bluuebunny/crossref_metadata_2025_split huggingface dataset:
SREBP‐1‐mediated lipogenesis confers resistance to ferroptosis and improves endothelial injury
Authors: Wang Xue , Chen Yanqiu , Meng Heyu , Ruan Jianjun , Meng Fanbo 
Published: July 2024

AbstractAtherosclerosis refers to a disease characterized by the formation of lipid plaque deposits within arterial walls, leading to reduced blood flow or blockage of blood outflow. The process of endothelial injury induced by oxidized low‐density lipoprotein (ox‐LDL) is considered the initial stage of atherosclerosis. Ferroptosis is a form of iron‐dependent, non‐apoptotic cell death, and current research suggests its association with coronary artery disease (CAD). In this study, we observed a correlation between reduced expression of SREBP‐1 and the occurrence of stable CAD. Additionally, during the process of endothelial injury induced by ox‐LDL, we also noted decreased expression of the SREBP‐1/SCD1/FADS2 and involvement in the ferroptosis process. Mechanistically, ox‐LDL induced endothelial injury by inhibiting the lipid biosynthesis process mediated by the SREBP‐1/SCD1/FADS2, thereby inducing lipid peroxidation and ferroptosis. On the contrary, overexpression of SREBP‐1 or supplementation with monounsaturated fatty acids counteracted iron accumulation, mitochondrial damage, and lipid peroxidation‐induced ferroptosis, thereby improving endothelial injury. Our study indicated that the decreased expression of peripheral blood SREBP‐1 mRNA is an independent risk factor for stable CAD. Furthermore, in endothelial cells, the lipid biosynthesis process mediated by SREBP‐1 could ameliorate endothelial injury by resisting ferroptosis. The study has been registered with the Chinese Clinical Trial Registry, which serves as a primary registry in the World Health Organization International Clinical Trials Registry Platform (ChiCTR2300074315, August 3rd, 2023).
On the enigmatic null effect of global methylation perturbation
Authors: Edrei Yifat , Hellman Asaf 
Published: July 2024

AbstractDespite the established role of DNA methylation in transcriptional silencing, most of the genes remain unchanged upon its global erasing from the genome, while expression of other genes is actually raised. Since its discovery a few decades ago, this unsolved enigma has hampered true understanding of DNA methylation role. By applying an updated mathematical model to the results of the original studies, we showed that this paradoxical effect is due to between-gene differences in the balance between methylation-guided enhancers and silencers, which protect particular disease-causing genes from the otherwise harsh effects of global methylation perturbation. Nevertheless, local methylation alternation may still affect these genes. The results a settle a long-standing wondering and suggest that DNA-methylation regulatory role is significantly greater than previously thought.
The first report on the effect of white and black truffle extracts on human semen parametersin vitro
Authors: Shelkovnikova Victoria , Dmitrieva Maria , Malygina Ekaterina , Imidoeva Natalia , Belyshenko Alexander , Morgunova Maria , Vlasova Anfisa , Telnova Tamara , Batalova Anna , Martynova Elena , Axenov-Gribanov Denis 
Published: July 2024

AbstractOur experiment aimed to evaluate the influence of extracts of white and black truffle mushrooms on human spermatozoa. The study utilized 28 samples of wild truffle fruiting bodies. In the experiment, we used ejaculate from male volunteers of active reproductive age (N=10, 25–35 years old). During the experiment, we assessed sixteen physiological parameters. Research has shown that extracts from black and white truffles related toTubersp. have a stimulating effect on spermatozoa. The average path sperm velocity, curvilinear velocity and beat cross-frequency were increased by 56%, 48% and 50% respectively. Linearity showed a significant increase by 56% and straightness by 48%. This could be useful in the development of drugs to enhance sperm activity and lifespan. Additionally, extracts from black truffles have been found to have negative effects on spermatozoa, which could be relevant for developing new contraceptive drugs. Our study demonstrated, for the first time, the influence of methanol extracts ofTubersp. mushrooms on male gametesin vitro.
Evaluating theories of neural information integration during visual search
Authors: Leite Abe , Adeli Hossein , McPeek Robert M. , Zelinsky Gregory J. 
Published: July 2024

AbstractThe brain routes and integrates information from many sources during behavior. A number of models explain this phenomenon within the framework of mixed selectivity theory, yet it is difficult to compare their predictions to understand how neurons and circuits integrate information. In this work, we apply time-series partial information decomposition [PID] to compare models of integration on a dataset of superior colliculus [SC] recordings collected during a multi-target visual search task. On this task, SC must integrate target guidance, bottom-up salience, and previous fixation signals to drive attention. We find evidence that SC neurons integrate these factors in diverse ways, including decision-variable selectivity to expected value, functional specialization to previous fixation, and code-switching (to incorporate new visual input).
Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species
Authors: Armstrong Ellie E. , Li Chenyang , Campana Michael G. , Ferrari Tessa , Kelley Joanna L. , Petrov Dmitri A. , Solari Katherine A. , Mooney Jazlyn A. 
Published: July 2024

AbstractDespite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favored for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for use in population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel user-friendly SNP selection pipeline for population assignment and individual identification, mPCRselect. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for species of conservation concern.
Cloud-Connected Patch-Worn Auscultation Device for Chest Sound Monitoring
Authors: Downen R. Scott , Li Baichen , Dong Quan , Li Zhenyu 
Published: July 2024

AbstractIn recent years, wearable electrocardiograms have risen in popularity as a solution for personal monitoring of heart activity. However, this technology has limitations in diagnostic capability and structural function monitoring. Meanwhile, auscultation of the heart remains a fundamental tool for physicians in diagnosis and monitoring of heart disease largely unaddressed in a convenient wearable format. The present work outlines a promising system currently under investigation, allowing user-initiated 10-second chest-sound recordings to be transmitted over Bluetooth-Low-Energy, with an innovative package design providing inherent noise reduction and a high signal-to-noise ratio. The device has been tested on healthy individuals, and system response has been validated against calibrated electrocardiogram recording equipment to analyze signal capture fidelity.Abstract Figure
Ultra-high temporal resolution 4D angiography using arterial spin labeling with subspace reconstruction
Authors: Shen Qijia , Wu Wenchuan , Chiew Mark , Ji Yang , Woods Joseph G. , Okell Thomas W. 
Published: July 2024

AbstractPurposeTo achieve ultra-high temporal resolution non-contrast 4D angiography with improved spatiotemporal fidelity.MethodsContinuous data acquisition using 3D golden-angle sampling following an arterial spin labeling preparation allows for flexibly reconstructing 4D dynamic angiograms at arbitrary temporal resolutions. However, k-space data is often temporally “binned” before image reconstruction, negatively affecting spatiotemporal fidelity and limiting temporal resolution. In this work, a subspace was extracted by linearly compressing a dictionary constructed from simulated curves of an angiographic kinetic model. The subspace was used to represent and reconstruct the voxelwise signal timecourse at the same temporal resolution as the data acquisition without temporal binning. Physiological parameters were estimated from the resulting images using a Bayesian fitting approach. A group of 8 healthy subjects were scanned and the in-vivo results reconstructed by different methods were compared. Due to the difficulty of obtaining ground truth 4D angiograms with ultra-high temporal resolution, the in-vivo results were cross-validated with numerical simulations.ResultsThe proposed method enables 4D time-resolved angiography with much higher temporal resolution (14.7 ms) than previously reported (∼50 ms) whilst maintaining high spatial resolution (1.1 mm isotropic). Blood flow dynamics were depicted in greater detail, thin vessel visibility was improved, and the estimated physiological parameters also exhibited more realistic spatial patterns with the proposed method.ConclusionIncorporating a subspace compressed kinetic model into the reconstruction of 4D ASL angiograms notably improved the temporal resolution and spatiotemporal fidelity, which was subsequently beneficial for accurate physiological modeling.
Quantifying Forest Biomass and Genetic Contribution using Light Detection and Ranging
Authors: Sano Haruka , Miura Naoko , Inamori Minoru , Unno Yamato , Guo Wei , Isobe Sachiko , Kusunoki Kazutaka , Iwata Hiroyoshi 
Published: July 2024

AbstractThe growing focus on the role of forests in carbon sequestration highlights the importance of accurately and efficiently measuring biophysical traits, such as diameter at breast height (DBH) and tree height. Understanding genetic contributions to trait variation is crucial for enhancing carbon storage through genetic improvement of forest trees. Light detection and ranging (LiDAR) has been used to estimate DBH and tree height; however, few studies have explored the heritability of these traits or assessed the accuracy of biomass increment selections based on these traits. Therefore, this study aimed to leverage LiDAR to measure DBH and tree height, estimate tree heritability, and evaluate the accuracy of timber volume selections based on these traits using 60-year-old larch as the study material. Unmanned aerial vehicle (UAV) and backpack LiDAR were compared against hand-measured values. The accuracy of DBH estimations using backpack LiDAR resulted in a root mean square error (RMSE) of 2.7 cm and a coefficient of determination of 0.67. Conversely, the accuracy achieved with UAV LiDAR was 4.0 cm in RMSE and a 0.24 coefficient of determination. The heritability of DBH was found to be higher for backpack LiDAR than for UAV LiDAR and even exceeded that of hand measurements. Comparisons of the accuracy of timber volume selections based on the measured traits demonstrated comparable performances between the backpack and UAV LiDAR. Overall, these findings underscore the potential of using LiDAR remote sensing to quantitatively measure forest tree biomass and facilitate their genetic improvement of carbon-sequestration ability based on these measurements.
Human-Mouse Chimeric Brain Models to Study Human Glial-Neuronal and Macroglial-Microglial Interactions
Authors: Jin Mengmeng , Ma Ziyuan , Zhang Haiwei , Papetti Ava V. , Dang Rui , Stillitano Alessandro C. , Zou Lisa , Goldman Steven A. , Jiang Peng 
Published: July 2024

AbstractHuman-mouse chimeric brain models, generated by transplanting human induced pluripotent stem cell (hiPSC)-derived neural cells, are valuable for studying the development and function of human neural cells in vivo. Understanding glial-glial and glial-neuronal interactions is essential for unraveling the complexities of brain function and developing treatments for neurological disorders. To explore these interactions between human neural cells in vivo, we co-engrafted hiPSC-derived neural progenitor cells together with primitive macrophage progenitors into the neonatal mouse brain. This approach creates human-mouse chimeric brains containing human microglia, macroglia (astroglia and oligodendroglia), and neurons. Using super-resolution imaging and 3D reconstruction techniques, we examine the dynamics between human neurons and glia, and observe human microglia pruning synapses of human neurons, and often engulfing neurons themselves. Single-cell RNA sequencing analysis of the chimeric brain uncovers a close recapitulation of the human glial progenitor cell population, along with a dynamic stage in astroglial development that mirrors the processes found in the human brain. Furthermore, cell-cell communication analysis highlights significant neuronal-glial and macroglial-microglial interactions, especially the interaction between adhesion molecules neurexins and neuroligins between neurons and astroglia, emphasizing their key role in synaptogenesis. We also observed interactions between microglia and astroglia mediated by SPP1, crucial for promoting microglia growth and astrogliosis, and the PTN-MK pathways, instrumental in homeostatic maintenance and development in macroglial progenitors. This innovative co-transplantation model opens up new avenues for exploring the complex pathophysiological mechanisms underlying human neurological diseases. It holds particular promise for studying disorders where glial-neuronal interactions and non-cell-autonomous effects play crucial roles.
Copy number variation contributes to parallel local adaptation in an invasive plant
Authors: Wilson Jonathan , Bieker Vanessa C. , van Boheemen Lotte , Connallon Tim , Martin Michael D. , Battlay Paul , Hodgins Kathryn A. 
Published: July 2024

AbstractAdaptation is a critical determinant of the diversification, persistence, and geographic range limits of species. Yet the genetic basis of adaptation is often unknown and potentially underpinned by a wide range of mutational types – from single nucleotide changes to large-scale alterations of chromosome structure. Copy number variation (CNV) is thought to be an important source of adaptive genetic variation, as indicated by decades of candidate gene studies that point to CNVs underlying rapid adaptation to strong selective pressures. Nevertheless, population- genomic studies of CNVs face unique logistical challenges not encountered by other forms of genetic variation. Consequently, few studies have systematically investigated the contributions of CNVs to adaptation at a genome-wide scale. We present a genome-wide analysis of CNV contributing to the adaptation of an invasive weed,Ambrosia artemisiifolia– the first such study in an invasive pest. CNVs show clear signatures of parallel local adaptation between North American (native) and European (invaded) ranges, implying widespread reuse of CNVs during adaptation to shared heterogeneous patterns of selection. We used a local principal component analysis to genotype CNV regions in whole-genome sequences of samples collected over the last two centuries. We identified 16 large CNV regions of up to 11.85 megabases in length, six of which show signals of rapid evolutionary change, with pronounced frequency shifts between historic and modern populations. Our results provide compelling genome-wide evidence that copy number variation underlies rapid adaptation over contemporary timescales of natural populations.Significance StatementUsing a population-genomic approach, we identified copy number variants – stretches of DNA that can be either present, absent, or in multiple copies – displaying parallel signatures of local adaptation across the native and introduced ranges of the invasive weedAmbrosia artemisiifolia. We further identified 16 large copy number variants, some associated with ecologically important traits including sex allocation and height, that show strong signatures of selection over space, along with dramatic temporal changes over the past several decades. These results highlight the importance of an often-overlooked form of genomic variation in both local adaptation and rapid adaptation of invasive species.
Transposable Element Expression and Sub-cellular Dynamics During hPSC Differentiation to Endoderm, Mesoderm, and Ectoderm Lineages
Authors: Babarinde Isaac A. , Fu Xiuling , Ma Gang , Li Yuhao , Akinwole Mobolaji T. , Zhou Xuemeng , Hutchins Andrew P. 
Published: July 2024

AbstractTransposable elements (TEs) are genomic elements that are found in multiple copies in mammalian genomes. TEs were previously thought to have little functional relevance but recent studies have reported TE roles in multiple biological processes, particularly in embryonic development. To investigate the expression dynamics of TEs during human early development, we used long-read sequence data generated fromin vitrodifferentiation of human pluripotent stem cells (hPSCs) to endoderm, mesoderm, and ectoderm lineages to construct lineage-specific transcriptome assemblies and accurately place TE sequences in their transcript context. Our analysis revealed that specific TE types, such as LINEs and LTRs, exhibit distinct expression patterns across different lineages. Notably, an expression outburst was observed in the ectoderm lineage, with multiple TE types showing dynamic expression trajectories. Additionally, certain LTRs, including HERVH and LTR7Y, were highly expressed in hPSCs and endodermal cells, but these HERVH and LTR7Y sequences originated from completely different transcripts. Interestingly, TE-containing transcripts exhibit distinct levels of transcript stability and subcellular localization across different lineages. Moreover, we showed a consistent trend of increased chromatin association of TE-containing transcripts in germ lineage cells compared to hPSCs. This study suggests that TEs contribute to human embryonic development through dynamic chromatin interaction.Key findingsDifferent loci of the same TEs are independently regulated in different cell statesEctoderm has the highest frequency of TE-containing transcriptsThe presence of TEs dynamically drives transcripts to different sub-cellular compartments in different cell stateshPSCs have the least stable TE transcripts with the weakest TE chromatin association, highlighting loose hPSC chromatin and potential roles in cell differentiation
Postprandial sleep in short-sleeping Mexican cavefish
Authors: Gallman Kathryn , Rastogi Aakriti , North Owen , O’Gorman Morgan , Hutton Pierce , Lloyd Evan , Warren Wes , Kowalko Johanna E. , Duboue Erik R. , Rohner Nicolas , Keene Alex C. 
Published: July 2024

AbstractInteraction between sleep and feeding behaviors are critical for adaptive fitness. Diverse species suppress sleep when food is scarce to increase the time spent foraging. Post-prandial sleep, an increase in sleep time following a feeding event, has been documented in vertebrate and invertebrate animals. While interactions between sleep and feeding appear to be highly conserved, the evolution of postprandial sleep in response to changes in food availability remains poorly understood. Multiple populations of the Mexican cavefish,Astyanax mexicanus,have independently evolved sleep loss and increased food consumption compared to surface-dwelling fish of the same species, providing the opportunity to investigate the evolution of interactions between sleep and feeding. Here, we investigate effects of feeding on sleep in larval and adult surface fish, and two parallelly evolved cave populations ofA. mexicanus.Larval surface and cave populations ofA. mexicanusincrease sleep immediately following a meal, providing the first evidence of postprandial sleep in a fish model. The amount of sleep was not correlated to meal size and occurred independently of feeding time. In contrast to larvae, postprandial sleep was not detected in adult surface or cavefish, that can survive for months without food. Together, these findings reveal that postprandial sleep is present in multiple short-sleeping populations of cavefish, suggesting sleep-feeding interactions are retained despite the evolution of sleep loss. These findings raise the possibility that postprandial sleep is critical for energy conservation and survival in larvae that are highly sensitive to food deprivation.
Mechanism of Proton Release during Water Oxidation in Photosystem II
Authors: Allgöwer Friederike , Pöverlein Maximilian C. , Rutherford A. William , Kaila Ville R. I. 
Published: July 2024

AbstractPhotosystem II (PSII) catalyzes the light-driven water oxidation that releases dioxygen into our atmosphere and provides the electrons needed for the synthesis of biomass. The catalysis occurs in the oxygen-evolving oxo-manganese-calcium (Mn4O5Ca) cluster that drives the stepwise oxidation and deprotonation of substrate water molecules leading to the O2formation. However, despite recent advances, the mechanism of these reactions remains unclear and much debated. Here we show that the light-driven Tyr161D1oxidation adjacent to the Mn4O5Ca cluster, significantly decreases the barrier for proton transfer from the putative substrate water molecule (W3/Wx) to Glu310D2, which is accessible to the luminal bulk. By combining hybrid quantum/classical (QM/MM) free energy calculations with atomistic molecular dynamics (MD) simulations, we probe the energetics of the proton transfer along the Cl1 pathway. We demonstrate that the proton transfer occurs via water molecules and a cluster of conserved carboxylates, driven by redox-triggered electric fields directed along the pathway. Glu65D1establishes a local molecular gate that controls the proton transfer to the luminal bulk, whilst Glu312D2acts as a local proton storage site. The identified gating region could be important in preventing back-flow of protons to the Mn4O5Ca cluster. The structural changes, derived here based on the dark-state PSII structure, strongly support recent time-resolved XFEL data of the S3→S4transition (Nature617, 2023), and reveal the mechanistic basis underlying deprotonation of the substrate water molecules. Our combined findings provide insight into the water oxidation mechanism of PSII and show how the interplay between redox-triggered electric fields, ion-pairs, and hydration effects control proton transport reactions.Significance StatementPhotosystem II is nature’s water splitting enzyme that produces the oxygen in the atmosphere and drives the synthesis of biomass. The water splitting reaction releases protons to the luminal bulk contributing to the protonmotive force that drives the synthesis of ATP. Key mechanistic principles of the light-driven water splitting reaction remain debated, amongst them the catalytically important deprotonation steps. Here we show how the oxygen-evolving oxo-manganese-calcium cluster transports protons via conserved carboxylates and water molecules in proton arrays that lead to the luminal bulk. We identify a local proton storage site and molecular gates that prevent wasteful back reactions by undergoing conformational changes, and we show how electric field effects control the protonation dynamics in Photosystem II.