bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital Light Processing 3D Printing enables High Throughput Fabrication of Human Engineered Heart Tissues for Disease Modeling
Authors: Dhand Abhishek P. , Juarros Miranda A. , Martin Thomas G. , Rodriguez-Rivera Gabriel J. , Hunt Dakota R. , Obenreder Mackenzie C. , Crosby Cody O. , Meurer-Zeman Bianca , McAfee Quentin , Valle-Ayala Henry , Zlotnick Hannah M. , Goddard Declan N. , Ebmeier Christopher C. , Burdick Jason A. , Leinwand Leslie A. 
Published: October 2024

ABSTRACT3Din vitroengineered heart tissue (EHT) models recapitulate aspects of native cardiac physiology but are often limited by scalability, cost, and reproducibility. Here, we report a simple, one-step method for rapid (∼minutes) fabrication of molds using digital light processing (DLP)-based 3D printing that support the formation of EHTs by human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) with high reproducibility (>95% efficiency) and varied designs (e.g., length, aspect ratio). Compared to 2D iPSC-CMs, 3D EHTs display enhanced maturity, including increased expression of β-oxidation genes, higher concentrations of sarcomeric myosins, improved sarcomere density and alignment, and enrichment of cardiac pathways (e.g., upregulation of sodium channels, action potentials, contraction). The technology is applied to model pathological cardiac hypertrophyin vitro, using either (i) acute adrenergic agonism or (ii) chronic culture within stiff hydrogel molds. Treated EHTs exhibit increased levels of pathology-associated gene expression and activation of signaling cascades involved in pathological remodeling compared to untreated controls or treated 2D iPSC-CMs. Thus, our method results in robust yet simpler, cheaper, and faster EHTs to study cardiac disease.
TheC. elegansLON-1 protein requires its CAP domain for function in regulating body size and BMP signaling
Authors: Serrano Maria Victoria , Cottier Stephanie , Wang Lianzijun , Moreira-Antepara Sergio , Nzessi Anthony , Liu Zhiyu , Williams Byron , Lee Myeongwoo , Schneiter Roger , Liu Jun 
Published: October 2024

ABSTRACTThe CAP (Cysteine-rich secretory proteins, Antigen-5, Pathogenesis-Related) proteins are widely expressed and have been implicated to play diverse roles ranging from mammalian reproduction to plant immune response. Increasing evidence supports a role of CAP proteins in lipid binding. TheC. elegansCAP protein LON-1 is known to regulate body size and Bone Morphogenetic Protein (BMP) signaling. LON-1 is a secreted protein with a conserved CAP domain and a C-terminal unstructured domain with no homology to other proteins. In this study, we report that the C-Terminal Domain (CTD) of LON-1 is dispensable for its function. Instead, key conserved residues located in the CAP domain are critical for LON-1 function in vivo. We further showed that LON-1 is capable of binding sterol, but not fatty acid, in vitro, and that certain key residues implicated in LON-1 function in vivo are also important for LON-1 sterol binding in vitro. These findings suggest a role of LON-1 in regulating body size and BMP signaling via sterol binding.ARTICLE SUMMARYTheC. elegansLON-1 protein is known to regulate body size and Bone Morphogenetic Protein (BMP) signaling. However, its molecular mode of action remains elusive. This study shows that LON-1 can bind sterol, but not fatty acid, in vitro. Furthermore, key conserved residues in the CAP domain of LON-1 are required for LON-1 function in vivo. These findings suggest a role of LON-1 in regulating body size and BMP signaling via sterol binding.
Structural basis for saxitoxin congener binding and neutralization by anuran saxiphilins
Authors: Zakrzewska Sandra , Nixon Samantha A. , Chen Zhou , Hajare Holly S. , Park Elizabeth R. , Mulcahy John V. , Arlinghaus Kandis M. , Neu Eduard , Konovalov Kirill , Provasi Davide , Leighfield Tod A. , Filizola Marta , Bois J. Du , Minor Daniel L. 
Published: October 2024

AbstractDinoflagellates and cyanobacteria in harmful ‘red tide’ algal blooms produce saxitoxin (STX) and ∼50 congeners that block voltage-gated sodium channel (NaV) function and disrupt bioelectrical signals1–4. Consuming seafood carrying these lethal toxins causes paralytic shellfish poisoning (PSP), a growing public health hazard due to climate change5–7that motivates efforts to detect these toxins and counteract their noxious effects. Although structural studies of NaVs8,9and anuran soluble STX binding proteins known as saxiphilins (Sxphs)10,11revealed convergent binding modes for the bis-guanidinium STX core10,11, the structural basis for STX congener recognition is unknown. Here, we show that American bullfrog (Rana catesbeiana)RcSxph10,11and High Himalaya frog (Nanorana parkeri)NpSxph10use a pre-organized pocket to sequester STX congeners through a binding mode shared with STX. This ‘lock and key’ recognition yields a tradeoff between a relatively rigid high-affinity toxin binding site in which bound waters are crucial and the ability of Sxphs to accommodate STX congener modifications. Importantly, functional studies show that Sxphs act as ‘toxin sponges’ that reverse NaVblock by multiple STX congeners and can detect these bis-guanidinium toxins in a radioligand receptor binding assay (RBA) for PSP toxin environmental testing12,13. Our findings establish how Sxphs sequester diverse neurotoxins and reveal structural factors underlying STX congener binding differences between Sxphs and NaVs that are rooted in the distinct toxin binding orientations on these two targets. These insights expand the molecular foundation required for understanding toxin sponge action and for guiding development of new means to monitor PSTs and mitigate their harmful effects.
Assessing Quantitative Performance and Expert Review of Multiple Deep Learning-Based Frameworks for Computed Tomography-based Abdominal Organ Auto-Segmentation
Authors: Ram Udbhav S. , Pogue Joel A. , Soike Michael , Pfister Neil T. , Jacob Rojymon , Cardenas Carlos E. 
Published: October 2024

ABSTRACTSegmentation of abdominal organs in clinical oncological workflows is crucial for ensuring effective treatment planning and follow-up. However, manually generated segmentations are time-consuming and labor-intensive in addition to experiencing inter-observer variability. Many deep learning (DL) and Automated Machine Learning (AutoML) frameworks have emerged as a solution to this challenge and show promise in clinical workflows. This study presents a comprehensive evaluation of existing AutoML frameworks (Auto3DSeg, nnU-Net) against a state-of-the-art non-AutoML framework, the Shifted Window U-Net Transformer (SwinUNETR), each trained on the same 122 training images, taken from the Abdominal Multi-Organ Segmentation (AMOS) grand challenge. Frameworks were compared using Dice Similarity Coefficient (DSC), Surface DSC (sDSC) and 95th Percentile Hausdorff Distances (HD95) on an additional 72 holdout-validation images. The perceived clinical viability of 30 auto-contoured test cases were assessed by three physicians in a blinded evaluation. Comparisons show significantly better performance by AutoML methods. nnU-Net (average DSC: 0.924, average sDSC: 0.938, average HD95: 4.26, median Likert: 4.57), Auto3DSeg (average DSC: 0.902, average sDSC: 0.919, average HD95: 8.76, median Likert: 4.49), and SwinUNETR (average DSC: 0.837, average sDSC: 0.844, average HD95: 13.93). AutoML frameworks were quantitatively preferred (13/13 OARs p>0.0.5 in DSC and sDSC, 12/13 OARs p>0.05 in HD95, comparing Auto3DSeg to SwinUNETR, and all OARs p>0.05 in all metrics comparing SwinUNETR to nnU-Net). Qualitatively, nnU-Net was preferred over Auto3DSeg (p=0.0027). The findings suggest that AutoML frameworks offer a significant advantage in the segmentation of abdominal organs, and underscores the potential of AutoML methods to enhance the efficiency of oncological workflows.
Association of Amygdala, Hippocampus, and Entorhinal cortex with thyroid function in older adults: Stratification’s value and relevance of bilateral volumetric analyses
Authors: Hallab Asma ,   Alzheimer’s Disease Neuroimaging Initiative
Published: October 2024

AbstractIntroductionThyroid hormones modulate the brain structure during neurogenesis and impact cognition and emotions during the lifetime. It is, therefore, important to understand their association with relevant brain structures during the aging process.MethodsA subset of 1348 older adults from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) was included. Linear regression was used to study the association between serum thyroid stimulating hormone (TSH) and the Amygdala, Hippocampus, and Entorhinal cortex volumes. Sex and neurodegeneration-related stratifications and comparative bilateral volumetric analyses were performed.ResultsFemales represented 667 (49%) of included cases, and 522 (38.72 %) were healthy controls (HC). A significant positive association was observed between TSH and total Hippocampus volume in mild cognitive impairment (MCI) (adj.ß=92 (23, 161),p- value=0.009), while a negative association in dementia participants remained statistically significant (ß=-177 (−295, −60),p-value=0.003 and adj.ß=-141 (−250, −32),p-value=0.012). There was a significant association between TSH and total Entorhinal cortex volume in the total study population (ß=44 (3.9, 85),p-value=0.032 and adj.ß=40 (5.1, 75),p-value=0.025). Stratification showed significant associations only in MCI (ß=80 (21, 138),p-value=0.007, and adj.ß=83 (27, 138),p-value=0.003), and males (adj.ß=54 (1.9, 106),p-value=0.042). Similar statistically significant associations were found only in the left Entorhinal cortex. The association between TSH and total Amygdala volume was positive in HC (ß=37 (1.6, 73),p- value=0.041) and negative in dementia participants (ß=-67 (−128, −6.4),p-value=0.030). None of those results remained statistically significant after adjusting the models. The bilateral volumetric analysis showed significant results only in the right Amygdala and dementia group.ConclusionsDepending on the stratum and side of the volumetric analysis, significant associations were observed between TSH and Hippocampus, Amygdala, and Entorhinal cortex volumes. It is, therefore, crucial to consider the role of sex, neurodegeneration, and laterality when exploring the thyroid-brain interaction in older adults.HighlightsHigher TSH levels are associated with lower Hippocampus volume on both sides in the dementia group.Lower TSH levels are associated with lower left Entorhinal cortex volume in the mild cognitive impairment and male strata.Higher TSH levels are associated with lower right Amygdala volume in the dementia group.Graphical abstract
Sub-functionalization and epigenetic regulation of a biosynthetic gene cluster inSolanaceae
Authors: Priego-Cubero Santiago , Knoch Eva , Wang Zhidan , Alseekh Saleh , Braun Karl-Heinz , Chapman Philipp , Fernie Alisdair , Liu Chang , Becker Claude 
Published: October 2024

AbstractBiosynthetic gene clusters (BGCs) are sets of often heterologous genes that are genetically and functionally linked. Among eukaryotes, BGCs are most common in plants and fungi, where they ensure the co-expression of the different enzymes coordinating the biosynthesis of specialised metabolites. Here, we report on a newly identified withanolide BGC inPhysalis grisea(ground-cherry), a member of the nightshade family (Solanaceae). A combination of transcriptomic, epigenomic and metabolic analyses, revealed that, following a duplication event, this BGC evolved two tissue-specifically expressed sub-clusters, containing eight pairs of paralogs that contribute to related but distinct biochemical processes; this sub- functionalisation is tightly associated with epigenetic features and the local chromatin environment. The two sub-clusters appear strictly isolated from each other at the chromatin structural level, each forming a highly self-interacting chromatin domain with tissue-dependent levels of condensation. This correlates with gene expression exclusively in either above- or below-ground tissue, thus spatially separating the production of different withanolide compounds. By comparative phylogenomic analysis, we show that the withanolide BGC most likely evolved before the diversification of theSolanaceaefamily and underwent lineage- specific diversifications and losses. The tissue-specific sub-functionalisation is common to species of thePhysalideaetribe but distinct from other, independent duplication events outside of this clade. In sum, our study reports on the first instance of an epigenetically modulated sub-functionalisation within a BGC and sheds light on the biosynthesis of withanolides, a highly diverse group of steroidal triterpenoids important in plant defence and amenable to pharmaceutical applications due to their anti-inflammatory, antibiotic and anti- cancer properties.
Determining sex differences in drug combinations targeting aortic valve myofibroblast activation using an artificial intelligence derived platform
Authors: Vogt Brandon J. , Wang Peter , Chavez Megan , Guo Peng , Chow Edward Kai-Hua , Ho Dean , Aguado Brian A. 
Published: October 2024

AbstractAortic valve stenosis (AVS) is a sexually dimorphic disease where aortic valve leaflets develop fibrosis and calcification, leading to heart failure if untreated. Sex differences in AVS progression depend on valvular interstitial cells (VICs) activating to myofibroblasts that drive aberrant extracellular matrix remodeling. To date, no treatment strategies have leveraged cellular sex differences to determine drug combinations that effectively target VIC myofibroblast activation. Here, we harnessed IDentif.AI, an artificial intelligence (AI)-derived drug optimization platform, to optimize sex-specific synergistic drug combinations that may prevent and reverse VIC myofibroblast activation on hydrogel biomaterials. The results reveal that anti-fibrotic drug efficacy and combinatorial interactions are dependent on cell sex. This study provides a framework for developing clinically relevant AVS treatment strategies through the integration of high-throughput hydrogel cell culture platforms and AI-driven drug optimization. The workflow towards designing targeted AVS drug combinations may help accelerate AVS drug development for male and female patients and address health disparities in AVS treatment outcomes.
Butterfly brains change in morphology and in gene splicing patterns after brief pheromone exposure
Authors: Dion Emilie , Toh YiPeng , Zhu Dantong , Monteiro Antónia 
Published: October 2024

AbstractHow insect brains differ between the sexes and respond to sex-specific pheromones is still not well understood. Here we briefly exposed femaleBicyclus anynanabutterflies to wild type (Wt) and modified male sex pheromone blends, previously shown to modify females’ sexual preferences, and examined how their brains were modified at the morphological and molecular levels, three days later. First, we 3D-reconstructed male and female brains of this species and documented sexual dimorphism in the size of seven of 67 glomeruli present in the olfactory lobe. Then we showed that several glomeruli changed in volume after blend exposures, implicating them in sex pheromone perception. Finally, we found that a few genes were differentially expressed but many more were differentially spliced between male and female naïve brains, and between naive and pheromone blend-exposed brains. These are primarily calcium-binding channels and RNA-binding genes, respectively. A learned preference for changed levels in a single pheromone component was linked to variants of proteins involved in synaptic transmission. Our work shows that naïve male and female brains differ primarily in gene splicing patterns and that a brief, 3-minute, exposure to pheromones produces slight changes in brain volume and large changes in the splicing of genes involved in neural development, that correlate with changes in sexual preferences in females.Significance statementHow brains differ between the sexes and respond to sex-specific cues is a hot research topic. Here we investigate how the brains of female butterflies differ from those of males and respond to male sex pheromones. We find that the sexes differ in the volume of a sub-set of olfactory lobe glomeruli, and the volume of some glomeruli also changes after exposure to pheromone blends. In addition, male and female brains differ primarily in hundreds of splice variants, both before and after pheromone exposure. These findings suggest that different proteins (splice variants) characterize male and female brains and that a brief exposure to pheromones can lead to changes in brain structure and in further gene splicing linked to altered sexual preferences in female butterflies.
Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations
Authors: Feczko Eric , Stoyell Sally M , Moore Lucille A. , Alexopoulos Dimitrios , Bagonis Maria , Barrett Kenneth , Bower Brad , Cavender Addison , Chamberlain Taylor A. , Conan Greg , Day Trevor KM , Goradia Dhruman , Graham Alice , Heisler-Roman Lucas , Hendrickson Timothy J. , Houghton Audrey , Kardan Omid , Kiffmeyer Elizabeth A , Lee Erik G , Lundquist Jacob T. , Lucena Carina , Martin Tabitha , Mummaneni Anurima , Myricks Mollie , Narnur Pranav , Perrone Anders J. , Reiners Paul , Rueter Amanda R. , Saw Hteemoo , Styner Martin , Sung Sooyeon , Tiklasky Barry , Wisnowski Jessica L , Yacoub Essa , Zimmermann Brett , Smyser Christopher D. , Rosenberg Monica D. , Fair Damien A. , Elison Jed T. 
Published: October 2024

AbstractReproducibility of neuroimaging research on infant brain development remains limited due to highly variable protocols and processing approaches. Progress towards reproducible pipelines is limited by a lack of benchmarks such as gold standard brain segmentations. Addressing this core limitation, we constructed the Baby Open Brains (BOBs) Repository, an open source resource comprising manually curated and expert-reviewed infant brain segmentations. Markers and expert reviewers manually segmented anatomical MRI data from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Anatomical images showed dramatic differences in myelination and intensities across the 1 to 9 month age range, emphasizing the need for densely sampled gold standard manual segmentations in these ages. The BOBs repository is publicly available through the Masonic Institute for the Developing Brain (MIDB) Open Data Initiative, which links S3 storage, Datalad for version control, and BrainBox for visualization. This repository represents an open-source paradigm, where new additions and changes can be added, enabling a community-driven resource that will improve over time and extend into new ages and protocols. These manual segmentations and the ongoing repository provide a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this repository provides a vitally needed foundation for early-life large-scale studies such as HBCD.
Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system
Authors: Sailer A.-L. , Brendel J. , Chernev A. , König S. , Bischler T. , Gräfenhan T. , Urlaub H. , Gophna U. , Marchfelder A. 
Published: October 2024

AbstractCRISPR-Cas is a sophisticated defence system used by bacteria and archaea to fend off invaders. CRISPR-Cas systems vary in their Cas protein composition and have therefore been divided into different classes and types. Type I systems of bacteria have been shown to contain the small Cas11 protein as part of the interference complex. Here we show for the first time that an archaeal CRISPR-Cas type I system also contains a Cas11 protein. In addition, we show for the first time an internal in-frame translation of an archaeal protein. The Cas11b protein from theHaloferax volcaniitype I-B system is encoded in thecas8bgene. Translation initiation at an internal methionine of thecas8bopen reading frame results in synthesis of Cas11b. Cas11b is required for an effective interference reaction and without Cas11b fewer Cascade complexes form. Comparison of transcriptomes from wild type and a Cas11b less strain show that the depletion of Cas11b results in differential regulation of many genes. Taken together Cas11b is important for the defence reaction of the type I-B CRISPR-Cas system and seems to play an additional cellular role.
Cryo-EM structural insights into Vγ9Vδ2 TCR activation via multiple butyrophilins
Authors: Zhang Mai , Wang Yiqing , Cai Ningning , Qu Yingying , Ma Xianqiang , Xue Jing , Chen Xiaorui , Zhang Xueguang , Xiao Junyu , Zhang Yonghui 
Published: October 2024

ABSTRACTHuman Vγ9Vδ2 T cells detect cancerous and pathogen-infected cells through an “inside-out” mechanism wherein intracellular domains of butyrophilin (BTN) proteins recognize phosphoantigens (pAgs) to prime BTN ectodomains to engage with the T cell receptor (TCR) to activate Vγ9Vδ2 T cells. Here, we present cryo-electron microscopy (cryo-EM) structures, including the full-length BTN3A1-BTN3A2–BTN2A1 complex stabilized by the pAg HMBPP and an HMBPP-primed BTN multimer complex engaged with the Vγ9Vδ2 TCR. The HMBPP-primed BTN3A1-BTN3A2–BTN2A1 complex confirms that this pAg bridges the intracellular B30.2 domains of BTN3A1 and BTN2A1, while also revealing an association of the ectodomains of BTN3A2 and BTN2A1. Upon TCR engagement, the TCR undergoes a substantial conformational change and BTN3A2–BTN2A1 ectodomain interaction dissociates, allowing BTN2A1 to bind to the lateral surface of the Vγ9 chain, while BTN3A2 binds to the apical surface of the Vδ2 chain. Beyond demonstrating that BTN3A2 as abona fideTCR ligand, this dissociation/binding sequence suggests a “pliers-like gripping” mechanism for TCR activation. We also obtained cryo-EM structures of BTN proteins in complex with functional antibodies, further elucidating the overall Vγ9Vδ2 T cell activation process. Thus, our structural insights into how BTN proteins sense antigens and drive TCR activation lay the groundwork for developing targeted γδ T cell immunotherapies.
Structural basis of SARS-Cov-2 spike recognition by engineered synthetic multivalent VHH antibodies
Authors: Lujan Hernandez Ana G. , Laughlin Zane T. , Patel Anamika , Yuan Tom Z. , Nugent Rebecca L. , Axelrod Fumiko , Ortlund Eric A. , Sato Aaron K. 
Published: October 2024

AbstractHigh-throughput technologies such as next-generation sequencing (NGS), microarray-based gene synthesis, and phage display have empowered the discovery and engineering of precisely defined, synthetic antibodies with high avidity and drug-like features. Here, we describe a scalable process for engineering homo- and hetero-hexavalent variable domains of camelid heavy-chain (VHH)-Fc antibodies against the severe acute respiratory coronavirus 2 (SARS-CoV-2) spike (S) protein. Overall, we demonstrate that VHH trimerization is an effective and modular approach for increasing the affinity of anti-S1 VHH-Fc antibodies for the highly mutated S proteins of SARS-CoV-2 variants. We show that one specific nanobody (named TB201-1) binds spike trimer protein at the interface of two neighboring RBDs, recognizing one distinct epitope on one RBD but making a set of secondary interactions with the neighboring RBD. From this structure, we determine the epitope-paratope residues responsible for spike-nanobody interaction and how mutations found in the SARS-CoV-2 variants contribute to oblate TB201-1 binding. This approach could be leveraged to improve existing antibody-based diagnostics and therapeutics targeting SARS-CoV-2 as the virus evolves.