bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective Down-Regulation of Neutrophil Mac-1 in Endotoxemic Hepatic Microcirculation via IL-10
Authors: Menezes Gustavo Batista , Lee Woo-Yong , Zhou Hong , Waterhouse Christopher Curtis Matchett , Cara Denise Carmona , Kubes Paul 
Published: November 2009

Abstract
Hepatic neutrophil adhesion during endotoxemia is an integrin-independent, CD44-dependent process. Because integrins function in other endotoxemic vasculatures, we used spinning disk confocal intravital microscopy to assess whether LPS down-modulated integrin functions in sinusoids. First, we applied fMLP onto the liver surface, and compared it with systemic LPS administration. Local fMLP caused neutrophil adhesion, crawling, and emigration for at least 2 h. Surprisingly, the number of adherent and crawling neutrophils was markedly reduced in Mac-1−/− and ICAM-1−/− mice, but not in mice treated with anti-CD44 mAb. By contrast, systemic LPS injection induced a robust accumulation of neutrophils in sinusoids, which was dependent on CD44, but not on integrins. Strikingly, local fMLP could not induce any integrin-dependent adhesion in endotoxemic mice treated with anti-CD44 mAb, indicating that Mac-1-dependent neutrophil adhesion was inhibited by LPS. This response was localized to the hepatic microvasculature because neutrophils still adhered via integrins in brain microvasculature. ICAM-1/ICAM-2 levels were not decreased, but following LPS treatment, Mac-1 was down-regulated in neutrophils localized to liver, but not in the circulation. Mac-1 down-regulation in neutrophils was not observed in IL-10−/− mice. In vitro neutrophil incubation with IL-10 induced direct decrease of Mac-1 expression and adhesivity in LPS-stimulated neutrophils. Therefore, our data suggest that Mac-1 is necessary for neutrophil adhesion and crawling during local inflammatory stimuli in sinusoids, but during systemic inflammation, neutrophils are exposed to high concentrations of IL-10, leading to a CD44-dependent, integrin-independent adhesion. This may be a mechanism to keep neutrophils in sinusoids for intravascular trapping.
Systematic Classification of Primary Immunodeficiencies Based on Clinical, Pathological, and Laboratory Parameters
Authors: Samarghitean Crina , Ortutay Csaba , Vihinen Mauno 
Published: November 2009

AbstractThe classification of diseases has several important applications ranging from diagnosis and choice of treatment to demographics. To date, classifications have been successfully created manually, often within international consortia. Some groups of diseases, such as primary immunodeficiencies (PIDs), are especially hard to nosologically cluster due, on one hand, to the presence of a wide variety of disorders and, in contrast, because of overlapping characteristics. More than 200 PIDs affecting components of the innate and adaptive immune systems have been described. Clinical, pathological, and laboratory characteristics were collected and used to group PIDs. A consensus of at least five independent methods provided a novel classification of 11 groups, which revealed previously unknown features and relationships of PIDs. Comparison of the classification to independent features, including the severity and therapy of the diseases, functional classification of proteins, and network vulnerability, indicated a strong statistical support. The method can be applied to any group of diseases.
CD39+Foxp3+ Regulatory T Cells Suppress Pathogenic Th17 Cells and Are Impaired in Multiple Sclerosis
Authors: Fletcher Jean M. , Lonergan Roisin , Costelloe Lisa , Kinsella Katie , Moran Barry , O'Farrelly Cliona , Tubridy Niall , Mills Kingston H. G. 
Published: November 2009

Abstract
Despite the fact that CD4+CD25+Foxp3+ regulatory T cells (Treg cells) play a central role in maintaining self-tolerance and that IL-17-producing CD4+ T cells (Th17 cells) are pathogenic in many autoimmune diseases, evidence to date has indicated that Th17 cells are resistant to suppression by human Foxp3+ Treg cells. It was recently demonstrated that CD39, an ectonucleotidase which hydrolyzes ATP, is expressed on a subset of human natural Treg cells. We found that although both CD4+CD25highCD39+ and CD4+CD25highCD39− T cells suppressed proliferation and IFN-γ production by responder T cells, only the CD4+CD25highCD39+, which were predominantly FoxP3+, suppressed IL-17 production, whereas CD4+CD25highCD39− T cells produced IL-17. An examination of T cells from multiple sclerosis patients revealed a normal frequency of CD4+CD25+CD127lowFoxP3+, but interestingly a deficit in the relative frequency and the suppressive function of CD4+CD25+CD127lowFoxP3+CD39+ Treg cells. The mechanism of suppression by CD39+ Treg cells appears to require cell contact and can be duplicated by adenosine, which is produced from ATP by the ectonucleotidases CD39 and CD73. Our findings suggest that CD4+CD25+Foxp3+CD39+ Treg cells play an important role in constraining pathogenic Th17 cells and their reduction in multiple sclerosis patients might lead to an inability to control IL-17 mediated autoimmune inflammation.
CD80 Blockade Enhance Glucocorticoid-Induced Leucine Zipper Expression and Suppress Experimental Autoimmune Encephalomyelitis
Authors: Dudhgaonkar Shailesh P. , Janardhanam Srihari B. , Kodumudi Krithika N. , Srinivasan Mythily 
Published: November 2009

Abstract
Designing mimetic of the interface functional groups of known receptor-ligand complexes is an attractive strategy for developing potential therapeutic agents that interfere with target protein-protein interactions. The CD80/CD86-CD28/CD152 costimulatory interactions transmit signals for CD4+ T cell activation and suppression and are critically involved in the initiation, progression, and reactivation of the immunopathology in multiple sclerosis. Differences in the pattern, levels, and kinetics of expression of CD80/CD86 molecules in conjunction with differences in the strength of the signals delivered upon binding CD28 or CD152 determine the outcome of the immune response. A temporal up-regulation of surface expression of CD80 relative to CD86 on APCs and CNS-infiltrating cells has been shown to correlate with disease progression in experimental autoimmune encephalomyelitis an animal model for multiple sclerosis. Hence blockade of the CD80 costimulatory axis has therapeutic potential in multiple sclerosis. In this study, we report the efficacy of a novel CD80-blocking agent CD80-competitive antagonist peptide (CD80-CAP) in suppressing clinical disease and relapse in experimental autoimmune encephalomyelitis. The CD80-CAP mediates protection by inhibiting proinflammatory cytokines and skewing toward anti-inflammatory response presumably by enhancing the expression of glucocorticoid-induced leucine zipper in activated CD4+ T cells.
Cutting Edge: Requirement of MARCH-I-Mediated MHC II Ubiquitination for the Maintenance of Conventional Dendritic Cells
Authors: Ohmura-Hoshino Mari , Matsuki Yohei , Mito-Yoshida Mari , Goto Eiji , Aoki-Kawasumi Masami , Nakayama Manabu , Ohara Osamu , Ishido Satoshi 
Published: November 2009

Abstract
MARCH-I (membrane-associated RING-CH I) has been suggested as a physiological E3 ubiquitin ligase for both MHC class II (MHC II) and B7-2. In this study, we show that MARCH-I-mediated MHC II ubiquitination is necessary for the maintenance of conventional dendritic cell (cDC) functions in the steady state. MARCH-I-deficient cDCs accumulated MHC II and B7-2 and exhibited low Ag-presenting ability for exogenous Ags and low cytokine-producing ability upon stimulation in vivo. Importantly, MHC II, but not B7-2, was required for impaired cDC function induced by loss of MARCH-I in vivo. Moreover, MHC II knockin mice whose MHC II was not ubiquitinated showed dysfunction of cDC similar to that of MARCH-I knockout mice. These results suggest that the accumulation of MHC II resulting from loss of ubiquitination caused cDC abnormality; therefore, MARCH-I may function as a housekeeper of cDC in the steady state.
MAPK, Phosphatidylinositol 3-Kinase, and Mammalian Target of Rapamycin Pathways Converge at the Level of Ribosomal Protein S6 Phosphorylation to Control Metabolic Signaling in CD8 T Cells
Authors: Salmond Robert J. , Emery Juliet , Okkenhaug Klaus , Zamoyska Rose 
Published: November 2009

Abstract
Ribosomal protein S6 (rpS6) is a key component of the translational machinery in eukaryotic cells and is essential for ribosome biogenesis. rpS6 is phosphorylated on evolutionarily conserved serine residues, and data indicate that rpS6 phosphorylation might regulate cell growth and protein synthesis. Studies in cell lines have shown an important role for the serine kinase mammalian target of rapamycin (mTOR) in rpS6 phosphorylation, further linking rpS6 to control of cellular metabolism. rpS6 is essential in T cells because its deletion in mouse double-positive thymocyte cells results in a complete block in T cell development; however, the signaling pathway leading to rpS6 phosphorylation downstream of TCR stimulation has yet to be fully characterized. We show that maximal TCR-induced rpS6 phosphorylation in CD8 T cells requires both Lck and Fyn activity and downstream activation of PI3K, mTOR, and MEK/ERK MAPK pathways. We demonstrate that there is cross-talk between the PI3K and MAPK pathways as well as PI3K-independent mTOR activity, which result in differential phosphorylation of specific rpS6 serine residues. These results place rpS6 phosphorylation as a point of convergence for multiple crucial signaling pathways downstream of TCR triggering.
MAp44, a Human Protein Associated with Pattern Recognition Molecules of the Complement System and Regulating the Lectin Pathway of Complement Activation
Authors: Degn Søren E. , Hansen Annette G. , Steffensen Rudi , Jacobsen Christian , Jensenius Jens C. , Thiel Steffen 
Published: November 2009

Abstract
Essential effector functions of innate immunity are mediated by complement activation initiated by soluble pattern recognition molecules: mannan-binding lectin (MBL) and the ficolins. We present a novel, phylogenetically conserved protein, MAp44, which is found in human serum at 1.4 μg/ml in Ca2+-dependent complexes with the soluble pattern recognition molecules. The affinity for MBL is in the nanomolar range (KD = 0.6 nM) as determined by surface plasmon resonance. The first eight exons of the gene for MAp44 encode four domains shared with MBL-associated serine protease (MASP)-1 and MASP-3 (CUB1-EGF-CUB2-CCP1), and a ninth exon encodes C-terminal 17 aa unique to MAp44. mRNA profiling in human tissues shows high expression in the heart. MAp44 competes with MASP-2 for binding to MBL and ficolins, resulting in inhibition of complement activation. Our results add a novel mechanism to those known to control the innate immune system.
Serine 649 Phosphorylation within the Protein Kinase C-Regulated Domain Down-Regulates CARMA1 Activity in Lymphocytes
Authors: Moreno-García Miguel E. , Sommer Karen , Haftmann Claudia , Sontheimer Clayton , Andrews Sarah F. , Rawlings David J. 
Published: November 2009

Abstract
Phosphorylation of CARMA1 is a crucial event initiating the assembly of IκB kinase and JNK signaling complexes downstream of activated Ag receptors. We previously mapped three protein kinase C (PKC) target sites in murine CARMA1 in vitro, and demonstrated that mutation of two of these serines (S564 and S657) resulted in reduced NF-κB activation, whereas mutation of the third serine (S649) had no clear effect. In this study, we report that when low concentrations of Ag receptor activators are used, loss of S649 (by mutation to alanine) promotes enhanced IκB kinase and JNK activation in both B and T cell lines. Reconstitution of CARMA1−/− DT40 B cells with CARMA1 S649A leads to increased cell death and reduced cell growth in comparison to wild-type CARMA1, likely a result of enhanced JNK activation. To directly determine whether S649 is modified in vivo, we generated phospho-specific Abs recognizing phospho-S649, and phospho-S657 as a positive control. Although phospho-S657 peaked and declined rapidly after Ag receptor stimulation, phospho-S649 occurred later and was maintained for a significantly longer period poststimulation in both B and T cells. Interestingly, phospho-S657 was completely abolished in PKCβ-deficient B cells, whereas delayed phosphorylation at S649 was partially intact and depended, in part, upon novel PKC activity. Thus, distinct PKC-mediated CARMA1 phosphorylation events exert opposing effects on the activation status of CARMA1. We propose that early phosphorylation events at S657 and S564 promote the initial assembly of the CARMA1 signalosome, whereas later phosphorylation at S649 triggers CARMA1 down-regulation.
Neutrophils Ameliorate Lung Injury and the Development of Severe Disease during Influenza Infection
Authors: Tate Michelle D. , Deng Yi-Mo , Jones Jessica E. , Anderson Gary P. , Brooks Andrew G. , Reading Patrick C. 
Published: November 2009

Abstract
The clinical response to influenza infection ranges from mild disease to severe pneumonia and it remains unclear whether the inflammatory response to infection is protective or pathogenic. We have defined a novel role for neutrophils in ameliorating lung injury during influenza infection, thereby limiting development of severe disease. Infection of neutrophil-depleted mice with influenza virus HKx31 (H3N2) led to rapid weight loss, pneumonia, and death. Neutropenia was associated with enhanced virus replication in the respiratory tract; however, viral titers were declining at the time of death, leading us to investigate other factors contributing to mortality. In addition to thymic atrophy, lymphopenia, and viremic spread, depletion of neutrophils led to exacerbated pulmonary inflammation, edema, and respiratory dysfunction. Thus, while it is well established that neutrophils contribute to lung injury in a range of pathological conditions, reduced numbers or impaired neutrophil function can facilitate progression of mild influenza to severe clinical disease.
TGFβ Neutralization within Cardiac Allografts by Decorin Gene Transfer Attenuates Chronic Rejection
Authors: Faust Susan M. , Lu Guanyi , Wood Sherri C. , Bishop D. Keith 
Published: November 2009

Abstract
Chronic allograft rejection (CR) is the leading cause of late graft failure following organ transplantation. CR is a progressive disease, characterized by deteriorating graft function, interstitial fibrosis, cardiac hypertrophy, and occlusive neointima development. TGFβ, known for its immunosuppressive qualities, plays a beneficial role in the transplant setting by maintaining alloreactive T cells in a hyporesponsive state, but has also been implicated in promoting graft fibrosis and CR. In the mouse vascularized cardiac allograft model, transient depletion of CD4+ cells promotes graft survival but leads to CR, which is associated with intragraft TGFβ expression. Decorin, an extracellular matrix protein, inhibits both TGFβ bioactivity and gene expression. In this study, gene transfer of decorin into cardiac allografts was used to assess the impact of intragraft TGFβ neutralization on CR, systemic donor-reactive T cell responses, and allograft acceptance. Decorin gene transfer and neutralization of TGFβ in cardiac allografts significantly attenuated interstitial fibrosis, cardiac hypertrophy, and improved graft function, but did not result in systemic donor-reactive T cell responses. Thus, donor-reactive T and B cells remained in a hyporesponsive state. These findings indicate that neutralizing intragraft TGFβ inhibits the cytokine’s fibrotic activities, but does not reverse its beneficial systemic immunosuppressive qualities.
Tyrosine Kinase 2 Plays Critical Roles in the Pathogenic CD4 T Cell Responses for the Development of Experimental Autoimmune Encephalomyelitis
Authors: Oyamada Akiko , Ikebe Hiori , Itsumi Momoe , Saiwai Hirokazu , Okada Seiji , Shimoda Kazuya , Iwakura Yoichiro , Nakayama Keiichi I. , Iwamoto Yukihide , Yoshikai Yasunobu , Yamada Hisakata 
Published: November 2009

AbstractTyrosine kinase 2 (Tyk2), a member of the JAK family, is involved in IL-12- and IL-23-mediated signaling. In the present study, we examined the roles of Tyk2 in the development of myelin oligodendrocyte glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE) by using Tyk2 knockout (KO) mice. In vitro differentiation of Th1 but not Th17 cells was severely impaired in Tyk2 KO CD4 T cells, although Tyk2 KO Th17 cells did not respond to IL-23. Tyk2 KO mice showed complete resistance against EAE with no infiltration of CD4 T cells in the spinal cord. Surprisingly, the number of MOG-specific Th17 cells in the periphery was comparable between KO and wild-type (WT) mice, whereas Th1 cells were greatly reduced in Tyk2 KO mice. Adoptive transfer of MOG-primed WT T cells induced EAE in Tyk2 KO recipients, indicating that Tyk2 in the environment was dispensable for the infiltration of effector T cells into the spinal cord. A reduced but significant number of Tyk2 KO T cells were detected in the spinal cord of mice with EAE, which had been reconstituted with bone marrow cells of WT and KO mice. Furthermore, MOG-immunized Tyk2 KO mice developed EAE after adoptive transfer of MOG-primed WT Th1 cells, which might trigger local inflammation that recruits Th17 cells. Taken together, these results indicate that Tyk2 is critically involved in the pathogenic CD4 T cell responses and thus could be a target molecule for the treatment of autoimmune diseases.
Immune Gene and Cell Enrichment Is Associated with a Good Prognosis in Ependymoma
Authors: Donson Andrew M. , Birks Diane K. , Barton Valerie N. , Wei Qi , Kleinschmidt-DeMasters Bette K. , Handler Michael H. , Waziri Allen E. , Wang Michael , Foreman Nicholas K. 
Published: November 2009

Abstract
Approximately 50% of children with ependymoma will suffer from tumor recurrences that will ultimately lead to death. Development of more effective therapies and patient stratification in ependymoma mandates better prognostication. In this study, tumor gene expression microarray profiles from pediatric ependymoma clinical samples were subject to ontological analyses to identify outcome-associated biological factors. Histology was subsequently used to evaluate the results of ontological analyses. Ontology analyses revealed that genes associated with nonrecurrent ependymoma were predominantly immune function-related. Additionally, increased expression of immune-related genes was correlated with longer time to progression in recurrent ependymoma. Of those genes associated with both the nonrecurrent phenotype and that positively correlated with time to progression, 95% were associated with immune function. Histological analysis of a subset of these immune function genes revealed that their expression was restricted to a subpopulation of tumor-infiltrating cells. Analysis of tumor-infiltrating immune cells showed increased infiltration of CD4+ T cells in the nonrecurrent ependymomas. No genomic sequences for SV40, BK, JC, or Merkel polyomaviruses were found in nonrecurrent ependymoma. This study reveals that up-regulation of immune function genes is the predominant ontology associated with a good prognosis in ependymoma and it provides preliminary evidence of a beneficial host proinflammatory and/or Ag-specific immune response.
Vision-Language Models for Feature Detection of Macular Diseases on Optical Coherence Tomography
Authors: Antaki Fares , Chopra Reena , Keane Pearse A. 
Published: May 2024

ImportanceVision-language models (VLMs) are a novel artificial intelligence technology capable of processing image and text inputs. While demonstrating strong generalist capabilities, their performance in ophthalmology has not been extensively studied.ObjectiveTo assess the performance of the Gemini Pro VLM in expert-level tasks for macular diseases from optical coherence tomography (OCT) scans.Design, Setting, and ParticipantsThis was a cross-sectional diagnostic accuracy study evaluating a generalist VLM on ophthalmology-specific tasks using the open-source Optical Coherence Tomography Image Database. The dataset included OCT B-scans from 50 unique patients: healthy individuals and those with macular hole, diabetic macular edema, central serous chorioretinopathy, and age-related macular degeneration. Each OCT scan was labeled for 10 key pathological features, referral recommendations, and treatments. The images were captured using a Cirrus high definition OCT machine (Carl Zeiss Meditec) at Sankara Nethralaya Eye Hospital, Chennai, India, and the dataset was published in December 2018. Image acquisition dates were not specified.ExposuresGemini Pro, using a standard prompt to extract structured responses on December 15, 2023.Main Outcomes and MeasuresThe primary outcome was model responses compared against expert labels, calculating F1 scores for each pathological feature. Secondary outcomes included accuracy in diagnosis, referral urgency, and treatment recommendation. The model’s internal concordance was evaluated by measuring the alignment between referral and treatment recommendations, independent of diagnostic accuracy.ResultsThe mean F1 score was 10.7% (95% CI, 2.4-19.2). Measurable F1 scores were obtained for macular hole (36.4%; 95% CI, 0-71.4), pigment epithelial detachment (26.1%; 95% CI, 0-46.2), subretinal hyperreflective material (24.0%; 95% CI, 0-45.2), and subretinal fluid (20.0%; 95% CI, 0-45.5). A correct diagnosis was achieved in 17 of 50 cases (34%; 95% CI, 22-48). Referral recommendations varied: 28 of 50 were correct (56%; 95% CI, 42-70), 10 of 50 were overcautious (20%; 95% CI, 10-32), and 12 of 50 were undercautious (24%; 95% CI, 12-36). Referral and treatment concordance were very high, with 48 of 50 (96%; 95 % CI, 90-100) and 48 of 49 (98%; 95% CI, 94-100) correct answers, respectively.Conclusions and RelevanceIn this study, a generalist VLM demonstrated limited vision capabilities for feature detection and management of macular disease. However, it showed low self-contradiction, suggesting strong language capabilities. As VLMs continue to improve, validating their performance on large benchmarking datasets will help ascertain their potential in ophthalmology.