bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Assessment of Blood-Brain Barrier Opening and Sterile Inflammatory Response: Unraveling the Therapeutic Window
Authors: Martinez Payton , Song Jane J. , Garay Francis G. , Song Kang-Ho , Mufford Toni , Steiner Jenna , DeSisto John , Ellens Nicholas , Serkova Natalie J. , Green Adam L. , Borden Mark 
Published: October 2023

AbstractMicrobubbles (MBs) combined with focused ultrasound (FUS) have emerged as a promising noninvasive technique to permeabilize the blood-brain barrier (BBB) for drug delivery to the brain. However, the safety and biological consequences of BBB opening remain incompletely understood. This study investigates the effects of varying microbubble volume doses (MVD) and ultrasound mechanical indices (MI) on BBB opening and the sterile inflammatory response (SIR) using high-resolution ultra-high field MRI-guided FUS in mouse brains. The results demonstrate that both MVD and MI significantly influence the extent of BBB opening, with higher doses and mechanical indices leading to increased permeability. Moreover, RNA sequencing reveals upregulated inflammatory pathways and immune cell infiltration after BBB opening, suggesting the presence and extent of SIR. Gene set enrichment analysis identifies 12 gene sets associated with inflammatory responses that are upregulated at higher doses of MVD or MI. A therapeutic window is established between significant BBB opening and the onset of SIR, providing operating regimes for avoiding each three classes of increasing damage from stimulation of the NFκB pathway via TNFL signaling to apoptosis. This study contributes to the optimization and standardization of BBB opening parameters for safe and effective drug delivery to the brain and sheds light on the underlying molecular mechanisms of the sterile inflammatory response.Significance StatementThe significance of this study lies in its comprehensive investigation of microbubble-facilitated focused ultrasound for blood-brain barrier (BBB) opening. By systematically exploring various combinations of microbubble volume doses and ultrasound mechanical indices, the study reveals their direct impact on the extent of BBB permeability and the induction of sterile inflammatory response (SIR). The establishment of a therapeutic window between significant BBB opening and the onset of SIR provides critical insights for safe and targeted drug delivery to the brain. These findings advance our understanding of the biological consequences of BBB opening and contribute to optimizing parameters for clinical applications, thus minimizing potential health risks, and maximizing the therapeutic potential of this technique.
Accurate Automated Segmentation of Autophagic Bodies in Yeast Vacuoles Using Cellpose 2.0
Authors: Marron Emily C. , Backues Jonathan , Ross Andrew M. , Backues Steven K. 
Published: October 2023

AbstractSegmenting autophagic bodies in yeast TEM images is a key technique for measuring changes in autophagosome size and number in order to better understand autophagy. Manual segmentation of these images can be very time consuming, particularly since hundreds of images are needed for accurate measurements. Here we describe a validated Cellpose 2.0 model that can segment these images with accuracy comparable to that of human experts. This model can be used for fully automated segmentation, eliminating the need for manual body outlining, or for model-assisted segmentation, which allows human oversight but is still five times as fast as the current manual method. The model and instructions for its use are presented here for the autophagy community.
Neutrophil Extracellular Traps have DNAzyme activity that drives bactericidal potential
Authors: Ku Ti-Hsuan , Ram-Mohan Nikhil , Zudock Elizabeth J , Abe Ryuichiro , Yang Samuel 
Published: October 2023

AbstractThe mechanisms of bacterial killing by neutrophil extracellular traps (NETs) are unclear. DNA, the largest component of NETs is believed to merely be a scaffold with minimal antimicrobial activity through the charge of the backbone. Here, we report that NETs DNA is beyond a scaffold and produces hydroxyl free radicals through the spatially concentrated G-quadruplex/hemin DNAzyme complexes, driving bactericidal effects. Immunofluorescence staining showed colocalization of G-quadruplex and hemin in extruded NETs DNA, and Amplex UltraRed assay portrayed its peroxidase activity. Proximity labeling of bacteria revealed localized concentration of radicals resulting from NETs bacterial trapping.Ex vivobactericidal assays revealed that G-quadruplex/hemin DNAzyme is the primary driver of bactericidal activity in NETs. NETs are DNAzymes that may have important biological consequences.One-Sentence SummaryG-quadruplex/hemin DNAzymes may be major contributors to biological consequences of neutrophil extracellular traps.
Platelet proteo-transcriptomic profiling validates mediators of thrombosis and proteostasis in patients with myeloproliferative neoplasms
Authors: Kelliher Sarah , Gamba Sara , Weiss Luisa , Shen Zhu , Marchetti Marina , Schieppati Francesca , Scaife Caitriona , Madden Stephen , Bennett Kathleen , Fortune Anne , Maung Su , Fay Michael , Áinle Fionnuala Ní , Maguire Patricia , Falanga Anna , Kevane Barry , Krishnan Anandi 
Published: October 2023

AbstractPatients with chronic Myeloproliferative Neoplasms (MPN) including polycythemia vera (PV) and essential thrombocythemia (ET) exhibit unique clinical features, such as a tendency toward thrombosis and hemorrhage, and risk of disease progression to secondary bone marrow fibrosis and/or acute leukemia. Although an increase in blood cell lineage counts (quantitative features) contribute to these morbid sequelae, the significant qualitative abnormalities of myeloid cells that contribute to vascular risk are not well understood. Here, we address this critical knowledge gap via a comprehensive and untargeted profiling of the platelet proteome in a large (n= 140) cohort of patients (from two independent sites) with an established diagnosis of PV and ET (and complement prior work on the MPN platelet transcriptome from a third site). We discover distinct MPN platelet protein expression and confirm key molecular impairments associated with proteostasis and thrombosis mechanisms of potential relevance to MPN pathology. Specifically, we validate expression of high-priority candidate markers from the platelet transcriptome at the platelet proteome (e.g.,calreticulin (CALR), Fc gamma receptor (FcγRIIA)and galectin-1 (LGALS1)pointing to their likely significance in the proinflammatory, prothrombotic and profibrotic phenotypes in patients with MPN. Together, our proteo-transcriptomic study identifies the peripherally-derived platelet molecular profile as a potential window into MPN pathophysiology and demonstrates the value of integrative multi-omic approaches in gaining a better understanding of the complex molecular dynamics of disease.HighlightsMPN patient platelet proteome identifies key pathobiological mediators of thrombosis and proteostasis. The MPN platelet proteomic profile validates our prior findings from the platelet transcriptome.
Selective Removal of 7KC by a Novel Atherosclerosis Therapeutic Candidate Reverts Foam Cells to a Macrophage-like Phenotype
Authors: Bhargava Prerna , Dinh Darren , Teramayi Fadzai , Silberg Ana , Petler Noa , Anderson Amelia M. , Clemens Daniel M. , O’Connor Matthew S. 
Published: October 2023

AbstractThe removal of the toxic oxidized cholesterol, 7-ketocholesterol (7KC), from cells through the administration of therapeutics has the potential to treat atherosclerosis and various other pathologies. While cholesterol is a necessary building block for homeostasis, oxidation of cholesterol can lead to the formation of toxic oxysterols involved in various pathologies, the most prominent of which is 7KC, which is formed through the non-enzymatic oxidation of cholesterol. Oxidized LDL (oxLDL) particles, highly implicated in heart disease, contain high levels of 7KC, and molecular 7KC is implicated in the pathogenesis of numerous diseases, including multiple sclerosis, hypercholesterolemia, sickle cell anemia, and multiple age related diseases. Of particular interest is the role of 7KC in the progression of atherosclerosis, with several studies associating elevated levels of 7KC with the etiology of the disease or in the transition of macrophages to foam cells. This research aims to elucidate the molecular mechanisms of UDP-003, a novel therapeutic, in mitigating the harmful effects of 7KC in mouse and human monocyte and macrophage cell lines. Experimental evidence demonstrates that administration of UDP-003 can reverse the foam cell phenotype, rejuvenating these cells by returning phagocytic function and decreasing both reactive oxygen species (ROS) and intracellular lipid droplet accumulation. Furthermore, our data suggests that the targeted removal of 7KC from foam cells with UDP-003 can potentially prevent and reverse atherosclerotic plaque formation. UDP-003 has the potential to be the first disease-modifying therapeutic approach to treating atherosclerotic disease.
Effect of homotypicvs. heterotypic interactions on the cellular uptake of extracellular vesicles
Authors: Jhaveri Jhanvi R. , Khare Purva , Pinky Paromita Paul , Kamte Yashika S. , Chandwani Manisha N. , Milosevic Jadranka , Abraham Nevil , Dave Kandarp M. , Zheng Si-yang , O’Donnell Lauren , Manickam Devika S 
Published: October 2023

AbstractExtracellular vehicles (EVs) are an emerging class of drug carriers and are primarily reported to be internalized into recipient cells via a combination of endocytic routes such as clathrin-mediated, caveolae-mediated and macropinocytosis pathways. In this work, (1) we investigated potential effects of homotypicvs. heterotypic interactions by studying the cellular uptake of homologous EVs (EV donor cells and recipient cells of the same type)vs. heterologous EVs (EV donor cells and recipient cells of different types) and (2) determined the route of EV internalization into low pinocytic/hard-to-deliver cell models such as brain endothelial cells (BECs). We used BECs and macrophages as low-pinocytic and phagocytic cell models, respectively, to study the effect of homotypicvs. heterotypic interactions on EV uptake in the recipient cells. Homotypic interactions led to a greater extent of uptake into the recipient BECs compared to heterotypic interactions. However, we did not see a complete reduction in EV uptake into recipient BECs when endocytic pathways were blocked using pharmacological inhibitors. Our results suggest that EVs primarily use membrane fusion to enter low-pinocytic recipient BECs instead of relying on endocytosis.Lipophilic PKH67 dye-labeled EVsbut not intravesicular esterase-activated calcein ester-labeled EVs severely reduced particle uptake into BECs while phagocytic macrophages internalized both types of EV-labeled particles to comparable extents. Our results also highlight the importance of carefully choosing labeling dye chemistry to study EV uptake, especially in the case of low pinocytic cells such as BECs.Graphical abstract
A novel genetic fluorescent reporter to visualize mitochondrial nucleoids
Authors: Deng Jingti , Swift Lucy , Zaman Mashiat , Shahhosseini Fatemeh , Sharma Abhishek , Bureik Daniela , Padovani Francesco , Benedikt Alissa , Jaiswal Amit , Brideau Craig , Grewal Savraj , Schmoller Kurt M. , Colarusso Pina , Shutt Timothy E. 
Published: October 2023

AbstractMitochondria have their own genome (mtDNA), which is present in hundreds of copies per cell and organized into nucleoid structures that are distributed throughout the dynamic mitochondrial network. Beyond encoding essential protein subunits for oxidative phosphorylation, mtDNA can also serve as a signalling molecule when it is present into the cytosol. Despite the importance of this genome, there are still many unknowns with respect to its regulation. To study mtDNA dynamics in living cells, we have developed a genetic fluorescent reporter, mt-HI-NESS, which is based on the HI-NESS reporter that uses the bacterial H-NS DNA binding domain. Here, we describe how this reporter can be used to image mtDNA nucleoids for live cell imaging without affecting the replication or expression of the mtDNA. In addition to demonstrating the adaptability of the mt-HI-NESS reporter for multiple fluorescent proteins, we also emphasize important factors to consider during the optimization and application of this reporter.
Borrowing Transcriptional Kinases to Activate Apoptosis
Authors: Sarott Roman , Gourisankar Sai , Karim Basel , Nettles Sabin , Yang Haopeng , Dwyer Brendan G. , Simanauskaite Juste M. , Tse Jason , Abuzaid Hind , Krokhotin Andrey , Zhang Tinghu , Hinshaw Stephen M. , Green Michael R. , Crabtree Gerald R. , Gray Nathanael S. 
Published: October 2023

ABSTRACTProtein kinases are disease drivers whose therapeutic targeting traditionally centers on inhibition of enzymatic activity. Here chemically induced proximity is leveraged to convert kinase inhibitors into context-specific activators of therapeutic genes. Bivalent molecules that link ligands of the transcription factor B-cell lymphoma 6 (BCL6) to ATP-competitive inhibitors of cyclin-dependent kinases (CDKs) were developed to re-localize CDK to BCL6-bound loci on chromatin and direct phosphorylation of RNA Pol II. The resulting BCL6-target proapoptotic gene expression translated into killing of diffuse large B-cell lymphoma (DLBCL) cells at 72 h with EC50s of 0.9 – 10 nM and highly specific ablation of the BCL6-regulated germinal center response in mice. The molecules exhibited 10,000-fold lower cytotoxicity in normal lymphocytes and are well tolerated in mice. Genomic and proteomic evidence corroborated a gain-of-function mechanism where, instead of global enzyme inhibition, a fraction of total kinase activity is borrowed and re-localized to BCL6-bound loci. The strategy demonstrates how kinase inhibitors can be used to context-specifically activate transcription, accessing new therapeutic space.
Brain enlargement with rostral bias in larvae from a spontaneously occurring female variant line ofXenopus; role of aberrant embryonic Wnt/β-catenin signaling
Authors: Hongo Ikuko , Yamaguchi Chihiro , Okamoto Harumasa 
Published: October 2023

ABSTRACTIncreased brain size and its rostral bias are hallmarks of vertebrate evolution, but the underlying developmental and genetic basis remains poorly understood. To provide clues to understanding vertebrate brain evolution, we investigated the developmental mechanisms of brain enlargement observed in the offspring of a previously unrecognized, spontaneously occurring female variant line ofXenopusthat appears to reflect a genetic variation. Brain enlargement in larvae from this line showed a pronounced rostral bias that could be traced back to the neural plate, the primordium of the brain. At the gastrula stage, the Spemann organizer, which is known to induce the neural plate from the adjacent dorsal ectoderm and give it the initial rostrocaudal patterning, was expanded from dorsal to ventral in a large proportion of the offspring of variant females. Consistently,siamoisexpression, which is required for Spemann organizer formation, was expanded laterally from dorsal to ventral at the blastula stage in variant offspring. This implies that the active region of the Wnt/β-catenin signaling pathway was similarly expanded in advance on the dorsal side, assiamoisis a target gene of this pathway. Notably, the earliest detectable change in variant offspring was in fertilized eggs, in which maternalwnt11bmRNA, a candidate dorsalizing factor that activates Wnt/β-catenin signaling, had a wider distribution in the vegetal cortical cytoplasm. Since lateral spreading ofwnt11bmRNA, and possibly that of other potential maternal dorsalizing factors in these eggs, is expected to facilitate lateral expansion of the active region of the Wnt/β-catenin pathway during subsequent embryonic stages, we concluded that aberrant Wnt/β-catenin signaling could cause rostral-biased brain enlargement via expansion ofsiamoisexpression and consequent expansion of the Spemann organizer inXenopus. Our studies of spontaneously occurring variations in brain development inXenopuswould help uncover genetic mutations that drive analogous morphogenetic variations during vertebrate brain evolution.
Plasma-based antigen persistence in the post-acute phase of SARS-CoV-2 infection
Authors: Peluso Michael J. , Swank Zoe N. , Goldberg Sarah A. , Lu Scott , Dalhuisen Thomas , Borberg Ella , Senussi Yasmeen , Luna Michael A. , Chang Song Celina , Clark Alexus , Zamora Andhy , Lew Megan , Viswanathan Badri , Huang Beatrice , Anglin Khamal , Hoh Rebecca , Hsue Priscila Y. , Durstenfeld Matthew S. , Spinelli Matthew A. , Glidden David V. , Henrich Timothy J. , Kelly J. Daniel , Deeks Steven G. , Walt David R. , Martin Jeffrey N. 
Published: October 2023

ABSTRACTBACKGROUNDPersistent symptoms among some persons who develop COVID-19 has led to the hypothesis that SARS-CoV-2 may, in some form or location, persist for long periods following acute infection. Several studies have shown data in this regard but are limited by non-representative and small study populations, short duration since acute infection, and lack of a true-negative comparator group to assess assay specificity.METHODSWe evaluated adults with RNA-confirmed COVID-19 at multiple time points following acute infection (pandemic-era participants) and adults with specimens collected prior to 2020 (pre-pandemic era). Using once-thawed plasma, we employed the Simoa® (Quanterix) single molecule array detection platform to measure SARS-CoV-2 spike, S1, and nucleocapsid antigens.RESULTSCompared to 250 pre-pandemic participants who had 2% assay positivity, detection of any SARS-CoV-2 antigen was significantly more frequent among 171 pandemic-era participants at three different time periods in the post-acute phase of infection. The absolute difference in SARS-CoV-2 plasma antigen prevalence was +11% (95% CI: +5.0% to +16%) at 3.0-6.0 months post-onset of COVID-19; +8.7% (95% CI: +3.1% to +14%) at 6.1 to 10.0 months; and +5.4% (95% CI: +0.42% to +10%) at 10.1-14.1 months. Hospitalization for acute COVID-19 and, among the non-hospitalized, worse self-reported health during acute COVID-19 were associated with greater post-acute phase antigen detection.CONCLUSIONSCompared to uninfected persons, there is an excess prevalence of SARS-CoV-2 antigenemia in SARS-CoV-2-infected individuals up to 14 months after acute COVID-19. These findings motivate an urgent research agenda regarding the short-term and long-term clinical manifestations of this viral persistence.
Children’s Residential Proximity, Spousal Presence and Modifiable Risk Factors for Dementia among Older Adults with Cognitive Impairment
Authors: Lin Zhuoer , Yin Xuecheng , Levy Becca R. , Yuan Yue , Chen Xi 
Published: October 2023

AbstractBackgroundCognitive impairment in older adults poses considerable challenges, and the role of family support becomes increasingly crucial. This study aims to examine the impact of children’s residential proximity and spousal presence on the key modifiable risk factors for dementia among older adults with cognitive impairment.MethodsUtilizing the Health and Retirement Study (HRS) data from 1995 to 2018, we analyzed 14,731 participants (35,840 person-waves) aged 50 and older with cognitive impairment. Family support was characterized based on the presence of a spouse and residential proximity to children. Smoking, depressive symptoms and social isolation were included as the key modifiable risk factors for dementia identified in later life. Using mixed-effects logistic regressions, associations between access to family support and the modifiable risk factors were determined, adjusting for various socio-demographic and health-related factors.ResultsSignificant associations were found between access to family support and modifiable risk factors for dementia. Cognitively impaired older adults with less available family support, characterized by distant-residing children and the absence of a spouse, had significantly higher risks of smoking, depressive symptoms, and social isolation. Moreover, we revealed a consistent gradient in the prevalence of the risk factors based on the degree of family support. Relative to older adults with a spouse and co-resident children, those without a spouse and with all children residing further than 10 miles displayed the highest risks of smoking, depressive symptoms, and social isolation.ConclusionAccess to family support, particularly from spouses and proximate children, plays a protective role against key modifiable risk factors for dementia in older adults with cognitive impairment. The findings highlight the need for bolstering family and social support systems to enhance the well-being of this vulnerable population.
A parametric bootstrap approach for computing confidence intervals for genetic correlations with application to genetically-determined protein-protein networks
Authors: Tsai Yi-Ting , Hrytsenko Yana , Elgart Michael , Tahir Usman , Chen Zsu-Zsu , Wilson James G , Gerszten Robert , Sofer Tamar 
Published: October 2023

AbstractGenetic correlation refers to the correlation between genetic determinants of a pair of traits. When using individual-level data, it is typically estimated based on a bivariate model specification where the correlation between the two variables is identifiable and can be estimated from a covariance model that incorporates the genetic relationship between individuals, e.g., using a pre-specified kinship matrix. Inference relying on asymptotic normality of the genetic correlation parameter estimates may be inaccurate when the sample size is low, when the genetic correlation is close to the boundary of the parameter space, and when the heritability of at least one of the traits is low. We address this problem by developing a parametric bootstrap procedure to construct confidence intervals for genetic correlation estimates. The procedure simulates paired traits under a range of heritability and genetic correlation parameters, and it uses the population structure encapsulated by the kinship matrix. Heritabilities and genetic correlations are estimated using the close-form, method of moment, Haseman-Elston regression estimators. The proposed parametric bootstrap procedure is especially useful when genetic correlations are computed on pairs of thousands of traits measured on the same exact set of individuals. We demonstrate the parametric bootstrap approach on a proteomics dataset from the Jackson Heart Study.
Estimating the maximum risk of measles outbreaks due to heterogeneous fall in immunization rates
Authors: Wu Nicholas , Moon Sifat Afroj , Falk Ami , Marathe Achla , Vullikanti Anil 
Published: October 2023

AbstractImmunization rates for childhoold vaccines, such as MMR, have seen a reduction over the recent years; this fall has only been accentuated after the COVID-19 pandemic. However, there is limited data on where the rates have reduced, and prior work has shown that heterogeneity in the drop in immunization rates has a significant impact on the risk of an outbreak. An important question from a public health perspective is: what is the maximum size of an outbreak in a region, when limited information is available on the fall in immunization rates within the region?This turns out to be a very hard computational problem. We develop a Bayesian optimization based approach for estimating the maximum outbreak size, and use it on a measles model for the state of Virginia. Our results show that the maximum outbreak size is several orders of magnitude higher than estimated in a baseline which assumes homogeneous fall. Even for a 5% reduction in the statewide immunzation rate, the expected outbreak size can be very high. The maximum outbreak size depends crucially on the importation location, i.e., where the disease starts, and importation in an urban region leads to a significantly higher outbreak. The outbreak size remains high even if the drop in immunization is bounded in health service areas in the state.