bluuebunny/crossref_metadata_2025_split huggingface dataset:
National Trends in Utilization of Normothermic Machine Perfusion in DCD Liver Transplantation
Authors: Abu-Gazala Samir , Tang Helen , Abt Peter , Mahmud Nadim 
Published: April 2024

Background.
In liver transplantation, advances in ex situ normothermic machine perfusion (NMP) have improved outcomes compared with traditional static cold storage (SCS) in donation after circulatory death (DCD) organs. We aimed to characterize trends in the utilization of NMP versus SCS in DCD liver transplantation in the United States.

Methods.
This retrospective cohort study used data from the United Network for Organ Sharing database to identify recipient–donor adult liver transplant pairs from DCD donors from January 2016 to June 2022. Utilization of NMP and changes in donor risk index (DRI) and components between NMP and SCS were assessed across transplant year eras (2016–2018, 2019–2020, and 2021–2022). Statistical comparisons were made using the Kruskal-Wallis test or the chi-square test.

Results.
A total of 3937 SCS and 127 NMP DCD donor transplants were included. Utilization of NMP ranged from ~0.4% to 3.5% from 2016 to 2021 and rose significantly to 11.2% in early 2022. Across transplant eras, median DRI increased significantly for SCS and NMP, but the magnitude of the increase was larger for NMP. With NMP DCDs, there were significant increases in median donor age, national share proportion, and “cold ischemic time” over time. Finally, there was a shift toward including higher DRI donors and higher model for end-stage liver disease score transplant recipients with NMP in later transplant eras.

Conclusions.
In recent years, NMP utilization has increased and expanded to donors with higher DRI and recipients with higher model for end-stage liver disease score at transplant, suggesting increasing familiarity and risk tolerance with NMP technology. As NMP remains a relatively new technique, ongoing study of patient outcomes, organ allocation practices, and utilization patterns is critical.
Gut Microbiome Changes in Patients With Idiopathic Normal Pressure Hydrocephalus
Authors: Brandt Emilia , Koivisto Anne , Pereira Pedro , Mustanoja Ella , Auvinen Petri , Saari Toni , Lehtola Juha-Matti , Hannonen Sanna , Rusanen Minna , Leinonen Ville , Scheperjans Filip , Kärkkäinen Virve 
Published: April 2024

Background:
The gut microbiome is a complex system within the human gastrointestinal tract. The bacteria play a significant role in human health, and some can promote inflammation and pathologic processes through chemical interactions or metabolites. Gut microbiome dysbiosis has been linked to some neurological and other diseases. Here we aimed to examine microbiome differences between patients with a progressive neurological disorder, idiopathic normal pressure hydrocephalus (iNPH), compared with healthy controls (CO).

Methods:
We recruited 37 neurologically healthy CO and 10 patients with shunted iNPH. We evaluated these participants’ cognition using the CERAD-NB test battery and CDR test, and collected a variety of information, including about dietary habits and health. We also collected fecal samples, which were subjected to 16S amplicon sequencing to analyze differences in gut microbiome composition.

Results:
We found that the iNPH group exhibited significantly different abundances of 10 bacterial genera compared with the CO group. The Escherichia/Shigella and Anaeromassilibacillus genera were most remarkably increased. Other increased genera were Butyrivibrio, Duncaniella, and an unidentified genus. The decreased genera were Agathobaculum, Paramuribaculum, Catenibacterium, and 2 unidentified genera.

Conclusions:
Here we report the first identified microbiome differences in iNPH patients compared with healthy controls.
Decrease in Purifying Selection Pressures on Wheat Homoeologous Genes: TetraploidizationvsHexaploidization
Authors: Ezoe Akihiro , Todaka Daisuke , Utsumi Yoshinori , Takahashi Satoshi , Kawaura Kanako , Seki Motoaki 
Published: April 2024

SummaryA series of polyploidizations in higher-order polyploids is the main event affecting the gene contents in a genome, and this is frequently observed in domesticated plants. Each polyploidization event is expected to lead to functional divergence because of the associated decrease in the selection pressures on the duplicated genes, but it is unclear whether the initial tetraploidization or the subsequent higher-order polyploidization has a greater evolutionary impact on the duplicated genes. To address this uncertainty, we focused on theTriticum–Aegilopscomplex lineage and compared the selection pressures before and after the tetraploidization and hexaploidization events. The results indicated that while both events decreased the selection pressures on homoeologous gene pairs (compared with the selection pressures on their ancestral diploid and tetraploid orthologous genes), the initial tetraploidization had a greater impact on the selection pressures on homoeologous gene pairs than the subsequent hexaploidization. This was supported by the analyzed expression patterns. Surprisingly, the decreases in the selection pressures on these homoeologous genes were independent of the existence of in-paralogs within the same subgenome. This result suggests that unique functions are maintained in the homoeologous genes, including the functions that are unlikely to be preserved in duplicate gene pairs derived from other duplication mechanisms. We also revealed their unique functions were different between the tetra- and hexaploidization (e.g., Reproductive system and chromosome segregation processes). The findings of this study imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially the initial tetraploidization, may have been a unique source of functional divergence.
Machine Learned Classification of Ligand Intrinsic Activities at Humanµ-Opioid Receptor
Authors: Oh Myongin , Shen Maximilian , Liu Ruibin , Stavitskaya Lidiya , Shen Jana 
Published: April 2024

AbstractOpioids are small-molecule agonists ofµ-opioid receptor (µOR), while reversal agents such as naloxone are antagonists ofµOR. Here we developed machine learning (ML) models to classify the intrinsic activities of ligands at the humanµOR based on the SMILE strings and two-dimensional molecular descriptors. We first manually curated a database of 983 small molecules with measuredEmaxvalues at the humanµOR. Analysis of the chemical space allowed identification of dominant scaffolds and structurally similar agonists and antagonists. Decision tree models and directed message passing neural networks (MPNNs) were then trained to classify agonistic and antagonistic ligands. The hold-out test AUCs (areas under the receiver operator curves) of the extra-tree (ET) and MPNN models are 91.5 ± 3.9% and 91.8 ± 4.4%, respectively. To overcome the challenge of small dataset, a student-teacher learning method called tri-training with disagreement was tested using an unlabeled dataset comprised of 15,816 ligands of human, mouse, or ratµOR,κOR, orδOR. We found that the tri-training scheme was able to increase the hold-out AUC of MPNN to as high as 95.7%. Our work demonstrates the feasibility of developing ML models to accurately predict the intrinsic activities ofµOR ligands, even with limited data. We envisage potential applications of these models in evaluating uncharacterized substances for public safety risks and discovering new therapeutic agents to counteract opioid overdoses.TOC Graphic
Sox9 marks limbal stem cells and is required for asymmetric cell fate switch in the corneal epithelium
Authors: Rice Gabriella , Farrelly Olivia , Huang Sixia , Kuri Paola , Curtis Ezra , Ohman Lisa , Li Ning , Lengner Christopher , Lee Vivian , Rompolas Panteleimon 
Published: April 2024

AbstractAdult tissues with high cellular turnover require a balance between stem cell renewal and differentiation, yet the mechanisms underlying this equilibrium are unclear. The cornea exhibits a polarized lateral flow of progenitors from the peripheral stem cell niche to the center; attributed to differences in cellular fate. To identify genes that are critical for regulating the asymmetric fates of limbal stem cells and their transient amplified progeny in the central cornea, we utilized an in vivo cell cycle reporter to isolate proliferating basal cells across the anterior ocular surface epithelium and performed single-cell transcriptional analysis. This strategy greatly increased the resolution and revealed distinct basal cell identities with unique expression profiles of structural genes and transcription factors. We focused on Sox9; a transcription factor implicated in stem cell regulation across various organs. Sox9 was found to be differentially expressed between limbal stem cells and their progeny in the central corneal. Lineage tracing analysis confirmed that Sox9 marks long-lived limbal stem cells and conditional deletion led to abnormal differentiation and squamous metaplasia in the central cornea. These data suggest a requirement for Sox9 for the switch to asymmetric fate and commitment toward differentiation, as transient cells exit the limbal niche. By inhibiting terminal differentiation of corneal progenitors and forcing them into perpetual symmetric divisions, we replicated the Sox9 loss-of-function phenotype. Our findings reveal an essential role for Sox9 for the spatial regulation of asymmetric fate in the corneal epithelium that is required to sustain tissue homeostasis.
Glycolytic enzymes form membrane-less condensates in the malaria parasitePlasmodium falciparumby sensing glucose levels
Authors: Ishii Ryuta , Sakura Takaya , Inaoka Daniel Ken , Tokumasu Fuyuki 
Published: April 2024

AbstractRecent studies have shown that liquid-liquid phase separation (LLPS) in cells can regulate essential cellular events, including metabolic processes. Glycolytic bodies (G-bodies) are biomolecular condensates formed through the LLPS of glycolytic enzymes, and they accelerate glycolysis to overcome hypoxic stress in several organisms. Although the asexual blood stage (ABS) of the human malaria parasitePlasmodium falciparumhighly depends on glycolysis for energy production, there have been no reports of the formation of such G-bodies throughout the parasite’s lifecycle. Using fluorescence tagging and live imaging, we found that G-body-like condensates containing phosphofructokinase 9 (PFK9) and phosphoglycerate kinase (PGK) were formed in the parasite cells after long-term culture under conditions of low glucose. These G-body-like structures appeared stable, but membrane staining and osmotic stress experiments suggested that the observed condensates were not associated with lipid membrane. Further microscopic observations and mathematical analyses of high signal-to-noise ratio images indicated that small condensates were formed transiently first, and these then gradually grew and stabilized in the cytosol. These results suggested that the formation of glycolytic enzyme condensates may be an important cellular response for adapting to blood sugar level oscillations in the host and maintaining the parasite’s multiplication in the ABS.Significance statementGlycolytic bodies (G-bodies), which are biomolecular condensates formed through the liquid-liquid phase separation of glycolytic enzymes, can accelerate glycolysis to produce energy and overcome hypoxic stress. The parasites that cause malaria depend on glycolysis for energy production, but there have been no reports that these parasites form G-bodies. We demonstrated that membrane-less G-body-like structures formed in media containing low levels of glucose. Small condensates appeared first and over time, the condensates became larger and more stable. The formation of glycolytic enzyme condensates may be important for the malaria parasite to adapt to fluctuating blood sugar levels in the host. These results further our understanding of the cellular mechanisms for the survival of malaria parasites.
Humanizedin vivobone marrow models orchestrate multi-lineage human hematopoietic cell development
Authors: Renou Laurent , Sun Wenjie , Friedrich Chloe , Galant Klaudia , Conrad Cecile , Plantier Evelia , Schallmoser Katharina , Krisch Linda , Barroca Vilma , Devanand Saryami , Déchamp Nathalie , Reinisch Andreas , Martinovic Jelena , Magnani Alessandra , Faivre Lionel , Calvo Julien , Perie Leila , Kosmider Olivier , Pflumio Françoise 
Published: April 2024

AbstractHematopoiesis develops in the bone marrow (BM) where multiple interactions regulate differentiation and preservation of hematopoietic stem/progenitor cells (HSPCs). Although murine BM has been extensively analyzed, the human BM microenvironment remains less understood. Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, which remains limited as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h)in vivoBM model, based on mesenchymal stromal cell (MSC) differentiation (called hOssicles (hOss)), and hematopoietic cell compartments generated 3 months post-transplant of CD34+cells using single-cell RNA sequencing and cellular barcoding. Serial isolation of MSCs and HSPCs from hOss and transplant experiments revealed the dynamic nature of these hBM niches. hOss altered human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels. Clonal tracking highlighted hematopoietic cell cross-talks between the murine BM and hOss, indicating the multipotent or more restricted lineage origin of human hematopoiesis shared in the BM sites.
Activity-dependent COX-2 proteolysis generates a catalytically inactive fragment that affects aerobic respiration and proliferation
Authors: Benishay Liat Hartal , Tal Sharon , Elkader Amal Abd , Ehsainieh Omar , Srouji-Eid Ranin , Mikl Martin , Barki-Harrington Liza 
Published: April 2024

SummaryCyclooxygenase-2 (COX-2) catalyzes arachidonic acid (AA) into PGH2, the single source of all prostaglandins (PGs), ligands that activate multiple inflammatory pathways. AA catalysis quickly results in suicide inactivation, rendering the enzyme catalytically inactive. We show that the catalytic activity also leads to controlled cleavage of COX-2, an event that is differentially regulated by fatty acids, and blocked by COX inhibitors. We also observe COX-2 cleavage in human colon tumors. Using mass spectrometry, we identify two adjacent cleavage points within the catalytic domain, which give rise to COX-2 fragments that are catalytically inactive and localize to different cellular compartments. One of these fragments significantly alters the expression of mitochondrial electron transport genes and functional assays show that it leads to reduced mitochondrial function, increased lactate production, and enhanced proliferation. We propose that in addition to its role in generating PGs, COX-2 has subsequent PG-independent cellular functions that may account for the complex role of COX-2 in proliferative diseases and chronic inflammation.Graphical Abstract
Coping with Cannabis During Pregnancy: Trajectories of Depression, Stress, and Cannabis Use across the Prenatal Period
Authors: Constantino-Pettit Anna , Tillman Rebecca , Wilson Jillian , Lashley-Simms Nicole , Vatan Naazanene , Atkinson Azaria , Leverett Shelby , Lenze Shannon , Smyser Christopher , Bogdan Ryan , Rogers Cynthia , Agrawal Arpana 
Published: April 2024

AbstractObjectiveWe examined trajectories of stress, depression, and cannabis use across the prenatal period. We also investigated whether individuals who reported using cannabis to alleviate stress and depressive symptoms experienced symptom relief across the prenatal period.MethodsPregnant individuals (n=436) with a history of lifetime cannabis use were recruited and identified either as prenatal cannabis users (PCU; continued cannabis use following knowledge of pregnancy in the first trimester) or non-prenatal cannabis users (NPCU; no cannabis use following knowledge of pregnancy in the first trimester). PCU individuals additionally reported on reasons for continued cannabis use during pregnancy. We employed longitudinal multivariate modeling to examine trajectories of depression (maternal self-report; Edinburgh Postnatal Depression Scale), stress (maternal self-report; Perceived Stress Scale), and cannabis use (maternal self-report and urinalysis) over time, stratified by motives for use during the perinatal period.ResultsStress, depression, and cannabis use decreased from the first to the third trimester (slopeB=-0.21, -0.35, and -0.31, respectively). While cannabis use and depression at the first trimester were correlated with one another, they did not affect the other’s rate of change. Cannabis use similarly did not affect the rate of change in stress. Finally, while individuals using cannabis to cope with mental health symptoms experienced a decrease in overall depression symptoms, this slope was roughly equivalent to individuals who were not using cannabis prenatally (slopeB=- 0.43 and -0.51, respectively).ConclusionOur sample experienced a collective decrease in depression, stress, and cannabis use prenatally. This decline in cannabis use – even among those who reported using to cope with mental health conditions – was not attributable to the decrease in depressive symptoms. This study lends valuable insight into the reasons why individuals continue to use cannabis during pregnancy, which providers can use to help tailor recommendations for other sources of coping and support to childbearing individuals.
Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment
Authors: Snabel Rebecca R. , Cofiño-Fabrés Carla , Baltissen Marijke , Schwach Verena , Passier Robert , Veenstra Gert Jan C. 
Published: April 2024

ABSTRACTStem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. Here we show how cardiac monolayer, embryoid body, and engineered heart tissue trajectories compare in a single-cell roadmap of atrial and ventricular differentiation conditions. Using a multiomic approach and gene-regulatory network inference, we identified regulators of the epicardial, atrial and ventricular cardiomyocyte lineages. We identifiedZNF711as a regulatory switch and safeguard for cardiomyocyte commitment. We show thatZNF711ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation by regulation of shared and complementary target genes, showing an interplay betweenZNF711and retinoic acid in cardiac lineage commitment.GRAPHICAL ABSTRACTHIGHLIGHTSWe present an atlas of cardiac differentiation under different culture conditions, showing progenitor trajectories and cell states reminiscent of the fetal heart.Multiome and chromatin accessibility analysis identified candidate regulators of cardiomyocyte and non-cardiomyocyte lineages.Distinct trajectories of lineage commitment and differentiation under different culture conditions shows plasticity of first and second heart field progenitors and different ratios of cardiomyocyte and non-myocyte lineages.ZNF711 is required for balanced commitment to epicardial and ventricular cardiomyocyte lineages. Retinoic acid rescues a requirement for ZNF711 in cardiomyocyte differentiation, promoting both atrial cardiomyocyte and epicardial differentiation.
Active state structures of a bistable visual opsin bound to G proteins
Authors: Tejero Oliver , Pamula Filip , Koyanagi Mitsumasa , Nagata Takashi , Afanasyev Pavel , Das Ishita , Deupi Xavier , Sheves Mordechai , Terakita Akihisa , Schertler Gebhard F.X. , Rodrigues Matthew J. , Tsai Ching-Ju 
Published: April 2024

AbstractOpsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption, causing conformational changes that result in receptor activation. Monostable opsins, responsible for vision in vertebrates, release the chromophore after activation and must bind another retinal molecule to remain functional. In contrast, bistable opsins, responsible for non-visual light perception in vertebrates and for vision in invertebrates, absorb a second photon in the active state to return the chromophore and protein to the inactive state. Structures of bistable opsins in the activated state have proven elusive, limiting our understanding of how they function as bidirectional photoswitches. Here we present active state structures of a bistable opsin, jumping spider rhodopsin isoform-1 (JSR1), in complex with its downstream signaling partners, the Gi and Gq heterotrimers. These structures elucidate key differences in the activation mechanisms between monostable and bistable opsins, offering essential insights for the rational engineering of bistable opsins into diverse optogenetic tools to control G protein signaling pathways.
Transdifferentiation is uncoupled from progenitor pool expansion during hair cell regeneration in the zebrafish inner ear
Authors: Beaulieu Marielle O. , Thomas Eric D. , Raible David W. 
Published: April 2024

ABSTRACTDeath of mechanosensory hair cells in the inner ear is a common cause of auditory and vestibular impairment in mammals, which have a limited ability to regrow these cells after damage. In contrast, non-mammalian vertebrates including zebrafish can robustly regenerate hair cells following severe organ damage. The zebrafish inner ear provides an understudied model system for understanding hair cell regeneration in organs that are highly conserved with their mammalian counterparts. Here we quantitatively examine hair cell addition during growth and regeneration of the larval zebrafish inner ear. We used a genetically encoded ablation method to induce hair cell death and observed gradual regeneration with correct spatial patterning over two weeks following ablation. Supporting cells, which surround and are a source of new hair cells, divide in response to hair cell ablation, expanding the possible progenitor pool. In parallel, nascent hair cells arise from direct transdifferentiation of progenitor pool cells uncoupled from progenitor division. These findings reveal a previously unrecognized mechanism of hair cell regeneration with implications for how hair cells may be encouraged to regenerate in the mammalian ear.SUMMARY STATEMENTHair cell regeneration in the zebrafish inner ear occurs through transdifferentiation after a transient wave of supporting cell proliferation that expands the precursor pool.