bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progress in Combined Liver–lung Transplantation at a Single Center
Authors: Connor Ashton A. , Huang Howard J. , Mobley Constance M. , Graviss Edward A. , Nguyen Duc T. , Goodarzi Ahmad , Saharia Ashish , Yau Simon , Hobeika Mark J. , Suarez Erik E. , Moaddab Mozhgon , Brombosz Elizabeth W. , Moore Linda W. , Yi Stephanie G. , Gaber A. Osama , Ghobrial Rafik Mark 
Published: April 2023

Background.
Combined liver–lung transplantation is an uncommon, although vital, procedure for patients with simultaneous end-stage lung and liver disease. The utility of lung–liver transplant has been questioned because of initial poor survival outcomes, particularly when compared with liver-alone transplant recipients.

Methods.
A single-center, retrospective review of the medical records of 19 adult lung–liver transplant recipients was conducted, comparing early recipients (2009–2014) with a recent cohort (2015–2021). Patients were also compared with the center’s single lung or liver transplant recipients.

Results.
Recent lung–liver recipients were older (P = 0.004), had a higher body mass index (P = 0.03), and were less likely to have ascites (P = 0.02), reflecting changes in the etiologies of lung and liver disease. Liver cold ischemia time was longer in the modern cohort (P = 0.004), and patients had a longer posttransplant length of hospitalization (P = 0.048). Overall survival was not statistically different between the 2 eras studied (P = 0.61), although 1-y survival was higher in the more recent group (90.9% versus 62.5%). Overall survival after lung–liver transplant was equivalent to lung-alone recipients and was significantly lower than liver-alone recipients (5-y survival: 52%, 51%, and 75%, respectively). Lung–liver recipient mortality was primarily driven by deaths within 6 mo of transplant due to infection and sepsis. Graft failure was not significantly different (liver: P = 0.06; lung: P = 0.74).

Conclusions.
The severity of illness in lung–liver recipients combined with the infrequency of the procedure supports its continued use. However, particular attention should be paid to patient selection, immunosuppression, and prophylaxis against infection to ensure proper utilization of scarce donor organs.
Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis
Authors: Hou Wenpin , Ji Zhicheng 
Published: April 2023

ABSTRACTCell type annotation is an essential step in single-cell RNA-seq analysis. However, it is a time-consuming process that often requires expertise in collecting canonical marker genes and manually annotating cell types. Automated cell type annotation methods typically require the acquisition of high-quality reference datasets and the development of additional pipelines. We assessed the performance of GPT-4, a highly potent large language model, for cell type annotation, and demonstrated that it can automatically and accurately annotate cell types by utilizing marker gene information generated from standard single-cell RNA-seq analysis pipelines. Evaluated across hundreds of tissue types and cell types, GPT-4 generates cell type annotations exhibiting strong concordance with manual annotations and has the potential to considerably reduce the effort and expertise needed in cell type annotation. We also developed GPTCelltype, an open-source R software package to facilitate cell type annotation by GPT-4.
Altered neutrophil extracellular traps in response toMycobacterium tuberculosisin persons living with HIV with no previous TB and negative TST and IGRA
Authors: Kroon EE , Correa-Macedo W , Evans R , Seeger A , Engelbrecht L , Kriel JA , Loos B , Okugbeni N , Orlova M , Cassart P , Kinnear CJ , Tromp GC , Möller M , Wilkinson RJ , Coussens AK , Schurr E , Hoal EG 
Published: April 2023

AbstractPersons living with HIV (PLWH) have an increased risk for tuberculosis (TB). After prolonged and repeated exposure, some PLWH never develop TB and test persistently negative in tests of immune sensitization tuberculin skin test (TST) and interferon gamma release assays (IGRA) forMycobacterium tuberculosis(Mtb). This group has been identified and defined as HIV+ persistently TB, tuberculin and IGRA negative (HITTIN). To investigate potential innate mechanisms unique to individuals with the HITTIN phenotype we compared their neutrophilMtbinfection response to that of PLWH, with no TB history, but who test persistently IGRA positive, and tuberculin positive (HIT). Neutrophil samples from 17 HITTIN (PMNHITTIN) and 11 HIT (PMNHIT) were isolated and infected withMtbH37Rv for 1h and 6h. RNA was extracted and used for RNAseq analysis. At 1h ofMtbinfection, PMNHITTINdisplayed 151 significantly upregulated and 40 significantly downregulated differentially expressed genes (DEGs) and PMNHIT98 significantly upregulated and 11 significantly downregulated DEGs. At the 6h timepoint, PMNHITTINdisplayed 3106 significantly upregulated and 3548 significantly downregulated DEGs while PMNHIThad 3816 significantly up- and 3794 significantly downregulated DEGs. There was no significant differential transcriptional response at 1h between infected PMNHITTINand PMNHIT.However, when contrasting the log2FC 6h infection response toMtbfrom PMNHITTINagainst PMNHIT, 2285 genes showed significant differential response between the two groups. Apoptosis and NETosis were key pathways linked to the enrichment of genes in PMNHITTINwhen contrasted to PMNHITafter 6h infection withMtb. Fluorescence microscopy revealed relatively lower neutrophil extracellular trap formation and cell loss in PMNHITTINcompared to PMNHIT, showing that PMNHITTINhave a distinct response toMtb.
The X chromosome of insects predates the origin of Class Insecta
Authors: Toups Melissa A. , Vicoso Beatriz 
Published: April 2023

AbstractSex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is shared among all insect orders and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. Therefore, the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we suggest that the shrinking of gene content the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.
Nuclear bodies protect phase separated proteins from degradation in stressed proteome
Authors: Jung Kwan Ho , Sun Jiarui , Hsiung Chia-Heng , Lian Xiaojun Lance , Liu Yu , Zhang Xin 
Published: April 2023

AbstractRNA-binding proteins (RBPs) containing intrinsically disordered domains undergo liquid-liquid phase separation to form nuclear bodies under stress conditions. This process is also connected to the misfolding and aggregation of RBPs, which are associated with a series of neurodegenerative diseases. However, it remains elusive how folding states of RBPs changes upon the formation and maturation of nuclear bodies. Here, we describe SNAP-tag based imaging methods to visualize the folding states of RBPs in live cells via time-resolved quantitative microscopic analyses of their micropolarity and microviscosity. Using these imaging methods in conjunction with immunofluorescence imaging, we demonstrate that RBPs, represented by TDP-43, initially enters the PML nuclear bodies in its native state upon transient proteostasis stress, albeit it begins to misfolded during prolonged stress. Furthermore, we show that heat shock protein 70 co-enters the PML nuclear bodies to prevent the degradation of TDP-43 from the proteotoxic stress, thus revealing a previously unappreciated protective role of the PML nuclear bodies in the prevention of stress-induced degradation of TDP-43. In summary, our imaging methods described in the manuscript, for the first time, reveal the folding states of RBPs, which were previously challenging to study with conventional methods in nuclear bodies of live cells. This study uncovers the mechanistic correlations between the folding states of a protein and functions of nuclear bodies, in particular PML bodies. We envision that the imaging methods can be generally applied to elucidating the structural aspects of other proteins that exhibit granular structures under biological stimulus.
Acis-regulatory point mutation at a R2R3-Myb transcription factor contributes to speciation by reinforcement inPhlox drummondii
Authors: Garner Austin G. , Cameron Andrew , Berardi Andrea E. , Hopkins Robin 
Published: April 2023

AbstractThe process of reinforcement, whereby selection favors the evolution of increased reproductive trait divergence to reduce costly hybridization between species, has been well documented in nature, yet we know very little about how this process evolves at the molecular level. In this study, we combine functional characterization and genetic association tests to identify the mutational basis of reinforcement in the Texas wildflowerPhlox drummondii. P. drummondiievolved from light to dark flower color intensity by selection to stop hybridization with the closely related speciesP. cuspidata, and previous research suggests differential expression of a R2R3-Myb transcription factor underlies this phenotypic transition. Using gene-silencing experiments, we demonstrate expression of this transcription factor does control variation in flower color intensity. We then apply association mapping across a large genomic region flanking the R2R3-Myb gene and identified a point mutation within the gene’s promoter that is highly associated with flower color intensity in nature. Alleles at this mutation site match the expected patterns of dominance, create variation in predicted cis-regulatory motifs within the R2R3-Myb proximal promoter, and occur in the direction of evolution predicted for flower color variation in this system. By identifying the mutational basis of reinforcement in this system we demonstrate that, as predicted by theory, reproductive isolation can evolve despite gene flow through a very simple genetic basis.
Galectin-3 Mediates Vascular Dysfunction in Obesity by Regulating NADPH Oxidase 1
Authors: Padgett Caleb A. , Bátori Róbert K. , Speese Andrew C. , Rosewater Cody L. , Bush Weston B. , Derella Cassandra C. , Haigh Stephen B. , Sellers Hunter G. , Corley Zachary L. , West Madison A. , Mintz James D. , Ange Brittany B. , Harris Ryan A. , Brands Michael W. , Fulton David J. R. , Stepp David W. 
Published: April 2023

AbstractRationaleObesity increases the risk of cardiovascular disease (CVD) through mechanisms that remain incompletely defined. Metabolic dysfunction, especially hyperglycemia, is thought to be a major contributor but how glucose impacts vascular function is unclear. Galectin-3 (GAL3) is a sugar binding lectin upregulated by hyperglycemia but its role as a causative mechanism of CVD remains poorly understood.ObjectiveTo determine the role of GAL3 in regulating microvascular endothelial vasodilation in obesity.Methods and ResultsGAL3 was markedly increased in the plasma of overweight and obese patients, as well as in the microvascular endothelium of diabetic patients. To investigate a role for GAL3 in CVD, mice deficient in GAL3 were bred with obesedb/dbmice to generate lean, lean GAL3 knockout (KO), obese, and obese GAL3 KO genotypes. GAL3 KO did not alter body mass, adiposity, glycemia or lipidemia, but normalized elevated markers of reactive oxygen species (TBARS) in plasma. Obese mice exhibited profound endothelial dysfunction and hypertension, both of which were rescued by GAL3 deletion. Isolated microvascular endothelial cells (EC) from obese mice had increased NOX1 expression, which we have previously shown to contribute to increased oxidative stress and endothelial dysfunction, and NOX1 levels were normalized in EC from obese mice lacking GAL3. EC-specific GAL3 knockout mice made obese using a novel AAV-approach recapitulated whole-body knockout studies, confirming that endothelial GAL3 drives obesity-induced NOX1 overexpression and endothelial dysfunction. Improved metabolism through increased muscle mass, enhanced insulin signaling, or metformin treatment, decreased microvascular GAL3 and NOX1. GAL3 increased NOX1 promoter activity and this was dependent on GAL3 oligomerization.ConclusionsDeletion of GAL3 normalizes microvascular endothelial function in obesedb/dbmice, likely through a NOX1-mediated mechanism. Pathological levels of GAL3 and in turn, NOX1, are amenable to improvements in metabolic status, presenting a potential therapeutic target to ameliorate pathological cardiovascular consequences of obesity.Figure 8.Visual abstract
SIV-specific neutralizing antibody induction following selection of a PI3K drive-attenuatednefvariant
Authors: Yamamoto Hiroyuki , Matano Tetsuro 
Published: April 2023

AbstractHIV and simian immunodeficiency virus (SIV) infections are known for impaired neutralizing antibody (NAb) responses. While sequential virus-host B cell interaction appears to be basally required for NAb induction, driver molecular signatures predisposing to NAb induction still remain largely unknown. Here we describe SIV-specific NAb induction following a virus-host interplay decreasing aberrant viral drive of phosphoinositide 3-kinase (PI3K). Screening of seventy difficult-to-neutralize SIVmac239-infected macaques found nine NAb-inducing animals, with seven selecting for a specific CD8+T-cell escape mutation in viralnefbefore NAb induction. This Nef-G63E mutation reduced excess Nef interaction-mediated drive of B-cell maturation-limiting PI3K/mammalian target of rapamycin complex 2 (mTORC2).In vivoimaging cytometry depicted preferential Nef perturbation of cognate Envelope-specific B cells, suggestive of polarized contact-dependent Nef transfer and corroborating cognate B-cell maturation post-mutant selection up to NAb induction. Results collectively exemplify a NAb induction pattern extrinsically reciprocal to human PI3K gain-of-function antibody-dysregulating disease, and indicate that harnessing the PI3K/mTORC2 axis may facilitate NAb induction against difficult-to-neutralize viruses including HIV/SIV.
Regulation of apico-basolateral trafficking polarity of homologous Copper-ATPases ATP7A and ATP7B
Authors: Ruturaj  , Mishra Monalisa , Saha Soumyendu , Maji Saptarshi , Rodriguez-Boulan Enrique , Schreiner Ryan , Gupta Arnab 
Published: April 2023

AbstractWe suggest a model of apico-basolateral sorting in polarized epithelia using homologous Cu-ATPases as membrane cargoes. In polarized epithelia, upon copper treatment, homologous copper-ATPases ATP7A and ATP7B traffic from trans-Golgi network (TGN) to basolateral and apical membranes respectively. We characterized sorting pathways of Cu-ATPases between TGN and plasma-membrane and identified the machinery involved. ATP7A and ATP7B reside on distinct domains of TGN and in high copper, ATP7A traffics directly to basolateral membrane, whereas ATP7B traverses common-recycling, apical-sorting and apical-recycling endosomesen-routeto apical membrane. Mass-spectrometry identified regulatory partners of ATP7A and ATP7B that include Adaptor Protein-1 complex. Upon knocking-out pan-AP-1, sorting of both copper-ATPases are disrupted. ATP7A loses polarity and localizes on both apical and basolateral surfaces in high copper. Contrastingly, ATP7B loses TGN-retention but retains apical polarity that becomes copper-independent. Using isoform-specific knockouts, we found that AP-1A provides directionality and TGN-retention for both Cu-ATPases, whereas, AP-1B governs polarized trafficking of ATP7B solely. Trafficking phenotypes of Wilson disease-causing ATP7B mutants that disrupts putative ATP7B-AP1 interaction further substantiates the role of AP-1 in apical sorting of ATP7B.Summary statementThe Adapter Protein-1 (AP-1) isoforms AP-1A and AP-1B governs the apico-basolateral trafficking polarities of the homologous Copper-ATPases, ATP7A and ATP7B at the trans-Golgi network.
Scabrous is distributed via signaling filopodia to modulate Notch response during bristle patterning in Drosophila
Authors: Presser Adam , Freund Olivia , Hassapelis Theodora , Hunter Ginger L 
Published: April 2023

AbstractDuring development, tissues must be patterned correctly in order to support tissue function and shape. The sensory bristles of the peripheral nervous system on the thorax of Drosophila melanogaster self-organize from an unpatterned epithelial tissue to a regular spot pattern during pupal stages. Wild type patterning requires Notch-mediated lateral inhibition. Scabrous is a protein that can bind to and modify Notch receptor activity. Scabrous can be secreted, but it is also known to be localized to basal signaling filopodia, or cytonemes, that play a role in long-range Notch signaling. Consistent with previous work, we show that Scabrous is primarily distributed basally, within the range of signaling filopodia extension. We show that signaling filopodia are required for the distribution of Scabrous protein during sensory bristle patterning stages. We show that the Notch response of epithelial cells is sensitive to the level of Scabrous protein being expressed by the sensory bristle precursor cell. Our findings at the cell-level suggest a model for how epithelial cells engaged in lateral inhibition at a distance are sensitive local levels of Scabrous protein.
Dissecting the molecular basis for the modulation of neurotransmitter GPCR signaling by GINIP
Authors: Luebbers Alex , Zhou Myles , Eyles Stephen J , Garcia-Marcos Mikel 
Published: April 2023

ABSTRACTIt is well-established that activation of heterotrimeric G-proteins (Gαβγ) by G-protein-coupled receptors (GPCRs) stimulated by neurotransmitters is a key mechanism underlying neuromodulation. Much less is known about how G-protein regulation after receptor-mediated activation contributes to neuromodulation. Recent evidence indicates that the neuronal protein GINIP shapes GPCR inhibitory neuromodulation via a unique mechanism of G-protein regulation that controls neurological processes like pain and seizure susceptibility. However, the molecular basis of this mechanism remains ill-defined because the structural determinants of GINIP responsible for binding Gαi subunits and regulating G-protein signaling are not known. Here, we combined hydrogen-deuterium exchange mass-spectrometry, protein folding predictions, bioluminescence resonance energy transfer assays, and biochemical experiments to identify the first loop of the PHD domain of GINIP as an obligatory requirement for Gαi binding. Surprisingly, our results support a model in which GINIP undergoes a long-range conformational change to accommodate Gαi binding to this loop. Using cell-based assays, we demonstrate that specific amino acids in the first loop of the PHD domain are essential for the regulation of Gαi-GTP and free Gβγ signaling upon neurotransmitter GPCR stimulation. In summary, these findings shed light onto the molecular basis for a post-receptor mechanism of G-protein regulation that fine-tunes inhibitory neuromodulation.
Interplay betweenATRXandIDH1mutations governs innate immune responses in diffuse gliomas
Authors: Hariharan Seethalakshmi , Whitfield Benjamin T. , Pirozzi Christopher J. , Waitkus Matthew S. , Brown Michael C. , Bowie Michelle L. , Irvin David M. , Roso Kristen , Fuller Rebecca , Hostettler Janell , Dharmaiah Sharvari , Gibson Emiley A. , Briley Aaron , Mangoli Avani , Fraley Casey , Shobande Mariah , Stevenson Kevin , Zhang Gao , Malgulwar Prit Benny , Roberts Hannah , Roskoski Martin , Spasojevic Ivan , Keir Stephen T. , He Yiping , Castro Maria G. , Huse Jason T. , Ashley David M. 
Published: April 2023

AbstractStimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations inATRX, defining molecular alterations inIDH-mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss andIDHmutation on innate immunity. To explore this, we generatedATRXknockout glioma models in the presence and absence of theIDH1R132Hmutation. ATRX-deficient glioma cells were sensitive to dsRNA-based innate immune agonism and exhibited impaired lethality and increased T-cell infiltrationin vivo. However, the presence ofIDH1R132Hdampened baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1R132Hinhibition. IDH1R132Hco-expression did not interfere with theATRXKO-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1R132Hreversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytoma.
The Cell Subtypes Selection by Genes (CSSG) algorithm for discovering cell populations in high resolution
Authors: Kubiś Jakub , Figiel Maciej 
Published: April 2023

AbstractThe recent massive improvements in transcriptomics and single-cell technologies have led to a rising volume of data and demand for advances in bioinformatics processing. Existing methods are not fully capable of discovering genetic markers responsible for high-resolution cellular tissue heterogeneity, cell lineages during organism development, and cell differentiation with rare intermediate populations. In response to demand, we have generated a new Cell Subtypes Selection by Genes (CSSG) algorithm which is supported by a dedicated and fully automatic JSEQ®pipeline. The new CSSG algorithm is iterative, parallel, and able to make decisions for discovering cell populations in tissues based on transcript occurrence in cells. The CSSG/JSEQ is complemented by a new strategy and specialized algorithm for the naming of cell populations. Our approach allows for high-resolution tracing of cell populations, finding relations and hierarchy between them, particularly important for complex tissues such as the brain. The pipeline allows the establishment of developmental, differentiation, and pathogenic trajectory and takes a “snapshot” of a current physiological or pathological cellular stage of the investigated organ at the transcriptional level.
Simulations suggest a scaffolding mechanism of membrane deformation by the caveolin 8S complex
Authors: Vasquez Rodriguez Sayyid Yobhel , Lazaridis Themis 
Published: April 2023

AbstractCaveolins form complexes of various sizes that deform membranes into polyhedral shapes. However, the recent structure of the 8S complex was disk-like with a flat membrane-binding surface. How can a flat complex deform membranes into nonplanar structures? Molecular dynamics simulations revealed that the 8S complex rapidly takes the form of a suction cup. Simulations on implicit membrane vesicles determined that binding is stronger when E140 gets protonated. In that case, the complex binds much more strongly to 5 and 10-nm radius vesicles. A concave membrane binding surface readily explains the membrane-deforming ability of caveolins by direct scaffolding. We propose that the 8S complex sits at the vertices of the caveolar polyhedra, rather than at the center of the polyhedral faces.SignificanceCaveolae are membrane invaginations that play important roles in eukaryotic cells. Crucial for their formation is the caveolin protein family, but the mechanism by which these proteins deform membranes is unclear. Molecular dynamics simulations revealed that a recently determined structure changes shape from flat to concave. With one titratable residue protonated, this structure binds more strongly to spherical membranes, thus providing a possible mechanism for the membrane-deforming ability of caveolins.