bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adolescent social anxiety is associated with diminished discrimination of anticipated threat and safety in the bed nucleus of the stria terminalis
Authors: Hur Juyoen , Tillman Rachael M. , Kim Hyung Cho , Didier Paige , Anderson Allegra S. , Islam Samiha , Stockbridge Melissa D. , De Los Reyes Andres , DeYoung Kathryn A. , Smith Jason F. , Shackman Alexander J. 
Published: November 2023

ABSTRACTSocial anxiety—which typically emerges in adolescence—lies on a continuum and, when extreme, can be devastating. Socially anxious individuals are prone to heightened fear, anxiety, and the avoidance of contexts associated with potential social scrutiny. Yet most neuroimaging research has focused on acute social threat. Much less attention has been devoted to understanding the neural systems recruited during the uncertain anticipation of potential encounters with social threat. Here we used a novel fMRI paradigm to probe the neural circuitry engaged during the anticipation and acute presentation of threatening faces and voices in a racially diverse sample of 66 adolescents selectively recruited to encompass a range of social anxiety and enriched for clinically significant levels of distress and impairment. Results demonstrated that adolescents with more severe social anxiety symptoms experience heightened distress when anticipating encounters with social threat, and reduced discrimination of uncertain social threat and safety in the bed nucleus of the stria terminalis (BST), a key division of the central extended amygdala (EAc). Although the EAc—including the BST and central nucleus of the amygdala—was robustly engaged by the acute presentation of threatening faces and voices, the degree of EAc engagement was unrelated to the severity of social anxiety. Together, these observations provide a neurobiologically grounded framework for conceptualizing adolescent social anxiety and set the stage for the kinds of prospective-longitudinal and mechanistic research that will be necessary to determine causation and, ultimately, to develop improved interventions for this often-debilitating illness.
Isolating Small Extracellular Vesicles from Small Volumes of Blood Plasma using size exclusion chromatography and density gradient ultracentrifugation: A Comparative Study
Authors: Kong Fang , Upadya Megha , Weng Andrew See Wong , Dalan Rinkoo , Dao Ming 
Published: November 2023

AbstractSmall extracellular vesicles (sEVs) are heterogeneous biological vesicles released by cells under both physiological and pathological conditions. Due to their potential as valuable diagnostic and prognostic biomarkers in human blood, there is a pressing need to develop effective methods for isolating high-purity sEVs from the complex milieu of blood plasma, which contains abundant plasma proteins and lipoproteins. Size exclusion chromatography (SEC) and density gradient ultracentrifugation (DGUC) are two commonly employed isolation techniques that have shown promise in addressing this challenge. In this study, we aimed to determine the optimal combination and sequence of SEC and DGUC for isolating sEVs from small plasma volumes, in order to enhance both the efficiency and purity of the resulting isolates. To achieve this, we compared sEV isolation using two combinations: SEC-DGUC and DGUC-SEC, from unit volumes of 500μlplasma. Both protocols successfully isolated high-purity sEVs; however, the SEC-DGUC combination yielded higher sEV protein and RNA content. We further characterized the isolated sEVs obtained from the SEC-DGUC protocol using flow cytometry and mass spectrometry to assess their quality and purity. In conclusion, the optimized SEC-DGUC protocol is efficient, highly reproducible, and well-suited for isolating high-purity sEVs from small blood volumes.
Concurrent response and action effect representations across the somatomotor cortices during novel task preparation
Authors: Palenciano Ana F. , González-García Carlos , De Houwer Jan , Liefooghe Baptist , Brass Marcel 
Published: November 2023

AbstractInstructions allow us to fulfill novel and complex tasks on the first try. This skill has been linked to preparatory brain signals that encode upcoming demands in advance, facilitating novel performance. To deepen insight into these processes, we explored whether instructions pre-activated task-relevant motoric and perceptual neural states. Critically, we addressed whether these representations anticipated activity patterns guiding overt sensorimotor processing, which could reflect that internally simulating novel tasks facilitates the preparation. To do so, we collected functional magnetic resonance imaging data while female and male participants encoded and implemented novel stimulus-response associations. Participants also completed localizer tasks designed to isolate the neural representations of the mappings-relevant motor responses, perceptual consequences, and stimulus categories. Using canonical template tracking, we identified whether and where these sensorimotor representations were pre-activated. We found that response-related templates were encoded in advance in regions linked with action control, entailing not only the instructed responses but also their somatosensory consequences. This result was particularly robust in primary motor and somatosensory cortices. While, following our predictions, we found a systematic decrease in the irrelevant stimulus templates’ representational strength compared to the relevant ones, this difference was due to below-zero estimates linked to the irrelevant category activity patterns. Overall, our findings reflect that instruction processing relies on the sensorimotor cortices to anticipate motoric and kinesthetic representations of prospective action plans, suggesting the engagement of motor imagery during novel task preparation. More generally, they stress that the somatomotor system could participate with higher-level frontoparietal regions during anticipatory task control.
Spoink, a LTR retrotransposon, invadedD. melanogasterpopulations in the 1990s
Authors: Pianezza Riccardo , Scarpa Almorò , Narayanan Prakash , Signor Sarah , Kofler Robert 
Published: November 2023

AbstractDuring the last few centuriesD. melanogasterpopulations were invaded by several transposable elements, the most recent of which was thought to be theP-element between 1950 and 1980. Here we describe a novel TE, which we namedSpoink, that has invadedD. melanogaster. It is a 5216nt LTR retrotransposon of the Ty3/gypsy superfamily. Relying on strains sampled at different times during the last century we show thatSpoinkinvaded worldwideD. melanogasterpopulations after theP-element between 1983 and 1993. This invasion was likely triggered by a horizontal transfer from theD. willistonigroup, much as theP-element.Spoinkis probably silenced by the piRNA pathway in natural populations and about 1/3 of the examined strains have an insertion into a canonical piRNA cluster such as42AB. Given the degree of genetic investigation ofD. melanogasterit is surprising thatSpoinkwas able to invade unnoticed.
Fasten with Pipes
Authors: Katz Lee S. , Den Bakker Henk C. 
Published: November 2023

AbstractFasten is a versatile bioinformatics tool suite developed to address gaps in the manipulation of sequence data files in the fastq format. Existing tools often lack support for interleaved fastq files and Unix-style pipe file control. Fasten provides a solution by allowing bioinformaticians to efficiently work with paired-end sequence data, facilitating data transformation, and offering competitive speeds. This suite, implemented in Rust, offers a comprehensive manual, continuous integration, and seamless integration into the command line with Unix pipes. Fasten is poised to become an invaluable resource for routine command-line bioinformatics tasks, enhancing the accessibility and flexibility of data processing in the field.
Extended-depth of field random illumination microscopy, EDF-RIM, provides super-resolved projective imaging
Authors: Mazzella Lorry , Mangeat Thomas , Giroussens Guillaume , Rogez Benoit , Li Hao , Creff Justine , Saadaoui Mehdi , Martins Carla , Bouzignac Ronan , Labouesse Simon , Idier Jérome , Galland Frédéric , Allain Marc , Sentenac Anne , LeGoff Loïc 
Published: November 2023

ABSTRACTThe ultimate aim of fluorescence microscopy is to achieve high-resolution imaging of increasingly larger biological samples. Extended depth of field presents a potential solution to accelerate imaging of large samples when compression of information along the optical axis is not detrimental to the interpretation of images. We have implemented an Extended Depth of Field (EDF) approach in a Random Illumination Microscope (RIM). RIM uses multiple speckled illuminations and variance data processing to double the resolution. It is particularly adapted to the imaging of thick samples as it does not require the knowledge of illumination patterns. We demonstrate highly-resolved projective images of biological tissues and cells. Compared to a sequential scan of the imaged volume with conventional 2D-RIM, EDF-RIM allows an order of magnitude improvement in speed and light dose reduction, with comparable resolution. As the axial information is lost in an EDF modality, we propose a method to retrieve the sample topography for samples that are organized in cell sheets.
4Pi MINFLUX arrangement maximizes spatio-temporal localization precision of fluorescence emitter
Authors: Rickert Julian D. , Held Marcus O. , Engelhardt Johann , Hell Stefan W. 
Published: November 2023

AbstractWe introduce MINFLUX localization with interferometric illumination through opposing objective lenses for maximizing the attainable precision in 3D-localization of single inelastic scatterers, such as fluorophores. Our 4Pi optical configuration employs three sequentially tilted counter-propagating beam pairs for illumination, each providing a narrow interference minimum of illumination intensity at the focal point. The localization precision is additionally improved by adding the inelastically scattered (fluorescence) photons collected through both objective lenses. Our 4Pi configuration yields the currently highest precision per detected photon among all localization schemes. Tracking gold nanoparticles as non-blinking inelastic scatterers rendered a position uncertainty < 0.4 nm3in volume at a localization frequency of 2.9 kHz. We harnessed the record spatio-temporal precision of our 4Pi MINFLUX approach to examine the diffusion of single fluorophores and fluorescent nanobeads in solutions of sucrose in water, revealing local heterogeneities at the nanoscale. Our results show the applicability of 4Pi MINFLUX to study molecular nano-environments of diffusion and its potential for quantifying rapid movements of molecules in cells and other material composites.
Stimulation of Neurons and Astrocytes via Temporally Interfering Electric Fields
Authors: Ahtiainen Annika , Leydolph Lilly , Tanskanen Jarno M.A. , Hunold Alexander , Haueisen Jens , Hyttinen Jari A.K. 
Published: November 2023

SummaryA novel non-invasive electrical stimulation method, temporal interference stimulation (TIS), has been proposed to enable spatially steerable stimulation and to selectively activate different brain regions. However, TIS has not been studied with cell cultures that can provide an indepth assessment of its effects on neuronal cells. We successfully established anin vitroTIS setup using rat cortical neurons on microelectrode arrays. Stimulations involved 1) TIS with 653 Hz and 643 Hz, resulting in a 10 Hz frequency envelope, 2) low-frequency stimulation (LFS) at 10 Hz, 3) high-frequency stimulation (HFS) at 653 Hz, and 4) no electrical stimulation (control/sham). HFS and LFS had the least effect on neuronal activity, but TIS elicited neuronal electrophysiological responses, especially 24 hours after stimulation. We also assessed TIS in neuron-astrocyte co-cultures. Interestingly, co-cultures seemed to counteract the TIS effects. Hence, our findings deepen the current understanding of the electrical modulation of neurons during TIS.HighlightsTemporal interference stimulation (TIS) is a new technique for brain stimulation.TIS setup was established and combined with microelectrode array (MEA) system.Rat cortical neurons and astrocytes were stimulated with TISin vitro.Neurons responded to TIS more prominently without astrocyte support.
Supramolecular Interactions of Teixobactin Analogues in the Crystal State
Authors: Yang Hyunjun , Kreutzer Adam G. , Nowick James S. 
Published: November 2023

ABSTRACTTeixobactin is a potent peptide antibiotic against Gram-positive bacteria that binds to lipid II and related peptidoglycan precursors and disrupts the cell membrane. This paper presents the X-ray crystallographic structure of theN-methylated teixobactin analogueN-Me-D-Gln4,Lys10-teixobactin (1).N-Methylation at position 4 prevents uncontrolled aggregation and enables the crystallization of the teixobactin analogue. Lysine at position 10 replaces the non-proteinogenic amino acidallo-enduracididine, which is not commercially available. Crystallization from aqueous solution with MgCl2and PEG3350 afforded crystals suitable for X-ray crystallography. The crystallographic phases were solved using SAD phasing on data sets collected at 2.0663 Å. Molecular replacement then enabled the determination of the structure at 1.50 Å resolution using a data set collected at 0.9997Å (PDB 8U78). Eight peptide molecules comprise the asymmetric unit, with each peptide molecule binding a chloride anion through hydrogen bonding with the amide NH group of residues 7, 8, 10, and 11. The peptide molecules form hydrogen-bonded antiparallel β-sheet dimers in the crystal lattice, with residues 1–3 comprising the dimerization interface. The dimers further assemble end-to-end in the crystal lattice. The β-sheet dimers are amphiphilic, with the side chains of the hydrophobic residues on one surface and the side chains of the hydrophilic residues on the other surface. The dimers pack in the lattice through hydrophobic interactions between the hydrophobic surfaces. The crystal structure of teixobactin analogue 1 recapitulates several aspects of the interaction of teixobactin with the cell membrane of Grampositive bacteria, including anion binding, supramolecular assembly through β-sheet formation, and hydrophobic interactions.
Lewy Body Radius Growth: The Hypothesis of the Cube Root of Time Dependency
Authors: Kuznetsov Andrey V. 
Published: November 2023

AbstractThis paper presents a model for the growth of Lewy bodies (LBs), which are pathological hallmarks of Parkinson’s disease (PD). The model simulates the growth of classical LBs, consisting of a core and a halo. The core is assumed to comprise lipid membrane fragments and damaged organelles, while the halo consists of radiating alpha-synuclein (α-syn) fibrils. The Finke-Watzky model is employed to simulate the aggregation of lipid fragments and α-syn monomers. By analytically and numerically exploring the solutions of the governing equations, approximate solutions were derived, which are applicable for large times. The application of these approximate solutions to simulate LB radius growth led to the discovery of the cube root hypothesis, which posits that the LB radius is proportional to the cube root of its growth time. Sensitivity analysis revealed that the LB radius is unaffected by the kinetic rates of nucleation and autocatalytic growth, with growth primarily regulated by the production rates of lipid membrane fragments and α-syn monomers. The model suggests that large LBs relevant to PD can only develop when the machinery responsible for degrading lipid membrane fragments, α-syn monomers, and their aggregates is dysfunctional.
ODL-BCI: Optimal deep learning model for brain-computer interface to classify students confusion via hyperparameter tuning
Authors: Miah Md Ochiuddin , Habiba Umme , Kabir Md Faisal 
Published: November 2023

AbstractBrain-computer interface (BCI) research has gained increasing attention in educational contexts, offering the potential to monitor and enhance students’ cognitive states. Real-time classification of students’ confusion levels using electroencephalogram (EEG) data presents a significant challenge in this domain. Since real-time EEG data is dynamic and highly dimensional, current approaches have some limitations for predicting mental states based on this data. This paper introduces an optimal deep learning (DL) model for the BCI, ODL-BCI, optimized through hyperparameter tuning techniques to address the limitations of classifying students’ confusion in real time. Leveraging the “confused student EEG brainwave” dataset, we employ Bayesian optimization to fine-tune hyperparameters of the proposed DL model. The model architecture comprises input and output layers, with several hidden layers whose nodes, activation functions, and learning rates are determined utilizing selected hyperparameters. We evaluate and compare the proposed model with some state-of-the-art methods and standard machine learning (ML) classifiers, including Decision Tree, AdaBoost, Bagging, MLP, Näıve Bayes, Random Forest, SVM, and XG Boost, on the EEG confusion dataset. Our experimental results demonstrate the superiority of the optimized DL model, ODL-BCI. It boosts the accuracy between 4% and 9% over the current approaches, outperforming all other classifiers in the process. The ODL-BCI implementation source codes can be accessed by anyone athttps://github.com/MdOchiuddinMiah/ODL-BCI.
Interdependence of cellular and network properties in respiratory rhythmogenesis
Authors: Phillips Ryan S. , Baertsch Nathan A. 
Published: November 2023

ABSTRACTHow breathing is generated by the preBötzinger Complex (preBötC) remains divided between two ideological frameworks, and the persistent sodium current (INaP) lies at the heart of this debate. AlthoughINaPis widely expressed, thepacemaker hypothesisconsiders it essential because it endows a small subset of neurons with intrinsic bursting or “pacemaker” activity. In contrast,burstlet theoryconsidersINaPdispensable because rhythm emerges from “pre-inspiratory” spiking activity driven by feed-forward network interactions. Using computational modeling, we discover that changes in spike shape can dissociateINaPfrom intrinsic bursting. Consistent with many experimental benchmarks, conditional effects on spike shape during simulated changes in oxygenation, development, extracellular potassium, and temperature alter the prevalence of intrinsic bursting and pre-inspiratory spiking without altering the role ofINaP. Our results support a unifying hypothesis whereINaPand excitatory network interactions, but not intrinsic bursting or pre-inspiratory spiking, are critical interdependent features of preBötC rhythmogenesis.SIGNIFICANCE STATEMENTBreathing is a vital rhythmic process originating from the preBötzinger complex. Since its discovery in 1991, there has been a spirited debate about whether respiratory rhythm generation emerges as a network property or is driven by a subset of specialized neurons with rhythmic bursting capabilities, endowed by intrinsic currents. Here, using computational modeling, we propose a unifying data-driven model of respiratory rhythm generation which bridges the gap between these competing theories. In this model, both intrinsic cellular properties (a persistent sodium current) and network properties (recurrent excitation), but not intrinsic bursting, are essential and interdependent features of respiratory rhythm generation.
Robust and Accurate Doublet Detection of Single-Cell Sequencing Data via Maximizing Area Under Precision-Recall Curve
Authors: Chen Yanshuo , Wu Xidong , Ni Ke , Hu Haoran , Yue Molin , Chen Wei , Huang Heng 
Published: November 2023

AbstractSingle-cell sequencing has revolutionized our understanding of cellular heterogeneity by offering detailed profiles of individual cells within diverse specimens. However, due to the limitations of sequencing technology, two or more cells may be captured in the same droplet and share the same barcode. These incidents, termed doublets or multiplets, can lead to artifacts in single-cell data analysis. While explicit experimental design can mitigate these issues with the help of auxiliary cell markers, computationally annotating doublets has a broad impact on analyzing the existing public single-cell data and reduces potential experimental costs. Considering that doublets form only a minor fraction of the total dataset, we argue that current doublet detection methods, primarily focused on optimizing classification accuracy, might be inefficient in performing well on the inherently imbalanced data in the area under the precision-recall curve (AUPRC) metric. To address this, we introduce RADO (Robust and Accurate DOublet detection) - an algorithm designed to annotate doublets by maximizing the AUPRC, effectively tackling the imbalance challenge. Benchmarked on 18 public datasets, RADO outperforms other methods in terms of doublet score and achieves similar performance to the current best methods in doublet calling. Furthermore, beyond its application in single-cell RNA-seq data, we demonstrate RADO’s adaptability to single-cell assays for transposase-accessible chromatin sequencing (scATAC-seq) data, where it outperforms other scATAC-seq doublet detection methods. RADO’s open-source implementation is available at:https://github.com/poseidonchan/RADO.
The landscape of the histone-organized chromatin of Bdellovibrionota bacteria
Authors: Marinov Georgi K. , Doughty Benjamin , Kundaje Anshul , Greenleaf William J. 
Published: November 2023

AbstractHistone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (aBacteriovoraxstrain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast,Bacteriovoraxchromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility inBacteriovoraxpositively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters,Bacteriovoraxpromoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, theBacteriovoraxgenome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.