bluuebunny/crossref_metadata_2025_split huggingface dataset:
Within-host adaptation of a foliar pathogen,Xanthomonas, on pepper in presence of quantitative resistance and ozone stress
Authors: Kaur Amanpreet , Russell Ivory , Liu Ranlin , Holland Auston , Bhandari Rishi , Potnis Neha 
Published: March 2024

SummaryThe evolving threat of new pathogen variants in the face of global environmental changes poses a risk to the plant health and can impact the efficacy of resistance-based disease management.Here, we studied short-term eco-evolutionary response of the pathogen,Xanthomonas perforans, on quantitative resistant and susceptible pepper during a single growing season in open-top chambers under the influence of elevated Ozone (O3).We observed increased disease severity, accompanied by higher variation on resistant cultivar under elevated O3, with no apparent change on the susceptible cultivar. This altered resistance response under elevated O3 is linked to altered eco-evolutionary dynamics of pathogen. While a single pathogen genotype remained prevalent on susceptible cultivar, resistant cultivar supported heterogenous pathogen population, with the evidence of short- term evolutionary modifications seeded byde novoparallel mutations. Altered O3 levels led to strain turnover on resistant cultivar with higher within-host polymorphism containing higher proportion of randomde novomutations lacking parallelism.Population heterogeneity is a mechanism of pathogen adaptation in response to the stressors. While parallel mutations in response to quantitative resistance may provide clues to predicting long-term pathogen evolution, high proportion of transient mutations suggest less predictable pathogen evolution under climatic alterations.
The role of many-to-one mapping of vertebral form to function in Psittaciform tripedal locomotion
Authors: Stuart Anna R. , Granatosky Michael C. , Felice Ryan N. , Marek Ryan D. 
Published: March 2024

AbstractParrots highlight the functional diversity of the avian neck by contributing to a range of behaviors, including arboreal locomotion. The parrot neck is used alongside the beak and hindlimb to allow them to successfully navigate arboreal habitats via tripedal locomotion. Whether specific morphological characteristics of the neck enable this behavior are currently unknown. By combining geometric morphometrics with phylogenetic comparative methods we investigate the factors correlate with shape variation in the cervical vertebrae of parrots. We find that phylogeny, allometry, integration, diet and tripedal locomotion all have a significant influence on the morphology of psittaciform cervical vertebrae. However, the influence of diet and tripedal locomotion is weak, with a high degree of morphospace overlap existing between dietary and neck use groups. Additionally, we find no evidence of convergence in parrot neck morphology due to the incidence of tripedal locomotion or dietary specialization. We thus conclude that changes to the neuromuscular control of the neck, not morphological adaptations, are primarily responsible for tripedal locomotion in parrots. We argue that many-to-one mapping of form to function allows parrots with similar neck morphologies to participate in a range of behaviors, and this may be a common feature amongst all birds.
Chromosome-level genome assembly of milk thistle (Silybum marianum(L.) Gaertn.)
Authors: Kim Kyung Do , Shim Jeehyoung , Hwang Ji-Hun , Kim Daegwan , El baidouri Moaine , Park Soyeon , Song Jiyong , Yu Yeisoo , Lee Keunpyo , Ahn Byoung-Ohg , Hong Su Young , Chin Joong Hyoun 
Published: March 2024

AbstractSilybum marianum(L.) Gaertn., commonly known as milk thistle, is a medicinal plant belonging to the Asteraceae family. This plant has been recognized for its medicinal properties for over 2,000 years. However, the genome of this plant remains largely undiscovered, having no reference genome at a chromosomal level. Here, we assembled the chromosome-level genome ofS. marianum, allowing for the annotation of 53,552 genes and the identification of transposable elements comprising 58% of the genome. The genome assembly from this study showed 99.1% completeness as determined by BUSCO assessment, while the previous assembly (ASM154182v1) showed 36.7%. Functional annotation of the predicted genes showed 50,329 genes (94% of total genes) with known protein functions in public databases. Comparative genome analysis among Asteraceae plants revealed a striking conservation of collinearity betweenS. marianumandC. cardunculus. The genomic information generated from this study will be a valuable resource for milk thistle breeding and for use by the larger research community.
Synthesis of arbitrary interference patterns using a single galvanometric mirror, and its application to Structured Illumination Microscopy
Authors: Guo Ke , Boualam Abderrahim , Manton James D , Rowlands Christopher J 
Published: March 2024

AbstractWe present a new interferometer concept called SWIFT, able to project arbitrary interference patterns constructed from small numbers of plane waves. SWIFT can control each plane wave’s orientation, intensity, polarization and phase using just a single galvanometric mirror. We demonstrate the application of SWIFT to both 2D and 3D Structured Illumination Microscopy, characterizing performance on fluorescent nanoparticles and iFluor 488 phalloidin-stained U-2 OS cells.
Machine learning-based spike sorting reveals how subneuronal concentrations of monomeric Tau cause a loss in excitatory postsynaptic currents in hippocampal neurons
Authors: Brockhoff Marius , Träuble Jakob , Middya Sagnik , Fuchsberger Tanja , Fernandez-Villegas Ana , Stephens Amberley , Robbins Miranda , Dai Wenyue , Haider Belquis , Vora Sulay , Läubli Nino F , Kaminski Clemens F , Malliaras George G , Paulsen Ole , Kaminski Schierle Gabriele S 
Published: March 2024

AbstractExtracellular recordings of neuronal activity constitute a powerful tool for investigating the intricate dynamics of neural networks and the activity of individual neurons. Microelectrode arrays (MEAs) allow for recordings with a high electrode count, ranging from 10s to 1000s, generating extensive datasets of neuronal information. Furthermore, MEAs capture extracellular field potentials from cultured cells, resulting in highly complex neuronal signals that necessitate precise spike sorting for meaningful data extraction. Nevertheless, conventional spike sorting methods face limitations in recognising diverse spike shapes, thereby constraining the full utilisation of the rich dataset acquired from MEA recordings. To overcome these limitations, we have developed a machine learning algorithm, namedPseudoSort, which employs advanced self-supervised learning techniques, a distinctive density-based pseudo-labelling strategy, and an iterative fine-tuning process to enhance spike sorting accuracy. Through extensive benchmarking on large-scale simulated datasets, we demonstrate the superior performance ofPseudoSortcompared to recently developed machine learning-based (ML) spike sorting algorithms. We showcase the practical application ofPseudoSortby utilising MEA recordings from hippocampal neurons exposed to subneuronal concentrations of monomeric Tau, a protein associated with Alzheimer’s disease (AD). Our results, validated against patch clamp experiments, unveil that monomeric Tau at subneuronal concentrations induces stimulation-dependent disruptions in both local and global activity of hippocampal neurons. Remarkably, patch clamp electrophysiology highlights the effect of combined Tau and neuronal stimulation treatment on excitatory postsynaptic currents, whereasPseudoSortexcels in identifying neuronal clusters that exhibit diminished firing capacity following Tau treatment alone,i.e., in the absence of stimulation. This comprehensive approach validates the prowess ofPseudoSortand unravels the intricate effects of Tau on neuronal activity, particularly in the context of AD.
MASCARA: coexpression analysis in data from designed experiments
Authors: White Fred T.G. , Heintz-Buschart Anna , Dong Lemeng , Bouwmeester Harro J. , Westerhuis Johan A. , Smilde Age K. 
Published: March 2024

AbstractExperiments in plant transcriptomics are usually designed to induce variation in a pathway of interest. Harsh experimental conditions can cause widespread transcriptional changes between groups. Discovering coexpression within a pathway of interest (here the strigolactone pathway) in this context is hampered by the dominant variance induced by the design. Minor changes in experimental conditions not controlled for may affect the plants, leading to small coordinated differences in genes within pathways of interest and related pathways between replicate plants in the same controlled experimental condition. These systematic differences are usually averaged out, but we argue here that they can be used to improve the detection of genes that co-express. We introduce a novel framework “MASCARA” which combines ANOVA simultaneous component analysis and partial least squares to remove the experimentally induced variance and investigate multivariate relationships in the non-designed variance. MASCARA is tested against a selection of competitors on simulated data, created to mimic a designed transcriptome study, where its benefit is demonstrated. In a coexpression analysis of a real dataset MASCARA detects several uncharacterised but relevant transcripts. Our results indicate that there is sufficient structure left in a typical dataset after correcting for experimental variance and that this residual information is useful to investigate coexpression.Author SummaryExperiments in the life sciences usually purposefully induce significant variance between different treatments, in order to activate or repress certain mechanisms of interest. Whilst this is necessary it can make it challenging to detect meaningful relationships within pathways of interest, particularly when the experimental conditions are drastically different. Instead of focusing on the drastic changes in response due to the different treatment, MASCARA uses the systematic synchronous variances between replicates to find related features within the pathway of interest. Through simulation studies and application to a real dataset, we demonstrate the effectiveness of MASCARA in detecting relevant transcripts and extracting coexpression patterns from gene expression data.
Self-reported preferences for seasonal Daylight Saving Time meet fundamentals of human physiology: correlations in the 2018 Public Consultation by the European Commission
Authors: Martín-Olalla José María , Mira Jorge 
Published: March 2024

We thoroughly analyze the results to question 2 (individual preferences for cancelling or keeping the current clock regulations) from the 2018 Public Consultation on summertime arrangements (DST) conducted by the European Commission.We reveal correlations in the shares of population for cancelling the regulations and the winter sunrise time (SRW) [R2= 0.177;p= 0.03;N= 25] and the onset of human activity [R2= 0.677;p= 5 × 10−5;N= 17].The results are in line with the rationale behind the regulations in the range of latitude 35°to 63°: larger values of SRW (larger latitude) brought larger shares against the regulations; and earlier onset of human activity relative to SRW brought larger shares against the regulations.The shares for cancelling the regulation did not show correlations with time offset (position in time zone), thus challenging the current view within the circadian community.
Bilayered Biofabrication Unlocks the Potential of Skeletal Muscle for Biohybrid Soft Robots
Authors: Balciunaite Aiste , Yasa Oncay , Filippi Miriam , Michelis Mike Y. , Katzschmann Robert K. 
Published: March 2024

AbstractThe emerging field of biohybrid robotics aims to create the next generation of soft and sustainable robots by using engineered biological muscle tissues integrated with soft materials as artificial muscles (bio-actuators). Both cardiac and skeletal muscle cells can be used for biohybrid actuation. Generally, cardiac bio-actuators take the shape of thin cellular films, while locomotive skeletal muscle bio-actuators form bulk tissues. The geometry of a bio-actuator should be optimized for the type of desired motion,e.g., thin film layers are optimal for swimming actuators mimicking fish. Until now, the geometry of skeletal muscle bio-actuators has been constrained to ring- or block-like tissues generally differentiated around a pair of pillars due to the need to oppose the contraction force exerted during the skeletal muscle differentiation process. In this work, we extend the possible geometry of skeletal muscle bio-actuators by demonstrating a bilayered design that mimics the motion of jellyfish. We take advantage of a volumetric printing method,i.e., xolography, which allows us to micropattern poly(ethylene glycol) diacrylate and gelatin methacrylate hydrogels to serve as scaffolds for seeding a layer of the skeletal muscle cell matrix. We demonstrate the locomotion speed of our bio-actuators is 3.4x faster than previously reported counterparts. In addition, our skeletal bio-actuators outperform most cardiac ones. Further optimization of our bilayer biofabrication for improved reproducibility of the maturation process of the skeletal muscle tissue will pave the way for the next generation of performant skeletal muscle-based actuators for biohybrid robots.
Acceleratingde novoSINE annotation in plant and animal genomes
Authors: Liao Herui , Sun Yanni , Ou Shujun 
Published: March 2024

AbstractGenome annotation is an important but challenging task. Accurate identification of short interspersed nuclear elements (SINEs) is particularly difficult due to their lack of highly conserved sequences. AnnoSINE is state-of-the-art software for annotating SINEs in plant genomes, but its homology-based module is not available for animals and it is computationally inefficient for large genomes. Therefore, we propose AnnoSINE_v2, which extends accurate SINE annotation for animal genomes with greatly optimized computational efficiency. Our results show that AnnoSINE_v2’s annotation of SINEs has over 20% higher F1-score compared to the existing tools on animal genomes and enables the processing of complicated genomes, like human and zebrafish, which were beyond the capabilities of AnnoSINE_v1. AnnoSINE_v2 is freely available on Conda and GitHub:https://github.com/liaoherui/AnnoSINE_v2.
Scvi-hub: an actionable repository for model-driven single cell analysis
Authors: Ergen Can , Pour Amiri Valeh Valiollah , Kim Martin , Streets Aaron , Gayoso Adam , Yosef Nir 
Published: March 2024

ABSTRACTThe accumulation of single-cell omics datasets in the public domain has opened new opportunities for reusing and leveraging the vast amount of information they contain. Such uses, however, are complicated by the need for complex and resource-consuming procedures for data transfer, normalization and integration that must be addressed prior to any analysis. Here we present scvi-hub: a platform for efficiently sharing and accessing single-cell omics datasets using pre-trained probabilistic models. We demonstrate that scvi-hub allows immediate access to a slew of fundamental tasks like visualization, imputation, annotation, outlier detection, and deconvolution of new (query) datasets, using state of the art algorithms and with a requirement for storage and compute resources that is much lower compared to standard approaches. We also show that the pre-trained models enable efficient analysis and new discoveries with existing references, including large atlases such as the CZ CELLxGENE Discover Census. Scvi-hub is built within the scvi-tools open source environment and integrated into scverse. It provides powerful and readily available tools for utilizing a large collection of already-loaded datasets while also enabling easy inclusion of new datasets, thus putting the power of atlas-level analysis at the fingertips of a broad community of users.
pTAC3 and pTAC14 are required for binding of plastid-encoded RNA polymerase to DNA
Authors: Wang Joyful , Palomar V. Miguel , Min Ji-Hee , Wierzbicki Andrzej T. 
Published: March 2024

ABSTRACTPlastid-encoded RNA polymerase (PEP) is a bacterial-type multisubunit RNA polymerase responsible for the majority of transcription in chloroplasts. PEP consists of four core subunits, which are orthologs of their cyanobacterial counterparts. InArabidopsis thaliana, PEP associates with 12 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function are still poorly understood. We use ptChIP-seq to show that PAP1/pTAC3, a peripheral subunit of PEP, binds to the same genomic loci as RpoB, a core subunit of PEP. Thepap1/ptac3mutant shows a complete loss of RpoB binding to DNA throughout the genome, indicating that PAP1/pTAC3 is necessary for RpoB binding to DNA. A similar loss of RpoB binding to DNA is observed in thepap7/ptac14mutant, which is defective in another peripheral PEP subunit. We propose that the peripheral subunits of PEP are required for the recruitment of core PEP subunits to DNA.KEY MESSAGEThe peripheral subunits of plastid-encoded RNA polymerase play a crucial role in recruiting the core PEP subunits to DNA in Arabidopsis chloroplasts.
Distinct neural bases of subcomponents of the attentional blink
Authors: Halder Swagata , Raya Deepak Velgapuni , Sridharan Devarajan 
Published: March 2024

AbstractThe attentional blink reflects a ubiquitous bottleneck with selecting and processing the second of two targets that occur in close temporal proximity. An extensive literature has examined the attention blink as a unitary phenomenon, As a result, which specific component of attention – perceptual sensitivity or choice bias – is compromised during the attentional blink, and their respective neural bases, remains unknown. Here, we address this question with a multialternative task and novel signal detection model, which decouples sensitivity from bias effects. We find that the attentional blink impairs specifically one component of attention – sensitivity – while leaving the other component – bias – unaffected. Distinct neural markers of the attentional blink mapped on to distinct subcomponents of the sensitivity deficits. Parieto-occipital N2p and P3 potential amplitudes characterized target detection deficits whereas long-range high-beta band (20-30 Hz) coherence between frontoparietal electrodes signalled target discrimination deficits. We synthesized these results with representational geometry analysis. The analysis revealed that detection and discrimination deficits were encoded along separable neural dimensions, whose configural distances robustly correlated with the neural markers of each. Overall, these findings shed new light on subcomponents of the attentional blink, and reveal dissociable neural bases underlying its detection and discrimination bottlenecks.Lay summaryIn daily life, our attention switches rapidly between different objects. For example, when driving, we may shift focus from a billboard on the roadside to a pedestrian in front, in quick succession. Yet, our ability to process the second object is severely compromised especially when it appears soon after the first: an impairment called the “attentional blink”. In previous work, the attentional blink has been studied essentially as a “monolithic” (indivisible) phenomenon. We design a behavioral model to divide the attentional blink into sub-components and show that the blink affects only one specific component (sensitivity). We also identify key neural markers for deficits associated with this component. Our findings may aid in understanding the neural origins of attention deficit disorders.
Activating soluble adenylyl cyclase protects mitochondria, rescues retinal ganglion cells, and ameliorates visual dysfunction caused by oxidative stress
Authors: Bastola Tonking , Perkins Guy A. , Huu Viet Anh Nguyen , Ju Saeyeon , Kim Keun-Young , Shen Ziyao , Skowronska-Krawczyk Dorota , Weinreb Robert N. , Ju Won-Kyu 
Published: March 2024

AbstractOxidative stress is a key factor causing mitochondrial dysfunction and retinal ganglion cell (RGC) death in glaucomatous neurodegeneration. The cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) signaling pathway is involved in mitochondrial protection, promoting RGC survival. Soluble adenylyl cyclase (sAC) is one of the key regulators of the cAMP/PKA signaling pathway. However, the precise molecular mechanisms underlying the sAC-mediated signaling pathway and mitochondrial protection in RGCs that counter oxidative stress are not well characterized. Here, we demonstrate that sAC plays a critical role in protecting RGC mitochondria from oxidative stress. Using mouse models of oxidative stress, we found that activating sAC protected RGCs, blocked AMP-activated protein kinase activation, inhibited glial activation, and improved visual function. Moreover, we found that this is the result of preserving mitochondrial dynamics (fusion and fission), promoting mitochondrial bioenergetics and biogenesis, and preventing metabolic stress and apoptotic cell death in a paraquat oxidative stress model. Notably, sAC activation ameliorated mitochondrial dysfunction in RGCs by enhancing mitochondrial biogenesis, preserving mitochondrial structure, and increasing ATP production in oxidatively stressed RGCs. These findings suggest that activating sAC enhances the mitochondrial structure and function in RGCs to counter oxidative stress, consequently promoting RGC protection. We propose that modulation of the sAC-mediated signaling pathway has therapeutic potential acting on RGC mitochondria for treating glaucoma and other retinal diseases.
Simultaneous calculation of elastic scattering, fusion, and direct cross sections for reactions of weakly bound projectiles
Authors: Maridi H. M. , Keeley N. , Rusek K. 
Published: March 2024

Simultaneous analyses are performed of cross-section data for elastic scattering, fusion, Coulomb breakup, and other direct yields for the He6+Bi209 system at near Coulomb-barrier energies. The bare and dynamical polarization potentials are constructed microscopically from the structure of the colliding nuclei and they reproduce all the data well with only two adjustable parameters. This method of calculation can be successfully applied to the reactions of weakly bound and exotic projectiles with heavy targets.

Published by the American Physical Society
2024