bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combination treatment of persistent COVID-19 in immunocompromised patients with remdesivir, nirmaltrevir/ritonavir and tixegavimab/cilgavimab
Authors: Brosh-Nissimov Tal , Ma’aravi Nir , Leshin-Carmel Daniel , Edel Yonatan , Barouch Sharon Ben , Segman Yafit , Cahan Amos , Barenboim Erez 
Published: April 2023

AbstractBackgroundLittle data exists to guide the treatment of persistent COVID-19 in immunocompromised patients. We have employed a unique protocol combining tixegavimab/cilgavimab, and short-term combination antivirals including remdesivir.MethodsA retrospective single-center analysis of persistent COVID-19 in immunocompromised patients. Response was assessed by symptom resolution, declining C-reactive protein (CRP) levels and increasing SARS-CoV-2-PCR cycle-threshold (Ct) values.ResultsFourteen patients were included, including 2 kidney transplant recipients, 11 with B-cell lymphoproliferative disease, treated with anti-CD20 or ibrutinib, and 1 with rheumatoid arthritis, treated with anti-CD20. Median Ct-value was 27 (interquartile range (IQR):24-32). All patients received tixegavimab/cilgavimab and a 5-day course of remdesivir. Eleven also received nirmaltrevir/ritonavir and one received molnupiravir. Median follow-up was 45 days (IQR:12-89). Eleven patients had complete responses including symptom resolution, decrease in CRP, and increase in Ct values (all with either a negative PCR or Ct value>30 on day 4-16). Three patients had a partial response with relapses requiring re-admission. One had died, and two responded to prolonged antiviral treatments.ConclusionsA combination of monoclonal antibodies with antivirals has led to complete resolution of persistent COVID-19 in most severely-immunocompromised patients. Controlled studies will further direct the treatment of these patients, while more effective antivirals are urgently needed.Key pointsSome immunocompromised patients develop persistent symptomatic SARS-CoV-2 infection. Combination of monoclonal antibodies plus one or more antivirals cured 11/14 patients. Non-responders benefitted from prolonged combination antiviral treatment. Controlled trials are needed to find optimal treatment of persistent COVID-19.
Endothelial Nitric Oxide Synthase Regulates Lymphatic Valve Specification By Controlling β - catenin Signaling During Embryogenesis
Authors: Iyer Drishya , Mastrogiacomo Diandra , Li Kunyu , Banerjee Richa , Yang Ying , Scallan Joshua P. 
Published: April 2023

ABSTRACTObjectiveLymphatic valves play a critical role in ensuring unidirectional lymph transport. Loss of lymphatic valves or dysfunctional valves are associated with several diseases including lymphedema, lymphatic malformations, obesity, and ileitis. Lymphatic valves first develop during embryogenesis in response to mechanotransduction signaling pathways triggered by oscillatory lymph flow. In blood vessels, eNOS (gene name:Nos3) is a well characterized shear stress signaling effector, but its role in lymphatic valve development remains unexplored.Approach and ResultsWe used globalNos3−/−mice and cultured hdLECs to investigate the role of eNOS in lymphatic valve development, which requires oscillatory shear stress signaling. Our data reveal a 45% reduction in lymphatic valve specification cell clusters and that loss of eNOS protein inhibited activation of β-catenin and its nuclear translocation. Genetic knockout or knockdown of eNOS led to downregulation of β-catenin target proteinsin vivoandin vitro. However, pharmacological inhibition of NO production did not reproduce these effects. Coimmunoprecipitation experiments reveal that eNOS forms a complex with β-catenin and their association is enhanced by oscillatory shear stress. Finally, genetic ablation of the Foxo1 gene enhanced FOXC2 expression and rescued the loss of valve specification in the eNOS knockouts.ConclusionIn conclusion, we demonstrate a novel, nitric oxide-independent role for eNOS in regulating lymphatic valve specification and propose a mechanism by which eNOS forms a complex with β-catenin to regulate its nuclear translocation and thereby transcriptional activity.
Novel technology to develop non-transmissible live influenza virus vaccines through alterations in M2/M42 ion channel expression
Authors: Kapczynski Darrell R. , Segovia Karen , Chrzastek Klaudia , Conceicao Carina , Suarez David L. , Vervelde Lonneke , Digard Paul 
Published: April 2023

AbstractContinued global outbreaks of H5Nx highly pathogenic avian influenza viruses (HPAIV) have been reported in poultry since the emergence of the Asian Goose/Guangdong lineage of HPAIV H5N1 in 1996. Consequently, vaccines have been developed and employed to protect commercial and non-commercial poultry flocks. However, constant changes in virus immunogenetics makes vaccine candidates that prevent morbidity, mortality, reduce shedding, and prevent transmission a moving target. Here, we tested the effects of disrupting the mRNA splice sites and thus expression of either of the two isoforms of the viral ion channel M2 and M42 expressed by the H5N2 low pathogenic avian influenza virus (LPAIV) progenitor of the 1983 Pennsylvania HPAIV outbreak. Both G52C (ΔM2) and G145A (ΔM42) versions of the A/chicken/Pennsylvania/1/83 (Ck/Penn) virus replicated wellin vitroandin ovo, but showed altered virion morphology, with the G145A virus exhibiting filamentous budding. The G52C and G145A viruses also infected chickens efficiently and stimulated robust immune responses; however, unlike the wild type virus, they did not transmit to naïve-contact birds. In protection studies, vaccination of birds with G52C or G145A viruses protected 100% of birds from lethal challenge with homologous and distant heterologous H5 HPAIV strains from North American and Asian lineages and significantly reduced virus shedding compared to controls. Furthermore, the live virus vaccines decreased virus shedding 10,000-fold more than corresponding inactivated forms of the vaccine virus. Taken together, these studies demonstrate a strategy for developing a non-transmittable but highly protective live attenuated virus for AIV.
Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their excreted vesicles
Authors: Oberholster Larise , Mathias Amandine , Perriot Sylvain , Blaser Emma , Canales Mathieu , Jones Samuel , Culebras Lucas , Gimenez Marie , Kaynor G. Campbell , Sapozhnik Alexey , Richetin Kevin , Goelz Susan , Pasquier Renaud Du 
Published: April 2023

AbstractJC polyomavirus (JCPyV) is an opportunistic virus that remains in a latent state in the kidneys of more than half of the human adult population. In rare cases of severe immune suppression, the virus is able to establish a lytic infection of glial cells in the brain, resulting in a debilitating, demyelinating disease known as progressive multifocal leukoencephalopathy (PML). Because of the exceptional species and tissue specificity of the virus, appropriate models of JCPyV infection in the brain are lacking, thus hampering progress towards the development of novel antiviral strategies and biomarkers of disease activity. While PML has traditionally been characterized as a lytic infection of oligodendrocytes, more recent findings suggest an important role for astrocytes during the initial stages of disease. Here, using human induced pluripotent stem cell (hiPSC) derived-astrocytes coupled with a multiparametric approach, we show that 1. JCPyV readily infects and replicates in astrocytes, 2. JCPyV strongly dysregulates the cell biology and 3. these findings adequately reflectex vivofindings. We perform an in-depth characterization of the effect of JCPyV on the cell proteome over time, demonstrating a strong dysregulation of the cell cycle and activation of the DNA damage response. Furthermore, we show that the proteomic signature observed for infected astrocytes is extended to excreted vesicles, underlining their potential to gain valuable insights into JCPyV propagation in the brain.
Wearable-ome meets epigenome: A novel approach to measuring biological age with wearable devices
Authors: Sugden Cameron , du Preez Franco B , Olivier Laurence R , Deffur Armin 
Published: April 2023

AbstractAging is an inevitable process of cellular and physiological decline. These markers of age can be measured on the molecular and functional level. Wearable devices offer a non-invasive continuous measure of physiological and behavioural features and how they pertain to aging. Wearable data can be used to extrapolate information derived from epigenetic biological age predictions and its underlying biology. LifeQ-enabled wearable devices were worn for 40 days to harvest data on 48 human participants. Thereafter blood was drawn and methylation levels determined using the Illumina EPIC array. Multiple epigenetic clock ages were calculated and compared with wearable features. Activity minutes correlated with VO2max (p = 0.003), subendocardial viability ratio (SEVR, p < 0.01), blood pressure index (BPI, p = 0.02), resting heart rate (RHR, p < 0.01) and heart outflow (HO, p < 0.01). Sedentary time correlated with RHR (p < 0.01), VO2max (p = 0.01), SEVR (p = 0.04), and HO (p = 0.04). VO2max, SEVR, small artery resistance (SAR), BPI and large artery stiffness index (LASI) correlated with multiple epigenetic age clock outputs and chronological age but were most strongly correlated with PCPhenoAge. VO2max, (p = 0.04) RHR (p < 0.01) and LASI (p = 0.04) were significantly correlated with PCPhenoAge acceleration. Weighted gene correlation network analysis (WGCNA) of the differentially methylated positions of PCPhenoAge acceleration was used to construct modules, identifying 3 modules correlating with wearable features. Behavioural features impact physiological state, measured by the wearable, which are associated with epigenetic age and age acceleration. Signal from the underlying biology of age acceleration can be picked up by the wearable, presenting a case that wearable devices can capture portions of biological aging.
An Azapeptide Platform in Conjunction with Covalent Warheads to Uncover High-Potency Inhibitors for SARS-CoV-2 Main Protease
Authors: Khatua Kaustav , Alugubelli Yugendar R. , Yang Kai S. , Vulupala Veerabhadra R. , Blankenship Lauren R. , Coleman Demonta D. , Atla Sandeep , Chaki Sankar P. , Geng Zhi Zachary , Ma Xinyu R. , Xiao Jing , Chen Peng-Hsun Chase , Cho Chia-Chuan Dean , Vatansever Erol C. , Ma Yuying , Yu Ge , Neuman Benjamin W. , Xu Shiqing , Liu Wenshe Ray 
Published: April 2023

ABSTRACTMain protease (MPro) of SARS-CoV-2, the viral pathogen of COVID-19, is a crucial nonstructural protein that plays a vital role in the replication and pathogenesis of the virus. Its protease function relies on three active site pockets to recognize P1, P2, and P4 amino acid residues in a substrate and a catalytic cysteine residue for catalysis. By converting the P1 Cα atom in an MProsubstrate to nitrogen, we showed that a large variety of azapeptide inhibitors with covalent warheads targeting the MProcatalytic cysteine could be easily synthesized. Through the characterization of these inhibitors, we identified several highly potent MProinhibitors. Specifically, one inhibitor, MPI89 that contained an aza-2,2-dichloroacetyl warhead, displayed a 10 nM EC50value in inhibiting SARS-CoV-2 from infecting ACE2+A549 cells and a selectivity index of 875. The crystallography analyses of MProbound with 6 inhibitors, including MPI89, revealed that inhibitors used their covalent warheads to covalently engage the catalytic cysteine and the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 represents one of the most potent MProinhibitors developed so far, suggesting that further exploration of the azapeptide platform and the aza-2,2-dichloroacetyl warhead is needed for the development of potent inhibitors for the SARS-CoV-2 MProas therapeutics for COVID-19.
Dietary protein shapes the profile and repertoire of intestinal CD4+T cells
Authors: Lockhart Ainsley , Reed Aubrey , Castro Tiago Rezende de , Herman Calvin , Canesso Maria Cecilia Campos , Mucida Daniel 
Published: April 2023

AbstractThe intestinal immune system must tolerate food antigens to avoid allergy, a process requiring CD4+T cells. Combining antigenically defined diets with gnotobiotic models, we show that food and microbiota distinctly influence the profile and T cell receptor repertoire of intestinal CD4+T cells. Independent of the microbiota, dietary proteins contributed to accumulation and clonal selection of antigen-experienced CD4+T cells at the intestinal epithelium, imprinting a tissue specialized transcriptional program including cytotoxic genes on both conventional and regulatory CD4+T cells (Tregs). This steady state CD4+T cell response to food was disrupted by inflammatory challenge, and protection against food allergy in this context was associated with Treg clonal expansion and decreased pro-inflammatory gene expression. Finally, we identified both steady state epithelium-adapted CD4+T cells and tolerance-induced Tregs that recognize dietary antigens, suggesting that both cell types may be critical for preventing inappropriate immune responses to food.
Native and engineered human megakaryocytic extracellular vesicles for targeted non-viral cargo delivery to blood stem cells
Authors: Das Samik , Thompson Will , Papoutsakis E. Terry 
Published: April 2023

AbstractNative and engineered extracellular vesicles (EVs) generated from human megakaryocytes (huMkEVs) or from the human megakaryocytic cell line CHRF (CHEVs) interact with tropism delivering their cargo to both human and murine hematopoietic stem and progenitor cells (HSPCs). 24 hours after intravenous infusion of huMkMPs into NOD-scidIL2Rγnull(NSG™) mice, they induced a nearly 50% increase in murine platelet counts relative to saline control, thus demonstrating the potential of these EVs, which can be stored frozen, for treating thrombocytopenias. PKH26-labeled huMkMPs or CHEVs localized to the HSPC-rich bone marrow preferentially interacting with murine HSPCs. Using engineered huMkEVs or CHEVs, their receptor-mediated tropism for HSPCs was explored to functionally deliver synthetic cargo, notably plasmid DNA coding for a fluorescent reporter, to murine HSPCs bothin vitroandin vivo.These data demonstrate the potential of these EVs as a non-viral, HSPC-specific cargo vehicle for gene therapy applications to treat hematological diseases.Native and engineered human megakaryocytic extracellular vesicles for targeted non-viral cargo delivery to blood stem cells(Table of Contents):Graphical Overview: Native and engineered human megakaryocytic extracellular vesicles (huMkEVs) for provide targeted non-viral cargo delivery to blood stem cells.We demonstrate that huMkEVs as a transformational cargo-delivery system to blood stem cells (hematopoietic stem and progenitor cells, HSPCs) in NOD-scid IL2Rγnull(NSG™) mice. Intravenous delivery of native huMkEVs enhancesde novoplatelet biogenesis by inducing megakaryocytic differentiation of murine HSPCs, thus demonstrating the desirable strong tropism of huMkEVs for murine HSPCs. Based on this tropism, we demonstrate that engineered huMkEVs can deliver functional plasmid-DNA cargo specifically to HSPCs.
Why flying insects gather at artificial light
Authors: Fabian Samuel T , Sondhi Yash , Allen Pablo , Theobald Jamie , Lin Huai-Ti 
Published: April 2023

AbstractFor millennia, humans have watched nocturnal insects flying erratically around fires and lamps. Explanations have included theories of “lunar navigation” and “escape to light”. However, without three-dimensional flight data to test them rigorously, this odd behaviour has remained unexplained. We employed high-resolution motion capture in the laboratory and stereo-videography in the field to reconstruct the 3D kinematics of insect flights around artificial lights. Contrary to the expectation of attraction, insects do not steer directly toward the light. Instead, insects turn their dorsum toward the light, generating flight bouts perpendicular to the source. Under natural sky light, tilting the dorsum towards the brightest visual hemisphere helps maintain proper flight attitude and control. Near artificial sources, however, this highly conserved dorsal-light-response can produce continuous steering around the light and trap an insect. Our guidance model demonstrates that this dorsal tilting is sufficient to create the seemingly erratic flight paths of insects near lights and is the most plausible model for why flying insects gather at artificial lights.
Astrovirus replication is dependent on induction of double membrane vesicles through a PI3K-dependent, LC3-independent pathway
Authors: Bub Theresa , Hargest Virginia , Tan Shaoyuan , Smith Maria , Vazquez-Pagan Ana , Flerlage Tim , Brigleb Pamela H. , Meliopoulos Victoria , Lindenbach Brett , Cortez Valerie , Crawford Jeremy Chase , Schultz-Cherry Stacey 
Published: April 2023

AbstractHuman astrovirus is a positive sense, single stranded RNA virus. Astrovirus infection causes gastrointestinal symptoms and can lead to encephalitis in immunocompromised patients. Positive strand RNA viruses typically utilize host intracellular membranes to form replication organelles, which are potential antiviral targets. Many of these replication organelles are double membrane vesicles (DMVs). Here we show that astrovirus infection leads to an increase in DMV formation, and this process is replication-dependent. Our data suggest that astrovirus infection induces rearrangement of endoplasmic reticulum fragments, which may become the origin for DMV formation. Transcriptional data suggested that formation of DMVs during astrovirus infection requires some early components of the autophagy machinery. Results indicate that the upstream class III phosphatidylinositol 3-kinase (PI3K) complex, but not LC3 conjugation machinery, is utilized in DMV formation. Inhibition of the PI3K complex leads to significant reduction in viral replication and release from cells. Elucidating the role of autophagy machinery in DMV formation during astrovirus infection reveals a potential target for therapeutic intervention for immunocompromised patients.ImportanceThese studies provide critical new evidence that astrovirus replication requires formation of double membrane vesicles, which utilize class III PI3K, but not LC3 conjugation autophagy machinery for biogenesis. These results are consistent with replication mechanisms for other positive sense RNA viruses. This suggests that targeting PI3K could be a promising therapeutic option for not only astrovirus, but other positive sense RNA virus infections.
Spatial proteomics of human diabetic kidney disease, from health to class III
Authors: Kondo Ayano , McGrady Monee , Nallapothula Dhiraj , Ali Hira , Trevino Alexandro E. , Lam Amy , Preska Ryan , D’Angio H. Blaize , Wu Zhenqin , Lopez Lauren , Badhesha Harshanna Kaur , Vargas Chenoa Rochel , Ramesh Achyuta , Wiegley Nasim , Han Seung Seok , Dall’Era Marc , Jen Kuang-Yu , Mayer Aaron T. , Afkarian Maryam 
Published: April 2023

ABSTRACTAims/HypothesisDiabetic kidney disease (DKD) remains a significant cause of morbidity and mortality in people with diabetes. Though animal models have taught us much about the molecular mechanisms of DKD, translating these findings to human disease requires greater knowledge of the molecular changes caused by diabetes in human kidneys. Establishing this knowledge base requires building carefully curated, reliable, and complete repositories of human kidney tissue, as well as tissue proteomics platforms capable of simultaneous, spatially resolved examination of multiple proteins.MethodsWe used the multiplexed immunofluorescence platform CO-Detection by indexing (CODEX) to image and analyze the expression of 21 proteins in 23 tissue sections from 12 individuals with diabetes and healthy kidneys (DM, 5 individuals), DKD classes IIA, and IIB (2 individuals per class), IIA-B intermediate (2 individuals), and III (one individual).ResultsAnalysis of the 21-plex immunofluorescence images revealed 18 cellular clusters, corresponding to 10 known kidney compartments and cell types, including proximal tubules, distal nephron, podocytes, glomerular endothelial and peritubular capillaries, blood vessels, including endothelial cells and vascular smooth muscle cells, macrophages, cells of the myeloid lineage, broad CD45+ inflammatory cells and the basement membrane. DKD progression was associated with co-localized increase in collagen IV deposition and infiltration of inflammatory cells, as well as loss of native proteins of each nephron segment at variable rates. Compartment-specific cellular changes corroborated this general theme, with compartment-specific variations. Cell type frequency and cell-to-cell adjacency highlighted (statistically) significant increase in inflammatory cells and their adjacency to tubular and αSMA+ cells in DKD kidneys. Finally, DKD progression was marked by substantial regional variability within single tissue sections, as well as variability across patients within the same DKD class. The sizable intra-personal variability in DKD severity impacts pathologic classifications, and the attendant clinical decisions, which are usually based on small tissue biopsies.Conclusions/InterpretationsHigh-plex immunofluorescence images revealed changes in protein expression corresponding to differences in cellular phenotypic composition and microenvironment structure with DKD progression. This initial dataset demonstrates the combined power of curated human kidney tissues, multiplexed immunofluorescence and powerful analysis tools in revealing pathophysiology of human DKD.
Color appearance of iridescent objects
Authors: Doerschner Katja , Ennis Robert , Börner Philipp , Maile Frank J. , Gegenfurtner Karl R. 
Published: April 2023

AbstractIridescent objects and animals are quite mesmerizing to look at, since they feature multiple intense colors whose distribution can vary quite dramatically as a function of viewing angle. These properties make them a particularly interesting and unique stimulus to experimentally investigate the factors that contribute to single color impressions of multi-colored objects. Our stimuli were 3D printed shapes of varying complexity that were covered with three different types of iridescent coatings. For each shape-color combination, participants performed single- and multi-color matches for different views of the stationary object, as well as single color matches for a corresponding rotating stimulus. In the multi-color matching task, participants subsequently rated the size of the surface area on the object that was covered by the match-identified color. Results show that single-color appearance of iridescent objects varied with shape complexity, view, and object motion. Moreover, hue similarity of color settings in the multi color match task best predicted single color appearance, however this predictor was weaker for predicting single color matches in the motion condition. Taken together our findings suggest that the single color appearance of iridescent objects may be modulated by chromatic factors, spatial-relations and the characteristic dynamics of color changes that are typical for this type of material.