bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering Temporally Compositional Neural Manifolds with Switching Infinite GPFA
Authors: Yu Changmin , Sahani Maneesh , Lengyel Máté 
Published: October 2024

AbstractGaussian Process Factor Analysis (GPFA) is a powerful latent variable model for extracting low-dimensional manifolds underlying population neural activities. However, one limitation of standard GPFA models is that the number of latent factors needs to be pre-specified or selected through heuristic-based processes, and that all factors contribute at all times. We propose the infinite GPFA model, a fully Bayesian non-parametric extension of the classical GPFA by incorporating an Indian Buffet Process (IBP) prior over the factor loading process, such that it is possible to infer a potentially infinite set of latent factors, and the identity of those factors that contribute to neural firings in a compositional manner ateachtime point. Learning and inference in the infinite GPFA model is performed through variational expectation-maximisation, and we additionally propose scalable extensions based on sparse variational Gaussian Process methods. We empirically demonstrate that the infinite GPFA model correctly infers dynamically changing activations of latent factors on a synthetic dataset. By fitting the infinite GPFA model to population activities of hippocampal place cells during spatial navigation, we identify non-trivial and behaviourally meaningful dynamics in the neural encoding process.
Rho/Rok-dependent regulation of actomyosin contractility at tricellular junctions controls epithelial permeability in Drosophila
Authors: Jacobs Thea , Isasti Sanchez Jone , Reger Steven , Luschnig Stefan 
Published: October 2024

SummaryCell contacts in epithelia are remodeled to regulate paracellular permeability and to control passage of migrating cells, but how barrier function is modulated while preserving epithelial integrity is not clear. In the follicular epithelium ofDrosophilaovaries, tricellular junctions (TCJs) open transiently in a process termed patency to allow passage of externally produced yolk proteins for uptake by the oocyte. Here we show that modulation of actomyosin contractility at cell vertices controls TCJ permeability. Before patency, circumferential actomyosin bundles are anchored at apical follicle cell vertices, where tension-sensing junctional proteins, Rho-associated kinase (Rok), and active Myosin II accumulate and maintain vertices closed. TCJ opening is initiated by redistribution of Myosin II from circumferential bundles to a medial pool, accompanied by decreasing tension on vertices. This transition requires activation of Cofilin-dependent F-actin disassembly by the phosphatase Slingshot and Myosin II inactivation by Myosin light chain phosphatase, and is counteracted by Rok. Accordingly, constitutive activation of Myosin or of Rho signaling prevent vertex opening, whereas reduced Myosin II or Rok activity cause excessive and premature vertex opening. Thus, opening of intercellular gaps in the follicular epithelium does not require actomyosin-based forces, but relies on a reduction of actomyosin contractility. Conversely, F-actin assembly is required for closing intercellular gaps after patency. Our findings are consistent with a force transduction model in which TCJ integrity is maintained by vertex-anchored contractile actomyosin. We propose that the cell-type-specific organization of actomyosin at cell vertices determines the mode of contractility-dependent regulation of epithelial permeability.
The A-C Linker controls centriole cohesion and duplication
Authors: Bournonville Lorène , Laporte Marine. H. , Borgers Susanne , Guichard Paul , Hamel Virginie 
Published: October 2024

AbstractCentrioles are evolutionarily conserved barrel-shaped organelles playing crucial roles in cell division and ciliogenesis. These functions are underpinned by specific structural sub-elements whose functions have been under investigation since many years. The A- C linker structure, connecting adjacent microtubule triplets in the proximal region, has remained unexplored due to its unknown composition. Here, using ultrastructure expansion microscopy, we characterized two recently identified A-C linker proteins, CCDC77 and WDR67, along with a newly discovered protein, MIIP. Our findings reveal that these proteins localize between microtubule triplets at the A-C linker, forming a complex. Depletion of A-C linker components disrupt microtubule triplet cohesion, leading to breakage at the proximal end. Co-removal of the A-C linker and the inner scaffold demonstrates their joint role in maintaining centriole architecture. Moreover, we uncover an unexpected function of the A-C linker in centriole duplication through torus regulation, underscoring the interplay between these protein modules.
A remarkable psyllomorph family from Cretaceous Burmese amber, Miralidae stat. nov. (= Dinglidae syn. nov.; Hemiptera: Sternorrhyncha)
Authors: Ivanov Grigory A. , Vorontsov Dmitry D. , Shcherbakov Dmitry E. 
Published: October 2024

ABSTRACTCretaceous resins have preserved a remarkable diversity of sternorrhynchans. Burmese amber, formed in the mid-Cretaceous tropics, contains more numerous and diverse Psyllomorpha than all other fossil localities of the period together. The genusDinglaSzwedo et Drohojowska, 2020, previously placed into a separate family and infraorder, turned out to be similar in all essential characters toMiralaBurckhardt et Poinar, 2019 andBurmalaLiu et al., 2021; therefore we synonymize Dinglidae Szwedo et Drohojowska, 2020 with Miralinae Shcherbakov, 2020 and raise the last subfamily to the full family status. A sister-group relationship between Dinglomorpha and Aleyrodomorpha in the cladistic analysis of Drohojowska et al. (2020a) was based on incorrect interpretation of characters.@@ala @@ioidesgen. et sp. nov. from Burmese amber differs from other miralid genera by spotted forewings without pterostigma and the structure of terminalia in both sexes. In Miralidae, we discovered a long annulated labium and compound wax pores on the ventral side of the abdomen—for the first time among Hemiptera. The compound wax pores may have helped prevent miralids from sticking to the honeydew excreted. The long, flexible second labial segment, reinforced by sclerotized rings, probably allowed the protrusible length of the stylet bundle to be increased by arching the labium, as in mosquitoes.
Application of modular isoxazoline-β2,2-amino acid-based peptidomimetic foldamers as a chemical model system for studying the tau misfolding mechanism
Authors: di Lorenzo Davide , Bisi Nicolo , Bucci Raffaella , Ennen Inga , Presti Leonardo Lo , Dodero Veronica , Brandt Roland , Ongeri Sandrine , Gelmi Maria-Luisa , Tonali Nicolo 
Published: October 2024

AbstractTauopathies are a group of neurodegenerative diseases characterized by the deposition of abnormal aggregates of tau protein into the brain. Tau is a microtubule-associated protein whose physiological role is related to the modulation of microtubule dynamics and the correct axonal transport in neurons. In tauopathies, the mechanism of conversion of the tau molecule from a physiological to a pathological form is still unclear. Nevertheless, two hexapeptide sequences, named PHF6 and PHF6*, located in the R3 and R2 repetition domains of tau, respectively, seem to be crucial in triggering the aggregation. In the native state, the hydrophobic residues of PHF6 and PHF6* are protected by a β-hairpin-like structure. Contrary to that, the misfolded protein exposes hydrophobic residues, which can form hydrophobic interactions and drive the self-assembly process. Chemical model systems, other than being more straightforward and easily accessible than full-length proteins, can provide valuable insight, which is difficult to tease out by studying the natural systems directly, and can especially be employed to examine the structures and modes of folding of amyloid proteins. Here, we exploit the use of chemical systems to modulate and study the mechanism of tau misfolding and aggregation. By employing a new non-natural β2,2-amino acid, we have induced the two hot spot sequences of tau (PHF6 and PHF6*) either to have a totally extended conformation or a β-hairpin, according to the(S)or(R)stereochemistry of the scaffold, respectively. The aim of this work was to provide, through the interchange between β-hairpin-like and extended conformations, a possible explanation for the mechanism of tau misfolding. We demonstrated that an extended conformation, exposing the hydrophobic residues of both sequences and driving away PHF6* from PHF6, can trigger the aggregation of tau and behaves as a seed-competent monomer model system. Conversely, a β-hairpin imitates the favorable folding of tau, allowing the protein to maintain its soluble monomeric form. Furthermore, a β-hairpin mimic, based on the chaperone protein Hsp90, demonstrated the further application of this type of peptidomimetic foldamers as both aggregation inhibitors and chaperone mimics for the corrective folding of tau in a neuronal environment.
Tag with Caution — How protein tagging influences the formation of condensates
Authors: Dörner Kerstin , Gut Michelle , Overwijn Daan , Cao Fan , Siketanc Matej , Heinrich Stephanie , Beuret Nicole , Sharpe Timothy , Lindorff-Larsen Kresten , Maria Hondele 
Published: October 2024

SummaryFluorescent proteins and peptide tags are essential tools in cellular biology, but can alter the biochemical properties of target proteins. Biomolecular condensates, which have emerged as key principles of cellular organization, are suggested to provide robustness to cells, yet they can also respond sensitively to small changes in environmental conditions—or tagging of their components, as our findings suggest. Here, we investigated the effects of sixteen widely used tags on condensate formation in various model organisms,in vitro, in cells and by computational modelling. We find that tagging strongly influenced condensation for some proteins, while others remained unaffected. Effects varied, with some tags enhancing and others decreasing condensation, and depended on the protein being tagged. Coarse-grained simulations suggest that the charge of the fluorescent protein tags is a critical factor modulating condensation behavior. Together, our results underscore the importance of rigorous experimental design and interpretation in condensate experiments.
Adult lifespan effects on functional specialization along the hippocampal long axis
Authors: Bowman Caitlin R. , Charles Cara I. , Birr Saisha M. 
Published: October 2024

AbstractThere has been increasing attention to differences in function along the hippocampal long axis, with posterior regions proposed to have properties that are well suited to representing fine-grained details and coarser representations in anterior regions. Whether long axis functional specialization persists into older age is not well understood, despite well documented memory changes in older age. In this study, we used a large database of fMRI data (n =323 humans of both sexes included) from across the adult lifespan (ages 18-88) to determine the degree of functional differentiation across the hippocampal posterior-anterior axis. Our first approach was to measure the similarity among signals within each hippocampal subregion. We found that intra-region signals within the most posterior hippocampal subregion became more similar in older age, but did not relate to episodic memory performance. As a second approach, we measured functional connectivity between hippocampal subregions and the rest of the brain. The functional connectivity profiles of the posterior and anterior hippocampal subregions became more distinct from one another with increasing age, and age-related reductions in connectivity were strongest for the intermediate portion of the hippocampus. In contrast, anterior hippocampal functional connectivity remained relatively stable across the adult lifespan, and stronger anterior hippocampus connectivity with the anterior cingulate was associated with better episodic memory in older adults, suggesting that the anterior hippocampus may help some older adults compensate for age-related changes to more posterior hippocampal regions to preserve episodic memory.Significance StatementThere is an increasing understanding that differences across the hippocampal long axis help give rise to multifaceted episodic memories. Yet, whether hippocampal long axis differentiation persists into older age is not well understood. Here, we show that older age exaggerates the differentiation along the hippocampal long axis due largely to changes in posterior and intermediate portions of the hippocampus. Anterior hippocampal signals were more stable and were sometimes associated with better episodic memory performance in older age. These findings suggest that functional declines in posterior hippocampus may be a normal part of healthy aging, but that some older adults offset this decline by upregulating anterior hippocampal function, which in turn helps maintain episodic memory.
Early auditory and adult mating experiences interact with singer identity to shape neural responses to song in female zebra finches
Authors: Catalano Isabella , Woolley Sarah C. 
Published: October 2024

ABSTRACTSocial and sensory experiences across the lifespan can shape social interactions, however, experience-dependent plasticity is widely studied within discrete life stages. In the socially monogamous zebra finch, in which females use learned vocal signals to identify individuals and form long-lasting pair bonds, developmental exposure to song is key for females to show species-typical song perception and preferences. While adult mating experience can still lead to pair-bonding and song preference learning even in birds with limited previous song exposure (“song-naïve”), whether similarities in adult behavioral plasticity between normally-reared and song-naïve females reflect convergent patterns of neural activity is unknown. We investigated this using expression of a marker of neural activity and plasticity (phosphorylated S6) in mated normally-reared and song-naïve females in response to song from either their mate, a neighbor, or an unfamiliar male. We found that, in portions of a secondary auditory region (the caudomedial nidopallium NCM) and in dopaminergic neurons of the caudal ventral tegmental area, hearing the mate’s song significantly increased pS6 expression in females from both rearing conditions. In contrast, within other NCM subregions, song-identity drove different patterns of pS6 expression depending on the rearing condition. These data suggest that developmental experiences can have long-lasting impacts on the neural signatures of behaviors acquired in adulthood and that socially-driven behavioral plasticity in adults may arise through both shared and divergent neural circuits depending on an individual’s developmental experiences.
Quality and noodle‐making performance of wheat flour with varied gluten strengths altered by addition of various arabinoxylans
Authors: Kim Jeongeon , Kweon Meera 
Published: October 2024

AbstractThis study examined the effects of adding different types of arabinoxylans (AXs) to wheat flour with varying gluten strengths on flour quality and noodle‐making performance, with the aim of utilizing AXs as health‐enhanced ingredients. Three flours (Goso, Hojoong, and Joongmo) with low, medium, and high gluten strengths were used, along with two water‐extractable AXs (E1 and E2) and one water‐unextractable AX (U) with diverse molecular weights and viscosities. The addition of 2% AXs increased the water and sucrose solvent retention capacity values and decreased the gluten performance index values for all flours, with a notable effect on Goso flour by U. The dough development time was prolonged in all flours, necessitating more water for development. The sodium dodecyl sulfate sedimentation volume increased with the addition of AXs, especially with E2 and U. Pasting properties remained unaffected, suggesting a minimal impact on starch‐related properties. However, noodles made with E2 and U showed deteriorated quality in terms of fresh noodle texture, weight gain, cooking water turbidity, and cooked noodle texture, in contrast to noodles made with E1 alone. Additionally, adjusting the water amount when adding U altered the textural properties, approaching that of noodles without added AXs. Overall, the impact of AXs on flour and noodle quality varied depending on their molecular weights, viscosities, and the gluten strength of the flour. Additionally, AXs could be successfully utilized by adjusting the water amount for the production of health‐enhancing noodles.Practical ApplicationArabinoxylans, as health‐promoting ingredients, can be utilized in noodle production by optimizing the water amount and mixing time.
Optimization of a gelatin/carboxymethylcellulose‐based probiotic microcapsule and its application in preventing dextran sodium sulfate–induced colitis in mice
Authors: Zhu Xiao , Zhi Yiming , Heng Xiaoyi , Zhou Lihui , Liu Chang , Zhao Yiwen , Wang Yijun , Liu Jun , Huang Jinbao 
Published: October 2024

AbstractOral administration of probiotics has demonstrated substantial potential in alleviating colitis. However, most of the ingested microorganisms struggle to survive the harsh conditions of the gastrointestinal tract, leading to decreased efficacy. In the present study, using double emulsification (W1/O/W2) and complex coacervation methods, we developed a gelatin/carboxymethyl cellulose (CMC)‐based probiotic microcapsule and analyzed the efficacy of encapsulated probiotics in preventing dextran sodium sulfate (DSS)‐induced colitis in mice. Our results reveal that nearly 90% of the encapsulated probiotics remained viable after 30‐day storage at 4°C and approximately 38.1% of viable bacteria (4.0 × 108 cfu/g) survived after 4‐h simulated gastrointestinal digestion. In a DSS‐induced colitis model, pretreatment with probiotics exerted significant protective effects, with the bacterial microcapsule‐treated group having superior outcomes to those of the bacterial suspension plus empty carrier group. Probiotic treatments, especially those administered in the encapsulated form, significantly increased fecal short‐chain fatty acid contents, and altered the intestinal microbial composition. The family Muribaculaceae, dominant bacteria in the mouse gut, may be the key microorganism involved in the BM regulation process. Our study presents an alternative approach to treating colitis using probiotics.Practical ApplicationThe encapsuled probiotic showed remarkable storage stability at 4°C, maintained good vitality after simulated digestion, and gained superior outcomes in preventing colitis. Our results offer an alternative approach for the probiotic preparations aiming to prevent the intestinal inflammation.
tert‐Butylhydroquinone alleviates a postharvest pericarp browning of longan fruit by regulating antioxidant metabolism
Authors: Yu Zhiqian , Kang Wenjing , Zhang Zhengke , Yang Ziqin , Jiang Yueming , Pan Yonggui , Yang Jiali 
Published: October 2024

AbstractHarvested longan fruit is prone to pericarp browning, which restricts preservation quality and shortens fruit shelf life. The antioxidant system can defend against oxidative stress–mediated quality deterioration such as fruit browning. This study aimed to evaluate the effect of tert‐butylhydroquinone (TBHQ) on anti‐browning ability of longan fruit in association with redox metabolism. The results indicated that the application of 0.02% TBHQ significantly suppressed the progression of pericarp browning. In comparison with control, TBHQ treatment decreased the contents of hydrogen peroxide (H2O2), superoxide radical (O2−⋅), and malondialdehyde, and retained high levels of ascorbic acid (AsA), glutathione (GSH), total phenolics as well as 1,1‐diphenyl‐2‐picrylhydrazyl scavenging rate. Enhanced enzymatic activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase, and dehydroascorbate reductase (DHAR), but decreased activities of polyphenol oxidase and peroxidase were also observed in TBHQ‐treated fruit. Gene expression analysis indicated that redox metabolism‐related genes, including DlSOD, DlCAT, DlGR, and DlAPX, were upregulated after TBHQ treatment. Correlation analysis suggested that antioxidants, including AsA, GSH, CAT, APX, SOD, and DHAR, were negatively correlated to reactive oxygen species production and percarp browning. These results suggest that TBHQ is effective in alleviating pericarp browning by increasing antioxidant capacity of longan fruit.
Efficient elimination of 3‐monochloropropane‐1,2‐diol fatty acid ester from palm oil via using activated carbon grafted with Tween80
Authors: Ji Junmin , Li Changjiang , Hou Jie , Xu Fengyao , Li Nannan 
Published: October 2024

AbstractIn the current study, we attempt to remove 3‐monochloropropane‐1,2‐diol fatty acid ester (3‐MCPD ester) from palm oil with developed composite adsorbent (Tween80 modified activated carbon [AC]), and scanning electron microscopy‐energy dispersive spectrometer, Fourier transform‐infrared spectroscopy, X‐ray diffraction, nitrogen content adsorption‐desorption and thermogravimetric analysis were used to characterize the modifications. We further examined the adsorption capability of the composite adsorbent for 3‐MCPD ester and found that the highest removal efficiency was 87.36% (5.3% of adsorbent dose at 104°C for 29 min). This is approximately three times higher than that of pristine AC, implying that the composite can be employed as a novel adsorbent for 3‐MCPD ester reduction. Along with the adsorption mechanism of Langmuir, Freundlich, Dubinin–Radushkevich, and Temkin models were also tested. It has been suggested that Freundlich model could best describe the adsorption process. Adsorption was found to be well‐fitted by pseudo‐second‐order kinetics according to the kinetic study. An endothermic and spontaneous adsorption mechanism was demonstrated by the thermodynamic studies.
Perpetuating ableism in engineering education: The role of user abstraction and expertise hierarchies in the design process
Authors: Hardin Jessica , Carter Anna , Smith Lee , Lama Pema , Pasquantonio Anna , Hakim Makenna 
Published: October 2024

AbstractThis ethnographic study investigates the teaching and learning of the design process in biomedical engineering classrooms. Through classroom fieldwork, we examine how faculty and students conceptualize and implement the design process, focusing on its linear teaching methods, the abstraction of users, and the reinforcement of expertise hierarchies. Our analysis reveals how these pedagogical practices perpetuate ableist assumptions within engineering education. This research contributes to the understanding of how educational practices in engineering shape professional identities and reinforce systemic biases.