bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome-level genome for the nudibranch gastropodBerghia stephanieaehelps parse clade-specific gene expression in novel and conserved phenotypes
Authors: Goodheart Jessica A. , Rio Robin A. , Taraporevala Neville F. , Fiorenza Rose A. , Barnes Seth R. , Morrill Kevin , Jacob Mark Allan C. , Whitesel Carl , Masterson Park , Batzel Grant O. , Johnston Hereroa T. , Ramirez M. Desmond , Katz Paul S. , Lyons Deirdre C. 
Published: August 2023

AbstractHow novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropodBerghia stephanieae(Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filteredBerghiagenome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability
Authors: Drexler Richard , Khatri Robin , Sauvigny Thomas , Mohme Malte , Maire Cecile L. , Ryba Alice , Zghaibeh Yahya , Dührsen Lasse , Salviano-Silva Amanda , Lamszus Katrin , Westphal Manfred , Gempt Jens , Wefers Annika K. , Neumann Julia , Bode Helena , Hausmann Fabian , Huber Tobias B. , Bonn Stefan , Jütten Kerstin , Delev Daniel , Weber Katharina J. , Harter Patrick N. , Onken Julia , Vajkoczy Peter , Capper David , Wiestler Benedikt , Weller Michael , Snijder Berend , Buck Alicia , Weiss Tobias , Keough Michael B. , Ni Lijun , Monje Michelle , Silverbush Dana , Hovestadt Volker , Suvà Mario L. , Krishna Saritha , Hervey-Jumper Shawn L. , Schüller Ulrich , Heiland Dieter H. , Hänzelmann Sonja , Ricklefs Franz L. 
Published: August 2023

ABSTRACTNeural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is nascent. We present an epigenetically defined neural signature of glioblastoma that independently affects patients’ survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals high abundance of stem cell-like malignant cells classified as oligodendrocyte precursor and neural precursor cell-like in high-neural glioblastoma. High-neural glioblastoma cells engender neuron-to-glioma synapse formationin vitroandin vivoand show an unfavorable survival after xenografting. In patients, a high-neural signature associates with decreased survival as well as increased functional connectivity and can be detected via DNA analytes and brain-derived neurotrophic factor in plasma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant.
MRIO: The Magnetic Resonance Imaging Acquisition and Analysis Ontology
Authors: Bartnik Alexander , Serra Lucas M. , Smith Mackenzie , Duncan William D. , Wishnie Lauren , Ruttenberg Alan , Dwyer Michael G. , Diehl Alexander D. 
Published: August 2023

AbstractObjectiveMagnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. However, there are many challenges inherent in managing and analyzing MRI data, due in large part to the heterogeneity of data acquisition.Materials and MethodsTo address this, we have developed MRIO, the Magnetic Resonance Imaging Acquisition and Analysis Ontology.ResultsMRIO provides well-reasoned classes and logical axioms for the acquisition of several MRI acquisition types and well-known, peer-reviewed analysis software, facilitating the use of MRI data. These classes provide a common language for the neuroimaging research process and help standardize the organization and analysis of MRI data for reproducible datasets. We also provide queries for automated assignment of analyses for given MRI types.DiscussionMRIO aids researchers in managing neuroimaging studies by helping organize and annotate MRI data and integrating with existing standards such as Digital Imaging and Communications in Medicine and the Brain Imaging Data Structure, enhancing reproducibility and interoperability. MRIO was constructed according to Open Biomedical Ontologies Foundry principals and has contributed several terms to the Ontology for Biomedical Investigations to help bridge neuroimaging data to other domains.ConclusionMRIO addresses the need for a “common language” for MRI that can help manage the neuroimaging research, by enabling researchers to identify appropriate analyses for sets of scans and facilitating data organization and reporting.
YAEL: Your Advanced Electrode Localizer
Authors: Wang Zhengjia , Magnotti John , Zhang Xiang , Beauchamp Michael S. 
Published: August 2023

AbstractIntracranial electroencephalography (iEEG) provides a unique opportunity to measure human brain function with implanted electrodes. A key step in neuroscience inference from iEEG is localizing the electrodes relative to individual subject anatomy and identified regions in brain atlases. While there are number of workflows for electrode localization, most suffer from one or more limitations. The first limitation is a lack of integration: scientists must install and use different software packages for each localization step. Second, they are inefficient: while most iEEG analysis steps can be automated, electrode localization is still largely a manual process. Third, most current tools are limited to the localization process itself, leaving users without the ability to create high-quality visualizations for clinical and research purposes. We developed YAEL (Your Advanced Electrode Localizer) to overcome these limitations. First, YAEL is completely integrated: a single easy-to-use graphical user interface (GUI) controls every step of the localization process. Second, YAEL uses a flexible 3D viewer and automation tools to make accurate localization of electrodes quick and easy. Third, after localization is complete, YAEL leverages the same viewer to create high-quality visualizations of electrode data including identified brain areas from atlases; the response to experimental tasks measured with iEEG; and clinical measures such as epileptiform activity or the results of electrical stimulation mapping. YAEL contains more than 30,000 lines of code, is free and open source, and can be installed in minutes on Mac, Windows and Linux platforms fromhttps://yael.wiki. User interactions with YAEL occur through a web browser ensuring a familiar user experience and consistent operation across platforms and whether YAEL is used locally or deployed in the cloud.
Progesterone receptor activation regulates sensory sensitivity
Authors: Joshi Suchitra , Williamson John , Moosa Shayan , Kapur Jaideep 
Published: August 2023

AbstractWomen develop chronic pain during their reproductive years more often than men, and estrogen and progesterone regulate this susceptibility. We tested whether brain progesterone receptor (PR) signaling regulates pain susceptibility. During the estrous cycle, animals were more sensitive to pain during the estrus stage than in the diestrus stage, suggesting a role for reproductive hormones, estrogen, and progesterone. We measured the pain threshold daily for four days in ovariectomized, estrogen-primed animals treated with progesterone. The pain threshold was lower 2 days later and stayed that way for the duration of the testing. A specific progesterone-receptor (PR) agonist, segesterone, promoted pain, and mice lacking PR in the brain (PRKO) did not experience lowered pain threshold when treated with progesterone or segesterone. PR activation increased the cold sensitivity but did not affect the heat sensitivity and had a small effect on light sensitivity. Finally, we evaluated whether PR activation altered experimental migraine. Segesterone and nitroglycerin (NTG) when administered sequentially, reduced pain threshold but not separately. These studies have uncovered a pain-regulating function of PRs. Targeting PRs may provide a novel therapeutic avenue to treat chronic pain in women.
Tomato Response Evaluation through Fertilization and PGRs application Under Temperature Differentiation in late Winter
Authors: Gomasta Joydeb , Hassan Jahidul , Sultana Hasina , Ozaki Yukio , Alamri Saud , Alfagham Alanoud T. , AL-Humaid Latifah A 
Published: August 2023

AbstractThis study evaluated the exogenous application of PGRs substitute chemical fertilization without compromising the growth and yield of tomato in fluctuated day-night temperature and humidity stressed late winter. Two-factor experiment comprising chemical fertilizers at 100, 110, 90 and 80 % of recommended doses besides control and PGRs of GA3; NAA, 4-CPA and SA @ 50 ppm including control was conducted where treatments were assigned in triplicates. Results revealed no significant variation among the fertilizer doses (80% to 110% of recommendation) regarding growth and yield contributing traits while among the PGRs, GA3@ 50 ppm produced maximum number of flower clusters plant-1(16.85), flowers (8.80) and fruits (5.79) cluster-1, single fruit weight (67.83 g) and fruit yield (6.61 kg plant-1) of tomato that was statistically identical with the findings of SA. But significant reduction in yield was noted in NAA and 4-CPA (1.20 kg and 1.21 kg plant-1, respectively). Interestingly, GA3and SA in combination with any doses of the studied fertilizers maximize the tomato morphological and reproductive traits while fertilizer plus NAA and 4-CPA interaction gave the inferior results. Further, correlation matrix and PCA findings revealed that five fertilizer doses have no distinctiveness whereas GA3and SA has distinct position than other PGRs with the maximum dependent variables those were contributed positively in the total variations. The study findings suggested that 20% fertilizer requirement could be reduced with the substitution of GA3and SA @ 50 ppm for successful cultivation of tomato in late winter having the extreme environmental issues.
IRE1 regulated autophagy and chaperone levels cooperatively modulate acquired thermotolerance inArabidopsis thaliana
Authors: Bajaj Mayur , Allu Annapurna Devi , Rao Basuthkar J 
Published: August 2023

AbstractRapidly changing global climatic conditions emphasize the urgent need for the development of heat stress-resilient plants. Priming, a stress-training program that aids in imparting tolerance to subsequent stress(es) emerged as a promising approach to improve stress tolerance. However, molecular mechanisms underlying priming-induced plant stress responses still remain largely elusive. In the current study, the impact of heat stress onArabidopsis thalianaseedlings pre-exposed to elevated temperature (primed) was found to be minimal, compared to naïve (unprimed) seedlings, which failed to survive. Our findings suggest that thermopriming-mediated heat stress tolerance operates through the activation of IRE1-bZIP60 cascade triggering unfolded protein response (UPR). Further, IRE1 activation triggers autophagy response through attenuation of autophagy-negative regulators such asBGLU21, ROSY1andPR-14via RIDD-mediated mRNA degradation. Alongside UPR and autophagy, priming temporally induces HSP levels, rendering plants tolerant to acute heat stress. Contrarily, unprimed seedlings fail to mount such temporally coordinated regulation, thus fail to survive. Moreover, loss of bZIP60 reduces the impact of priming-induced response, suggesting its role in the maintenance of stress memory. Taken together, the current study suggests that priming-mediated regulation of protein homeostasis through the temporal regulation of autophagy in concert with chaperone synthesis promotes heat stress tolerance.
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Proteins?
Authors: Xie Tengyu , Huang Jing 
Published: August 2023

AbstractUnderstanding the conformational dynamics of proteins, such as the inward-facing (IF) and outward-facing (OF) transition observed in transporters, is vital for elucidating their functional mechanisms. Despite significant advances in protein structure prediction (PSP) over the past three decades, most efforts have been focused on single-state prediction, leaving multi-state or alternative conformation prediction (ACP) relatively unexplored. This discrepancy has led to the development of highly accurate PSP methods such as AlphaFold, yet their capabilities for ACP remain limited. To investigate the performance of current PSP methods in ACP, we curated a dataset, named IOMemP, consisting of 32 experimentally determined high-resolution IF and OF structures of 16 membrane proteins. We benchmarked 12 representative PSP methods, along with two recent multi-state methods based on AlphaFold, against this dataset. Our findings reveal an escalating bias towards one specific state in deep learning-based methods and a remarkably consistent preference for specific states across various PSP methods. We elucidated how coevolution information in MSAs influences the state preference. Moreover, we showed that AlphaFold, when excluding coevolution information, estimated similar energies between the experimental IF and OF conformations, indicating that the energy model learned by AlphaFold is not biased towards any particular state. Our IOMemP dataset and benchmark results are anticipated to advance the development of robust ACP methods.
Benchmarking computational methods for single-cell chromatin data analysis
Authors: Luo Siyuan , Germain Pierre-Luc , Robinson Mark D. , Meyenn Ferdinand von 
Published: August 2023

AbstractSingle-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics datasets continue, challenges in analyzing such sparse, noisy, and high-dimensional data become pressing. Specifically, one challenge relates to optimizing the processing of chromatin-level measurements and efficiently extracting information to discern cellular heterogeneity. This is of critical importance, since the identification of cell types is a fundamental step in current single-cell data analysis practices.We benchmarked 8 feature engineering pipelines derived from 5 recent methods to assess their ability to discover and discriminate cell types. By using 10 metrics calculated at the cell embedding, shared nearest neighbor graph, or partition levels, we evaluated the performance of each method at different data processing stages. This comprehensive approach allowed us to thoroughly understand the strengths and weaknesses of each method and the influence of parameter selection.Our analysis provides guidelines for choosing analysis methods for different datasets. Overall, feature aggregation, SnapATAC, and SnapATAC2 outperform latent semantic indexing-based methods. For datasets with complex cell-type structures, SnapATAC and SnapATAC2 are preferred. With large datasets, SnapATAC2 and ArchR are most scalable.
Large-scale lensless microscopy with fast acquisition and region-wise focusing
Authors: Zhou You , Song Weizhi , Wu Linyuan , Fan Lin , Wang Junjia , Jiang Shaowei , Ma Zhan , Xiong Bo , Cao Xun 
Published: August 2023

AbstractThe imaging field of view (FOV) of lensless microscope is consistent with the size of image sensor in use, enabling the observation of sample areas larger than 20 mm2. Combined with high-performance and even super-resolution phase retrieval algorithms, micron and sub-micron resolution can be achieved, ultimately realizing wide-field and high-resolution imaging performance simultaneously. However, high-throughput lensless imaging poses significant challenges in terms of rapid data acquisition and large-scale phase retrieval. Additionally, when observing biological samples over a large FOV, the focus plane often exhibits inconsistency among different regions, necessitating further parameter calibration. In this study, we propose a fast acquisition and efficient reconstruction strategy for coherent lensless imaging based on a multi-height imaging model. Multiple measurements are manually modulated using an axial translation stage and continuously captured by an image sensor, facilitating rapid data acquisition within seconds and requiring no hardware synchronization. The efficiency and accuracy of phase retrieval are enhanced through precise parameter calibration algorithms, as well as techniques such as region-wise parallel computing and region-wise auto-focusing. Experimental results demonstrate 7.4×5.5 mm2FOV and 1.55 μm half-pitch resolution imaging of human skin and lung tumor sections with region-wise focusing, requiring only an approximate 0.5-s acquisition time and 44-s reconstruction time. Furthermore, by incorporating the pixel super-resolution principle, the 1.10 μm half-pitch imaging resolution is demonstrated in full-FOV peripheral blood smears without additional data required, beneficial to the identification of hollow shape and segmentation of blood cells.
Methods and techniques enabling multi-kilobase long-range genomic rewrite/replace editing
Authors: Piggott Christopher A , Tjang Laurentia V , Chen Selina , Tatu Utsav , Hirou Hannah , Jaroszewska Antonina , McIntyre Emma , Chen Jocelin , Faybishenko Joelle V , Gavan Richard V , Hackley Chris R 
Published: August 2023

AbstractCRISPR enabled cell and gene therapies have the potential to revolutionize the field of genetic medicine. However, the vast majority of rare diseases remain untreatable due to the limitations of current tools and techniques. To date, most corrective therapeutic approaches have been restricted to mutation-by-mutation approaches, where either HDR, or newer techniques such as base or prime editing, rewrite small regions of DNA at a time (∼1-100 bp). While these approaches are powerful, short editing windows (relative to the size of human genes) are financially and/or technically incompatible with most rare-disease mutation profiles. Here, we demonstrate for the first time that CRISPR/Cas9 can be used to “rewrite” 7kb+ sections of the human genome simultaneously via a selection-free process we have named “long-range rewriting”. Long-range rewriting approaches are compatible with multiple nucleases, cell types and genomic loci, and can be used with both double-strand break (DSB) and non-DSB based approaches.
Woody plant taxonomic, functional, and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests: environmental filtering and arrival of temperate taxa
Authors: Bañares-de-Dios Guillermo , Macía Manuel J. , Arellano Gabriel , Granzow-de la Cerda Íñigo , Vega-Álvarez Julia , Arnelas Itziar , Espinosa Carlos I. , Salinas Norma , Cayuela Luis 
Published: August 2023

ABSTRACTAimMountains are paramount for exploring biodiversity patterns and their causes due to the rich mosaic of topographies and climates encompassed over short geographical distances. Biodiversity changes along elevational gradients have traditionally been explored in terms of taxonomic diversity, but other aspects must be considered. For first time, we simultaneously assessed elevational trends in the taxonomic, functional, and phylogenetic diversity of woody plants in Andean tropical montane forests (TMFs) and explored their underlying ecological and evolutionary causing processes.LocationTropical AndesTime period2011/2012 and 2017/2019Tropical AndesMajor TaxaWoody plantsMethodsWe investigated taxonomic, functional, and phylogenetic diversity along four transects (traversingca. 2,200 m altitudinal gradients) encompassing 114 0.1 ha plots across a broad latitudinal range (ca. 10°). We used Hill numbers to quantify differences in the abundance-based diversity of 37,869 woody plant individuals with DBH ≥ 2.5 cm.ResultsTaxonomic, functional, and phylogenetic diversity decreased as elevation increased. The decrease was less pronounced for Hill numbers of higher orders. The only exception was a slight increase in phylogenetic diversity when more weight was given to dominant species. These results were consistent between transects.Main conclusionsThe decrease in taxonomic and functional diversity with elevation might be due to an environmental filtering process where the increasingly harsher conditions towards highlands exclude species and functional strategies. Besides, the differences in the steepness of the decrease between Hill orders suggest that rare species contribute disproportionately to functional diversity. The shifting elevational trend in the phylogenetic diversity between Hill orders indicates a greater than previously considered influence in central tropical Andean highlands of species originated in lowlands with strong niche conservatism relative to distantly related temperate lineages. This could be explained by a decreasing presence and abundance of extratropical taxa towards the central Andes relative to northern or southern Andes.BIOSKETCHGuillermo Bañares-de-Dios is a plant ecologist with interests in community assembly, biodiversity patterns, and global change. He completed his PhD in 2020 and belongs to “Grupo de Ecología Tropical”, an international network of researchers from different institutions with broad interests in tropical biology (http://www.grupoecologiatropical.com/?lang=en). Currently he works as Project Manager implementing the European Pollinator Monitoring Scheme in Spain.