collection of short nucleotide sequences with a myriad of functionalities. These oligonucleotides are often studied for their function as molecular binding sites, regulatory motifs or sequence probes. The field of Bioinformatics uses a similar concept under the term “k-mers,” which is central to various tasks, like comparing the similarity of different DNA sequences in phylogenetic tree reconstruction. The present study explores ifk-mers experience selection pressure in the course of evolution. Our meta-analysis, spanning multiple organisms, suggests positive selection of genetic changes, where the associatedk-mersare more redundant in the genome, relative to their wild-type counterparts.
Abundance, diversity and evolution of tyrosinase enzymes involved in the adhesive systems of mussels and tubeworms
Authors: Duthoo Emilie , Delroisse Jérôme , Maldonado Barbara , Sinot Fabien , Mascolo Cyril , Wattiez Ruddy , Lopez Pascal Jean , de Weerdt Cécile Van , Harrington Matthew J. , Flammang Patrick 
Published: July 2024

AbstractThe blue mussel (Mytilus edulis) and the honeycomb tubeworm (Sabellaria alveolata) have evolved similar adhesive systems to cope with the hydrodynamic conditions of the intertidal environment where they live. Both organisms can establish a permanent adhesion through the secretion of adhesive proteins rich in DOPA (3,4-dihydroxyphenylalanine), a post-translationally modified amino acid playing essential roles in interfacial adhesion and bulk cohesion. DOPA is produced by the hydroxylation of tyrosine residues by tyrosinase enzymes, which can also in some cases oxidise it further into dopaquinone Compared to the detailed knowledge available on mussel and tubeworm adhesive proteins, little information exists about the tyrosinases involved in their adhesive systems. By combining different molecular analyses, a catalogue of tyrosinase candidates potentially involved in the adhesive systems ofM. edulisandS. alveolatawas identified. Some of these candidates were shown to be expressed in the adhesive glands byin situhybridization, with a high gland-specificity in mussels but not in tubeworms. The diversity of tyrosinases highlighted in the two species suggests the coexistence of different functions (monophenol monooxygenase or catechol oxidase activity) or different substrate specificities. However, the exact role of the different enzymes needs to be further investigated. Phylogenetic analyses support the hypothesis of independent expansions and parallel evolution of tyrosinases involved in adhesive protein maturation in both lineages, supporting the convergent evolution of their DOPA-based adhesion.