bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concept maps as a dynamic tool for teaching scientific thinking
Authors: Thompson Scott Beckett , Pugh-Bernard Aimee 
Published: January 2023

Abstract
Scientific thinking often involves understanding interrelated and multidimensional topics. We have employed the concept map as an active learning method for teaching a diversity of concepts in an undergraduate scientific thinking course. Here we describe our implementation of concept maps and how it can be used as tool for instruction, assessment and team building. A concept map is a diagram used to organize ideas and depict their relationships, typically constructed of information presented in boxes with labeled lines drawn between them to indicate connections. In our educational implementation, students write key concepts from assigned reading onto sticky notes and work in small groups using these notes and dry-erase markers to create a concept map on a white board. The modular nature of this approach enables students to dynamically edit and rearrange concepts both during the initial construction and throughout a class period to incorporate new ideas. Students have created concept maps on topics including the scientific method, the diagnostic process for physicians and scientific research articles. When students have disagreements on ideas, the collaborative and flexible nature of these concept maps enable a constructive resolution and the addition of alternative thoughts and ideas. Additionally, throughout the semester the sophistication of the concept maps evolves thus serving as qualitative assessment of student growth. Concept mapping enables students to collaboratively work towards understanding scientific ideas and to think critically about the relationships between them. Visualization of how students organize knowledge facilitates the assessment of student growth and the diversity of understanding within a class.
Appropriate Contextualisation of Immunology based STEM and Health teaching for undergraduate Medical Sciences Education
Authors: Sika-Paotonu Dianne , Chandra Pratik , De Silva Hashini , Hermann Zsófia , Lowry Fionnuala , Papalii Sophie , Rajakumaran Priyanka , Simpson Emma , Walton Michaela , Mitchell Maxine 
Published: January 2023

Abstract
Clinically relevant examples are needed to support knowledge application of Immunology teaching content within undergraduate Medical Sciences Education frameworks. The appropriate contextualisation of these Immunology teaching examples is essential, particularly when presenting health related issues that are of significance and relevance to Māori and Pacific population groups living in New Zealand (NZ) and the Pacific Region. Acute Rheumatic Fever (ARF) is an autoimmune condition that results from untreated Group A Streptococcal (GAS) infection of the throat (and skin). Repeated or severe episodes of ARF that remain untreated can lead to Rheumatic Heart Disease (RHD) or permanent heart damage. Māori, Pacific and Indigenous Aboriginal population groups are affected disproportionately by ARF and RHD. This work involved Immunologically related ARF and RHD teaching examples were presented to 4th year undergraduate Medical Science Education students that were contextualized, and relevant to current health priorities for Māori and Pacific population groups. Sound understanding was demonstrated by students participating in these classes. Strong interest in Immunologically related ARF/RHD research and teaching examples with positive feedback expressed by students within written and verbal teaching feedback platforms. A subset of students were motivated to undertake research placements to contribute to the NZ based ARF and RHD related Penicillin reformulation work. Overall, the contextualisation of the Immunologically related ARF/RHD research and teaching examples supported knowledge application and helped raise awareness of health issues for Māori and Pacific population groups living in NZ and the Pacific Region.
Graduate training in T cell immunotherapy and CAR-T cell therapy
Authors: Sterner Rosalie , Hedin Karen E. , Hayden Richard E. , Nowakowski Grzegorz S. , Wyles Saranya P. , Greenberg-Worisek Alexandra J. , Terzic Andre , Kenderian Saad S. 
Published: January 2023

Abstract
The objective was to evaluate the impact of an interdisciplinary graduate level course on students’ knowledge and interests in immunotherapy and CAR-T cell therapy. It was a one week course conducted in November 2018. Students were surveyed before and after the course. The survey included questions regarding background, self-perceived knowledge/confidence in skills, and interests/predicted behaviors. Students were assigned to work in interdisciplinary teams to develop a research proposal. A total of 25 students taking the course for graduate level credit were surveyed. Of these, all 25 (100%) completed the surveys. Students came from variable backgrounds and were at different stages of graduate training. After completion of the course, there was a statistically significant increase in self-perceived knowledge of immunotherapy (mean±standard deviation score of 3.6±0.9 post-course vs 2.6±1.0 pre-course, on a 5 point Likert scale, P&lt;0.001), knowledge of the benchtop research to clinic translational process (3.7±0.8 post-course vs 3.0±0.9 pre-course, P&lt;0.001), confidence in critical reading skills (4.3±0.6 post-course vs 4.0±0.5 pre-course, P=0.008), confidence in immunotherapy focused grant writing skills (3.6±0.9 post-course vs 2.8±1.1 pre-course, P&lt;0.001), interest in working in interdisciplinary teams (4.8±0.4 post-course vs 4.6±0.6 pre-course, P=0.02), and interest in attending immunotherapy educational events (3.5±1.3 post-course vs 3.2±1.3 pre-course, P≤0.05). In conclusion, this course helps trainees to build knowledge and interest in the fields of immunotherapy and CAR-T cell therapy and can potentially serve as a platform for future educational courses in interdisciplinary, translational research.
Bridging statistics and life sciences education for immunologists: Exploring a significantly impactful collaboration
Authors: Singh Jastaranpreet , White Bethany , Tong Lilin 
Published: January 2023

Abstract
Statistical tests and graphs are an important part of any immunological research publication or presentation. However, not all immunologists have the statistical expertise to choose the best methods to evaluate and represent their experiments, and the formal statistics training required by undergraduate immunology curricula is often quite limited. How can we prepare future immunologists for statistical practice in research? As a collaborative effort between the Department of Statistical Sciences and the Human Biology Program at the University of Toronto, a second-year undergraduate course was developed to integrate statistics instruction with research design to improve the quantitative training of life sciences students. In a Scholarship of Teaching and Learning (SoTL) study conducted within the course, student attitudes and self-efficacies for statistics, as well as their abilities to recognize and handle problems related to statistical practice in life sciences research, were assessed through surveys administered at the beginning and end of the course (n=126). Here, we present our team-teaching model and strategies for promoting meaningful connections between statistics and life sciences research through course design, activities and assessments. We also highlight results from our SoTL study, which revealed that 77% of students felt more confident about choosing the correct statistical procedure, while 74% indicated that the course helped increase their confidence with respect to results interpretation. We hope that insights from this teaching partnership and our SoTL findings will help inform future course offerings to better prepare our students to effectively engage with statistics in immunological research.
Citrullination modulates MHC class II antigen processing and presentation by revealing cryptic epitopes
Authors: Curran Ashley M , Jang Yura , Thomas Mekha A , Girgis Alexander A , Crawford Jonathan D , O’Meally Robert N , Cole Robert N , Na Chan Hyun , Darrah Erika 
Published: January 2023

Abstract
Cryptic peptides, hidden from the immune system under physiologic conditions, are revealed by changes to MHC class II processing and can facilitate loss of tolerance to self-antigens. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by immune responses to citrullinated self-antigens, in which arginine residues are converted to citrullines; however, the initiating events in RA remain poorly understood. We investigated the hypothesis that citrullination exposes cryptic epitopes by modifying protein structure and proteolysis in a manner sufficient to activate a previously ignorant repertoire of self-reactive T cells. We first utilized in vitro proteolytic mapping to define the effect of citrullination on four well-defined RA autoantigens-. We then used a natural antigen processing assay to elucidate the molecular mechanisms of citrullination-modulated processing and evaluated autoantigen-specific T cell responses against the unique peptide repertoire. We show that citrullination alters MHC class II processing and presentation of RA autoantigens, resulting in the destruction of dominant epitopes and the generation and presentation of cryptic epitopes, composed primarily of native peptide sequences. The citrullination-dependent repertoire stimulates T cells from RA patients with anti-citrullinated protein antibodies more robustly than the native repertoire and control T cells. The generation of this unique repertoire is achieved through altered protease affinity and protein destabilization, rather than direct presentation of citrulline-containing epitopes, suggesting a novel paradigm for the role of protein citrullination in the breach of immune tolerance in RA.
Supported by a grant from the Rheumatology Research Foundation and by the Luke Evnin and Deann Wright Fellowship
Aquaporin 4 Is A Mediator Of Essential Dendritic Cell Function
Authors: Nicosia Michael , Beavers Ashley , Yamamoto Yosuke , Thompson Trevor , Zindrick Thomas , Valujskikh Anna 
Published: January 2023

Abstract
Aquaporins are transmembrane water channels implicated in a range of physiologic functions. We previously reported that Aquaporin 4 (AQP4) is expressed by T cells and treatment with a small molecule AQP4 inhibitor (AER-270) significantly delays T cell mediated mouse heart allograft rejection. Our findings did not exclude a role for antigen presenting cells (APCs), and the purpose of this study is to investigate the requirement for AQP4 in dendritic cell (DC) functions.
Stimulation with AQP4−/− spleen APCs with the addition of antigenic peptide, resulted in reduced frequencies of IFNγ producing MAR T cells compared to WT APCs. We confirmed that splenic DCs express AQP4. Bone marrow derived dendritic cells (BMDCs) from WT and AQP4−/− mice were stimulated with LPS or protein antigen, the absence or inhibition of AQP4 resulted in no defects in up-regulation of maturation markers following stimulation. WT and AQP4−/− BMDCs were pulsed with Lucifer Yellow, FITC-dextran and OVA-AF647 to assess antigen uptake with no observable defect after AQP4 inhibition or in AQP4−/− BMDCs. However, AQP4−/− BMDCs pulsed with OVA protein had reduced expression of SIINFEKL peptide-MHC-I complexes. In contrast, when pulsed with OVA-derived SIINFEKL peptide, AER-270 treated WT BMDCs or AQP4−/− BMDCs showed no change in peptide-MHC complex expression suggesting a role for AQP4 in antigen processing. Consistent with this, the absence or inhibition of AQP4 resulted in decreased DQ-OVA signal, indicating that AQP4 is required for the antigen loading into the lysosome.
Our data indicate that AQP4 plays a critical role in the processing of antigens by dendritic cells that impacts their ability to prime T cells, and can be therapeutically targeted in a transplant setting.
Supported by grants from NIH (R56AI152368-01)
Dynamic features of tapasin as revealed by structures of two tapasin/Fab complexes
Authors: Taylor Daniel Kyle , Jiang Jiansheng , Boyd Lisa F , Cresswell Peter , Mage Michael G , Margulies David H , Natarajan Kannan 
Published: January 2023

Abstract
Intracellular loading of major histocompatibility complex class I (MHC-I) molecules occurs within the peptide loading complex and is accomplished through the concerted action of several proteins, including the chaperone/catalyst tapasin. In the absence of tapasin, peptide loading is compromised, resulting in decreased cell surface expression of some, though not all, MHC-I allelomorphs. To gain a mechanistic understanding of tapasin’s function we have produced recombinant Fab fragments of two anti-tapasin antibodies, PaSta1 and PaSta2, and investigated their binding to human recombinant soluble tapasin by surface plasmon resonance methods and X-ray crystallography. Both antibody Fabs bind with nanomolar affinities characterized by slow off rates. PaSta1 and PaSta2 recognize distinct epitopes as tapasin captured on a surface immobilized with one PaSta Fab binds the other PaSta Fab with nanomolar affinity. However, tapasin captured on a PaSta2 Fab surface is not able to bind peptide/HLA-B*44:05/beta-2 microglobulin complexes while tapasin captured on a PaSta1 Fab surface can, indicating that PaSta2 sterically competes for the MHC-I binding site. This finding was echoed in the structural characterization of PaSta Fab-tapasin complexes by X-ray crystallography. PaSta1 binds to an extended N-terminal region of tapasin, a site accessible even in the tapasin/ERp57 complex. By contrast, PaSta2 binds at the junction of the N-terminal and C-terminal domains of tapasin, where tapasin may interact with HLA-I molecules. Comparison of conformations of tapasin in complex with PaSta1, PaSta2, HLA-B*44:05, and ERp57 reveals the dynamic nature of tapasin, a versatile chaperone and catalyst.
Supported by the intramural research program of the NIAID, NIH
Autophagy in antigen presenting cells enhances the adjuvant effect by promoting antigen processing.
Authors: Hashimoto Kahoko , Ootomo Takuya , Sonobe Tsubasa , Kurosaki Naoko , Hasegawa Akihiro , Nakayama Toshinori 
Published: January 2023

Abstract
Previously, we proposed that LPS or IFNγ treated DC and macrophage induced cell proliferation, cytokine production, antigen presentation and autophagy function were detected. Among DC subset, CD8 positive DC enhances autophagy function with cross presentation but the similar effect was not shown in macrophages. To understand the difference, we studied that how DC are enhanced antigens processing through ubiquitin proteasome pathway, as well as autophagy pathway. Three different types of DC in vitro cultured mice DC with GM-CSF, DC with GM-CSF and IL-4, or GM-CSF and IL-15 were prepared, these DCs or macrophages were stimulated by using LPS or IFNg before antigen uptake. GM-CSF induced DC or GM-CSF and IL-15 induced DC showed enhanced antigen processing with active autophagy function, however GM-CSF and IL-4 induced DC showed active antigen presenting within 60 min, still autophagy function was not detected. Contrary to active antigen processing, GM-CSF and IL-4 - DC did not show inducible effect after adjuvant treatment, but GM-CSF or GM-CSF and IL-15-DC increased autophagy function after adjuvant treatment that was assessed by using fluorescent labeled phagosome or lysosome function analysis. Additionally, we investigated gene expression pattern related to autophagy such as ATG5 or ATG18 by q-PCR, and western blotting. Cultured DC with GM-CSF and IL-15 indicated prominent active autophagy related gene expression pattern. To induce more effective immune response on vaccination or immune therapy, effect of adjuvant treatment for autophagy function in DC and macrophage are required.
MATERNAL AUTOANTIBODIES AS A POSSIBLE ASD-RISK BIOMARKER
Authors: Celis Nora Alexandra Ramirez , Van de Water Judy A 
Published: January 2023

Abstract
Maternal autoantibody-related ASD (MAR ASD) is a subtype of autism in which pathogenic maternal autoantibodies (IgG) can cross the placenta, access the developing brain, and cause neurodevelopmental alterations and behaviors associated with autism in the exposed offspring. We previously reported maternal IgG response to eight proteins (CRMP1, CRMP2, GDA LDHA, LDHB, NSE, STIP1, and YBOX) and that reactivity two or more specific proteins (MAR ASD patterns) can be used to predict ASD risk in a discovery study.

Objective
In the current study, we aimed to validate the previously described MAR ASD patterns (CRMP1+GDA, CRMP1+CRMP2, NSE+STIP1, CRMP2+STIP1, LDHA+YBOX, LDHB+YBOX, GDA+YBOX, STIP1+YBOX, and CRMP1+STIP1) and their accuracy to predict ASD risk in a prospective cohort.

Methods
We used plasma from mothers of autistic children (ASD= 540) and general population controls (not verified as typically developing) (GP=420) collected by the Early Markers of Autism (EMA) study. We evaluated maternal IgG reactivity against each of the eight fetal brain proteins by ELISA and used Fisher Exact Test (p &lt; 0.05) to compare the association for each pattern with child outcome (ASD vs GP).

Results
We found reactivity to at least one protein in more than 50% of the samples in the case and control groups, suggesting that reactivity to a single antigen is not diagnosis-specific. However, when we tested the nine previously identified MAR ASD patterns, we found highly-specific reactivity in 10% ASD group vs 1% of the GP controls and increased the odds for an ASD outcome nearly 8-fold (p&lt; 0.001, OR 7.81, 95% CI from 3.32 to 22.43) demonstrating that the MAR ASD patterns are highly specific for the case group and could be used to assess ASD risk prior to symptoms.
Supported by EPA2P01ES011269-11, 83543201, R01ES015359, NICHD funded IDDRC P50 (P50HD103526), CONACYT-UC MEXUS Doctoral Fellowships 2015.
Autoantigen specific T-cell receptor induces organ-specific autoimmunity by escaping T cell negative selection
Authors: Yin Mianmian , Smith Jennifer A , Chou Marissa , Chan Jackie , Hu Yongmei , Lowell Clifford A , Gould Douglas B , Anderson Mark S , DeFranco Anthony L 
Published: January 2023

Abstract
Previously we reported a new model of spontaneous autoimmune uveitis in which mice with a hypomorphic mutation of Aire (AireGW/+) are combined with deletion of Lyn. The key autoantigen in this model is interphotoreceptor retinoid-binding protein (IRBP) as AireGW/+ Lyn−/− IRBP−/− mice failed to develop uveitis. We performed single-cell RNA-seq with TCR sequencing for IRBP 271–290 (P2)-specific CD4+ T cells from eye-draining lymph nodes (LN) of these mice with and without uveitis. Both mice showed an expansion of these T cells in eye-draining LNs, but it was greater in mice with disease. A remarkable clonal diversity of TCRs was seen. Expansions of particular T cell clonotypes were more evident in LN of mice with disease, and even greater in the retinas of mice with disease. We reconstituted several P2–specific TCR clonotypes in a T cell hybridoma line and verified their specificity. One of the TCRs was expressed in thymocytes by retroviral transduction of bone marrow stem cells from Rag2−/− mice and transplanted into WT or AireGW/+ recipient mice. Remarkably, the small residual expression of IRBP in the thymus of AireGW/+ mice was sufficient to induce substantial negative selection of thymocytes with this TCR. In addition, we generated TCR transgenic mice with this TCR clonotype. The TCR transgenic mice spontaneously developed uveitis with expansion of P2-specific CD4+ T cells. Combined with AireGW/+ or IRBP−/−, there were more P2-specific CD4+ T cells in the thymus of TCR transgenic mice. Thus, suboptimal Aire function in AireGW/+ Lyn−/− mice results in a partial defect in negative selection of T cells recognizing IRBP in the thymus, promoting development of uveitis. This disease is accelerated in mice expressing a TCR transgene recognizing IRBP.
Supported by AI138479
Type III interferon enhances thymic B cell licensing
Authors: Martinez Ryan J , Breed Elise , Worota Yosan , Ashby Katherine , Qian Lily , Hogquist Kristin Ann 
Published: January 2023

Abstract
The activation of thymic B cells is critical for their licensing as antigen presenting cells and resulting ability to mediate central immune tolerance. The processes leading to thymic B cell licensing are still not fully understood. By comparing thymic B cells to activated Peyer’s Patch B cells at steady state, we found that thymic B cell activation starts during the neonatal period and is characterized by immunoglobulin class switch recombination (CSR) without germinal center B cell phenotypes or structures. Transcriptional profiling supported the finding of extrafollicular activation of thymic B cells, but also demonstrated a strong interferon signature distinct from peripheral B cell activation. Removal of type I, II and III IFN receptors revealed thymic B cell activation and CSR were partially dependent on type III IFN signaling, while type I and II IFN signaling showed minimal contribution. Loss of type III IFN signaling in thymic B cells resulted in reduced licensing and alterations in self-antigen presentation. Together, these findings reveal the importance of type III IFN in generating tolerogenic thymic B cells and suggests inflammation in the thymus has a significant impact on the generation of central immune tolerance to B cell self-antigens.
The impact of pulmonary fibrosis on neutrophil aging and trafficking
Authors: Warheit-Niemi Helen I , Moore Bethany B 
Published: January 2023

Abstract
Neutrophil aging is the process through which neutrophils released from the bone marrow into circulation acquire specific phenotypic and functional changes over time. After neutrophils age in circulation, they return to the bone marrow or other organs for clearance. Aged neutrophils are highly proinflammatory and can potentially contribute to tissue injury if their return to and clearance within the bone marrow is dysregulated. We have found that the development of pulmonary fibrosis in mice is associated with decreased numbers of aged neutrophils within the bone marrow compared to non-fibrotic mice 21 days after induction of fibrosis, indicating that neutrophils are not returning to the bone marrow for clearance after aging in circulation. Indeed, we observed a corresponding increase in the numbers of aged neutrophils in peripheral blood and bronchioalveolar fluid (BALF) of fibrotic mice compared to non-fibrotic mice, supporting the idea that pulmonary fibrosis prevents neutrophil migration back to the bone marrow after aging. Pulmonary fibrosis is a disease characterized by aberrant wound healing and lung and vascular injury. In accordance with this, we have observed increased levels of extracellular DNA and neutrophil elastase in plasma and BALF of mice 21 days after induction of fibrosis. These products are released in high levels by aged neutrophils during the formation of neutrophil extracellular traps, suggesting that aberrant aged neutrophil behavior may contribute to lung and vascular injury in pulmonary fibrosis. Our study seeks to understand the role of neutrophils in fibrotic disease progression by evaluating how fibrosis may alter the trafficking of aged, highly proinflammatory neutrophils.
Supported by grants from NIH (R35 HL144481, F31 HL152509) and the Scleroderma Foundation (Arnold Postlethwaite, M.D. Memorial Pre-Doctoral Summer Fellowship Award)