Did the students' satisfaction rates at Avalon University School of Medicine correlate with the occurrence of accreditation site visits?

INTRODUCTION: Accreditation of medical education programs can be observed from different perspectives. Regulatory/accreditation agencies consider it vital to assure a certain level of quality. Other stakeholders may perceive the accreditation process as a negative experience, draining resources, and efforts. Although accreditation may improve the program's governance and administration, its direct or indirect impact on students must be further investigated. This study explores the relationship between the occurrence of accreditation site visits and student satisfaction rates at Avalon University School of Medicine. METHODS: A comparison study was conducted with retrospective satisfaction data from two accreditation cycles at AUSOM. We used the Caribbean Accreditation Authority for Education in Medicine and Other Health Professions (CAAM-HP) student surveys for data collection, and data from 2017, 2019, and 2022 were used. The response rate was 70% (n = 71), 72% (n = 47), and 60% (n = 56) for basic science students and 80% (n = 111), 82% (n = 115), and 70% (n = 76) for clinical students in 2017, 2019, and 2022, respectively. The survey for basic sciences students included 37 questions/items, and the survey for clinical students included 39 questions/items. The responses for the questionnaire were on the five-point Likert scale. The retrospective data were evaluated using the unpaired Wilcoxon-rank sum test. RESULTS: The ratings for the basic science students' survey increased from 2017 to 2019 (first accreditation cycle) only for 11 items/questions and they were increased from 2019 to 2022 for all items/questions. The ratings for clinical science students' surveys increased from 2017 to 2019 (the first accreditation cycle) for all items/questions with a statistically significant p-value. They increased for 28 questions/items from 2019 to 2022, and two items (availability and adequacy of career counseling) showed statistically significant p-values. CONCLUSIONS: The pre-accreditation preparation and the self-evaluation process while correcting the program's deficiencies are essential triggers for the quality improvement process associated with accreditation.

B-Cell Responses in Chronic Chagas Disease: Waning of Trypanosoma cruzi-Specific Antibody-Secreting Cells Following Successful Etiological Treatment.

BACKGROUND: A drawback in the treatment of chronic Chagas disease (American trypanosomiasis) is the long time required to achieve complete loss of serological reactivity, the standard for determining treatment efficacy. METHODS: Antibody-secreting cells and memory B cells specific for Trypanosoma cruzi and their degree of differentiation were evaluated in adult and pediatric study participants with chronic Chagas disease before and after etiological treatment. RESULTS: T. cruzi-specific antibody-secreting cells disappeared from the circulation in benznidazole or nifurtimox-treated participants with declining parasite-specific antibody levels after treatment, whereas B cells in most participants with unaltered antibody levels were low before treatment and did not change after treatment. The timing of the decay in parasite-specific antibody-secreting B cells was similar to that in parasite-specific antibodies, as measured by a Luminex-based assay, but preceded the decay in antibody levels detected by conventional serology. The phenotype of total B cells returned to a noninfection profile after successful treatment. CONCLUSIONS: T. cruzi-specific antibodies in the circulation of chronically T. cruzi-infected study participants likely derive from both antigen-driven plasmablasts, which disappear after successful treatment, and long-lived plasma cells, which persist and account for the low frequency and long course to complete seronegative conversion in successfully treated participants.

Depot buprenorphine as an opioid agonist therapy in New South Wales correctional centres: a costing model.

BACKGROUND: In 2019 daily liquid methadone and sublingual buprenorphine-naloxone were primary opioid agonist treatments for correctional centres in New South Wales, Australia. However, both had significant potential for diversion to other patients, and their daily administration was resource intensive. An alternative treatment in the form of subcutaneous depot buprenorphine became a viable option following a safety trial in 2020 - the UNLOC-T study. Depot preparation demonstrated advantages over current treatments as more difficult to divert and requiring fewer administrations. This paper reports the results of economic modelling of staffing costs in medication administration comparing depot buprenorphine, methadone, and sublingual buprenorphine provision in UNLOC-T trial facilities. METHODS: The costing study adopted a micro-costing approach involving the synthesis of cost data from the UNLOC-T clinical trial as well as data collected from Justice Health and Forensic Mental Health Network records. Labour and materials data were collected during site observations and interviews. Costs were calculated from two payer perspectives: a) the New South Wales (state) government which funds custodial and health services; and b) the Australian Commonwealth government, which pays for medications. The analysis compared the monthly-per-patient cost for each of the three medications in trial-site facilities during July 2019. This was followed by simulation of depot buprenorphine implementation across the study population. Costs associated with medical assessment and reviews were excluded. RESULTS: The monthly-per-patient New South Wales government service costs of depot buprenorphine, methadone and sublingual buprenorphine were: $151, $379 and $1,529 respectively while Commonwealth government medication costs were $434, $80 and $525. The implementation simulation found that service costs of depot buprenorphine declined as patients transitioned from weekly to monthly administration. Costs of treatment using the other medications increased as patient numbers decreased alongside fixed costs. At 12 months, monthly-per-patient service costs for depot buprenorphine, methadone and sublingual buprenorphine-which would be completely phased out by month 13-were $92, $530 and $2,162 respectively. CONCLUSIONS: Depot buprenorphine was consistently the least costly of the treatment options. Future modelling could allow for dynamic patient populations and downstream impacts for participants and the state health system. TRIAL REGISTRATION: ACTRN12618000942257 . Registered 4 June 2018.

Evaluating cost-effectiveness in the management of neuroendocrine neoplasms.

The rapid evolution of novel, costly therapies for neuroendocrine neoplasia (NEN) warrants formal high-quality cost-effectiveness evaluation. Costs of individual investigations and therapies are high; and examples are presented. We aimed to review the last ten years of standalone health economic evaluations in NEN. Comparing to published standards, EMBASE, Cochrane library, Database of Abstracts of Reviews of Effects (DARE), NHS Economic Evaluation Database and the Health Technology Assessment (HTA) Database were searched for health economic evaluations (HEEs) in NEN published between 2010 and October 2019. Of 12 economic evaluations, 11 considered exclusively pharmacological treatment (3 studies of SSAs, 7 studies of sunitinib, everolimus and/or 177Lu-DOTATATE and 1 study of telotristat ethyl) and 1 compared surgery with intraarterial therapy. 7 studies of pharmacological treatment had placebo or best supportive care as the only comparator. There remains a paucity of economic evaluations in NEN with the majority industry funded. Most HEEs reviewed did not meet published health economic criteria used to assess quality. Lack of cost data collected from patient populations remains a significant factor in HEEs where clinical expert opinion is still often substituted. Further research utilizing high-quality effectiveness data and rigorous applied health economic analysis is needed.

Non-isocyanate Polyurethanes from 1,1'-Carbonyldiimidazole: A Polycondensation Approach.

1,1'-Carbonyldiimidazole (CDI) provides a platform to generate high molecular weight polyurethanes from industrially relevant diols and diamines. CDI, which is described in the literature for its use in amidation and functionalization reactions, enables the production of well-defined and stable polyurethane precursors, thus eliminating the need for isocyanates. Herein, the functionalization of 1,4-butanediol with CDI yields an electrophilic biscarbamate, bis-carbonylimidazolide (BCI), which is suitable for further step-growth polymerization in the presence of amines. Elevated reaction temperatures enable the solvent-, catalyst-, and isocyanate-free polycondensation reaction between the BCI monomer and various diamines. The thermoplastic polyurethanes produced from this reaction demonstrate high thermal stability, tunable glass transition temperatures based on incorporation of flexible polyether segments, and mechanically ductile thin films. CDI functionalized diols will allow the preparation of diverse polyurethanes without the use of isocyanate-containing monomers.

Physics-informed machine learning: case studies for weather and climate modelling.

Machine learning (ML) provides novel and powerful ways of accurately and efficiently recognizing complex patterns, emulating nonlinear dynamics, and predicting the spatio-temporal evolution of weather and climate processes. Off-the-shelf ML models, however, do not necessarily obey the fundamental governing laws of physical systems, nor do they generalize well to scenarios on which they have not been trained. We survey systematic approaches to incorporating physics and domain knowledge into ML models and distill these approaches into broad categories. Through 10 case studies, we show how these approaches have been used successfully for emulating, downscaling, and forecasting weather and climate processes. The accomplishments of these studies include greater physical consistency, reduced training time, improved data efficiency, and better generalization. Finally, we synthesize the lessons learned and identify scientific, diagnostic, computational, and resource challenges for developing truly robust and reliable physics-informed ML models for weather and climate processes. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

Early-Cannulation Arteriovenous Grafts Are Safe and Effective in Avoiding Recurrent Tunneled Central Catheter Infection.

OBJECTIVES: Tunneled central venous catheter infection (TCVCi) is a common complication that often necessitates removal of the TCVC and replacement by a further TCVC. Theoretically, insertion of an early - cannulation graft (ecAVG) early after TCVC infection is possible but not widely practiced with concerns over safety and infection in the ecAVG. With 8 years of ecAVG experience, the aim of this study was to compare the outcomes following TCVC infection, comparing replacement with TCVC (TCVCr) versus immediate ecAVG (ecAVGr). DESIGN: Retrospective comparison of 2 cohorts, who underwent replacement of an infected TCVC either by an early cannulation graft (n = 18) or by a further central catheter (n = 39). METHODS: Data were abstracted from a prospectively completed electronic patient record and collected on patient demographics, TCVC insertion, duration and infection, including culture proven bacteriaemia and subsequent access interventions. RESULTS: Eighteen of 299 patients identified from 2012 to 2020 had an ecAVG implanted as treatment for a TCVCi. In a 1-year time-period (January 1, 2015-December 31, 2015) out of 222 TCVC inserted, 39 were as a replacement following a TCVCi. No patient with an ecAVGr developed an immediate infection, nor complication from the procedure. The rate of subsequent vascular access infection was significantly more frequent for those with a TCVCr than with an ecAVGr (0.6 vs. 0.1/patient/1000 HD days, P< 0.000). The number of further TCVC required was significantly higher in the TCVCr group (7.1 vs. 0.4/patient/1000 HD days, P= 0.000). CONCLUSIONS: An ecAVG early following a TCVC infection is safe, reduces the incidence of subsequent infectious complications and reduces the number of TCVC required, with a better functional patency.

From 'OPAT' to 'COpAT': implications of the OVIVA study for ambulatory management of bone and joint infection.

Bone and joint infection contributes significantly to clinical activity within outpatient parenteral antimicrobial therapy (OPAT) services. The OVIVA (oral versus intravenous antibiotics for bone and joint infection) randomized study has challenged the practice of prolonged intravenous therapy, because non-inferiority of oral antibiotic therapy was demonstrated, thereby implying that early transition to oral therapy is an appropriate alternative to prolonged intravenous therapy. We examine the caveats to the study and discuss the implications for OPAT practice, highlighting the importance of careful oral antibiotic selection with attention to bioavailability, bone penetration, drug interactions, compliance and toxicity monitoring. We emphasize that ambulatory antibiotic therapy (whether intravenous or oral) in this patient group requires expert multidisciplinary management, monitoring and follow-up, and ideally should be undertaken within existing OPAT or, more accurately, complex outpatient antibiotic therapy (COpAT) services.

Geographic variation in the use of lymphadenectomy and external-beam radiotherapy for endometrial cancer: a cross-sectional analysis of population-based data.

OBJECTIVE: To quantify geographic variation in the use of lymphadenectomy and/or external-beam radiotherapy (EBRT) for endometrial cancer in England. DESIGN: Cross-sectional analysis of population-based data. SETTING: English cancer registry data, linked to chemotherapy, radiotherapy and hospital episodes statistics data. POPULATION: Twenty-two thousand four hundred and eighty-three women with endometrial cancer presenting without clinical or radiological evidence of distant metastatic spread, diagnosed in England from 2013 to 2016. METHODS: Proportions of patients receiving lymphadenectomy and/or EBRT were compared across 19 Cancer Alliances, to identify variations in clinical practice. Two separate logistic regression models assessed the impact on variation of adjustment for tumour and patient characteristics. MAIN OUTCOME MEASURES: Receipt of lymphadenectomy, receipt of EBRT. RESULTS: There was substantial variation by Cancer Alliance in the adjusted proportion of women with endometrial cancer receiving lymphadenectomy (range 5% [95% CI 4-6%] to 48% [95% CI 45-52%]) and EBRT (range 10% [95% CI 7-12%] to 31% [95% CI 28-33%]), after adjusting for variation in pathological grade, age, comorbidities, deprivation, ethnic group and (EBRT only) FIGO stage. Different approaches to clinical practice were identified; (i) one Cancer Alliance had significantly higher than average lymphadenectomy and significantly lower than average EBRT use, (ii) three had high use of both lymphadenectomy and EBRT, (iii) one had low lymphadenectomy use and high EBRT use, and (iv) three had low use of both lymphadenectomy and EBRT. CONCLUSIONS: Lymphadenectomy is probably used to triage for EBRT when lymphadenectomy use is high and EBRT use is low. This is probably a result of variation in local endometrial cancer management guidelines, suggesting that UK recommendations should be clarified. TWEETABLE ABSTRACT: There is geographic variation in England in the use of lymphadenectomy and radiotherapy to treat endometrial cancer.

Advances in Polymeric Materials for Electromechanical Devices.

Electroactive polymers (EAP) provide lightweight and cost-effective materials that enable the next generation of electromechanical devices. Commercial polymers have historically dominated research in EAP devices due to their availability. However, several drawbacks of these materials have limited their commercial applications, necessitating new materials for the commercial success of future EAP devices. This review highlights recent advances in novel EAPs for ionic polymer-metal composites (IPMC) and dielectric elastomer actuators (DEA). Ion-containing block copolymers and charged segmented condensation polymers demonstrate suitable electromechanical properties competitive with Nafion-based IPMCs. In addition, swelling ionic polymer membranes with free ionic liquid enhances ionic conductivity and promotes electromechanical actuation. Synthetic approaches to increasing permittivity in dielectric elastomers are also explored as a method of producing more efficient DEAs. Incorporating polar functional groups into siloxane and acrylic elastomers through grafting or blending provides high-dielectric elastomers for use in DEAs with low driving voltages.

Providers' preferences for pediatric oral health information in the electronic health record: a cross-sectional survey.

BACKGROUND: The majority of primary care physicians support integration of children's oral health promotion and disease prevention into their practices but can experience challenges integrating oral health services into their workflow. Most electronic health records (EHRs) in primary care settings do not include oral health information for pediatric patients. Therefore, it is important to understand providers' preferences for oral health information within the EHR. The objectives of this study are to assess (1) the relative importance of various elements of pediatric oral health information for primary care providers to have in the EHR and (2) the extent to which practice and provider characteristics are associated with these information preferences. METHODS: We surveyed a sample of primary care physicians who conducted Medicaid well-child visits in North Carolina from August - December 2013. Using descriptive statistics, we analyzed primary care physicians' oral health information preferences relative to their information preferences for traditional preventive aspects of well-child visits. Furthermore, we analyzed associations between oral health information preferences and provider- and practice-level characteristics using an ordinary least squares regression model. RESULTS: Fewer primary care providers reported that pediatric oral health information is "very important," as compared to more traditional elements of primary care information, such as tracking immunizations. However, the majority of respondents reported some elements of oral health information as being very important. Also, we found positive associations between the percentage of well child visits in which oral health screenings and oral health referrals are performed and the reported importance of having pediatric oral health information in the EHR. CONCLUSIONS: Incorporating oral health information into the EHR may be desirable for providers, particularly those who perform oral health screenings and dental referrals.

Acquired Factor Xiii Deficiency: An Uncommon But Easily Missed Cause Of Severe Bleeding

Factor XIII (FXIII) is a plasma clotting protein involved in clot stabilization. Severe FXIII deficiency may present with severe, even fatal bleeding. Critically however, routine coagulation assays may be normal and only specific FXIII assays will detect the abnormality. Herein we discuss a case report of a patient with acquired FXIII deficiency in order to highlight the clinical challenges associated with establishing the diagnosis and discuss the treatment approach. A 70-year-old man presented with a gluteal haematoma despite no preceding personal history of bleeding. Extensive initial haemostatic investigations were normal until a specific FXIII assay showed a marked reduction in FXIII levels. With directed treatment, bleeding episodes ceased and remission was achieved. Clinical awareness of FXIII deficiency is important, so appropriate testing can be implemented in patients with unexplained bleeding diatheses, particularly those in whom bleeding responds poorly to standard replacement therapy.

A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency.

BACKGROUND: Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS: Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS: Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.

ClonEvol: clonal ordering and visualization in cancer sequencing.

BACKGROUND: Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation. MATERIALS AND METHODS: ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution. RESULTS: ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones throughout metastatic progression observed in the tumors of a published breast cancer patient. CONCLUSIONS: ClonEvol has broad applicability for longitudinal monitoring of clonal populations in tumor biopsies, or noninvasively, to guide precision medicine. AVAILABILITY: ClonEvol is written in R and is available at https://github.com/ChrisMaherLab/ClonEvol.

Production of a gonadotropin-releasing hormone 2 receptor knockdown (GNRHR2 KD) swine line.

Swine are the only livestock species that produce both the second mammalian isoform of gonadotropin-releasing hormone (GNRH2) and its receptor (GNRHR2). Previously, we reported that GNRH2 and GNRHR2 mediate LH-independent testosterone secretion from porcine testes. To further explore this ligand-receptor complex, a pig model with reduced GNRHR2 expression was developed. Small hairpin RNA sequences targeting porcine GNRHR2 were subcloned into a lentiviral-based vector, lentiviral particles were generated and microinjected into the perivitelline space of zygotes, and embryos were transferred into a recipient. One GNRHR2 knockdown (KD) female was born that subsequently produced 80 piglets from 6 litters with 46 hemizygous progeny (57% transgenic). Hemizygous GNRHR2 KD (n = 10) and littermate control (n = 7) males were monitored at 40, 100, 150, 190, 225 and 300 days of age; body weight and testis size were measured and serum was isolated and assayed for testosterone and luteinizing hormone (LH) concentrations. Body weight of GNRHR2 KD boars was not different from littermate controls (P = 0.14), but testes were smaller (P < 0.05; 331.8 vs. 374.8 cm3, respectively). Testosterone concentrations tended (P = 0.06) to be reduced in GNRHR2 KD (1.6 ng/ml) compared to littermate control (4.2 ng/ml) males, but LH levels were similar (P = 0.47). The abundance of GNRHR2 mRNA was reduced (P < 0.001) by 69% in testicular tissue from mature GNRHR2 KD (n = 5) versus littermate control (n = 4) animals. These swine represent the first genetically-engineered model to elucidate the function of GNRH2 and its receptor in mammals.

Progression of hepatitis C in the haemophiliac population in Ireland, after 30 years of infection in the pre-DAA treatment era.

INTRODUCTION: Prior to the introduction of viral inactivation of factor concentrates and screening of blood, 225 people with haemophilia became infected with hepatitis C (HCV) in Ireland. AIM: Our aim was to assess liver disease progression and mortality in this population after 30 years of infection. METHODS: Demographic and clinical data were collected from medical records in five hepatology units and one infectious disease unit retrospectively in 2005, and on four subsequent occasions. RESULTS: The participation rate was 73% (165/225). Eighty three percent of patients, who had been tested for RNA (n = 106/128), developed chronic HCV infection. Thirty four percent were co-infected with HIV. All-cause mortality, after approximately 30 years of infection with chronic HCV, was 44% in HIV positive patients and 29% in HIV negative patients. Liver-related mortality was 12.5% and did not vary significantly by HIV status. Thirty seven percent of patients had developed advanced liver disease, including 20% with cirrhosis and 9% with hepatocellular carcinoma. In the pre-interferon-free direct acting antivirals era, 57% (n = 60/106) of patients were treated for HCV, 65% of whom achieved a sustained virological response. Successfully treated patients had few adverse liver outcomes. CONCLUSION: After 30 years of infection, 40% of the patients who had evidence of chronic HCV had developed advanced liver disease, such as cirrhosis and HCC, or had died from liver-related causes. This proportion is high relative to similar international cohorts despite good anti-HCV treatment uptake and responses.

Tunable synthetic control of soft polymeric nanoparticle morphology.

With a growing variety of nanoparticles available, research probing the influence of particle deformability, morphology, and topology on the behavior of all polymer nanocomposites is also increasing. In particular, the behavior of soft polymeric nanoparticles in polymer nanocomposites has displayed unique behavior, but their precise performance depends intimately on the internal structure and morphology of the nanoparticle. With the goal of providing guidelines to control the structure and morphology of soft polymeric nanoparticles, we have examined monomer starved semi-batch nano-emulsion polymerizations that form organic, soft nanoparticles, to correlate the precise structure of the nanoparticle to the rate of monomer addition and crosslinking density. The synthesis method produces 5-20 nm radii polystyrene nanoparticles with tunable morphologies. We report small angle neutron scattering (SANS) results that correlate synthetic conditions to the structural characteristics of soft polystyrene nanoparticles. These results show that the measured molecular weight of the nanoparticles is controlled by the monomer addition rate, the total nanoparticle radius is controlled by the excess surfactant concentration, and the crosslinking density has a direct effect on the topology of each nanoparticle. These studies thus provide pathways to control these 3 structural characteristics of the nanoparticle. This research, therefore provides a conduit to thoroughly investigate the effect of structural features of soft nanoparticles on their individual properties and those of their polymer nanocomposites.

Parvovirus B19 infection in an adult presenting with connective tissue disease-like symptoms: a report of the clinical and histological findings.

Parvovirus B19 infections in adults are usually associated with nonspecific and mild symptoms. However, cases presenting with a lupus-like syndrome have been described, leading to the hypothesis that parvovirus infection can induce connective tissue disease. Various histopathologic features of cutaneous manifestations of parvovirus have been reported, including features which overlap with those of connective tissue disease. Herein, we discuss an unusual case of Parvovirus  B19 infection in a middle-aged woman. The biopsy results showed granulomatous vasculitis and were consistent with the previously described superantigen id reaction. This case demonstrates that infectious causes should be considered in the differential diagnosis for granulomatous vasculitis and clinicopathologic correlation is required for accurate diagnosis. We also provide a review of the literature highlighting the possible role of parvovirus in induction of a connective tissue disease-like presentation.

An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data.

Expression quantitative trait loci (eQTL) studies have functionalized nucleic acid variants through the regulation of gene expression. Although most eQTL studies only examine the effects of single variants on transcription, a more complex process of variant-variant interaction (epistasis) may regulate transcription. Herein, we describe a tool called interaction QTL (iQTL) designed to efficiently detect epistatic interactions that regulate gene expression. To maximize biological relevance and minimize the computational and hypothesis testing burden, iQTL restricts interactions such that one variant is within a user-defined proximity of the transcript (cis-regulatory). We apply iQTL to a data set of 183 smallpox vaccine study participants with genome-wide association study and gene expression data from unstimulated samples and samples stimulated by inactivated vaccinia virus. While computing only 0.15% of possible interactions, we identify 11 probe sets whose expression is regulated through a variant-variant interaction. We highlight the functional epistatic interactions among apoptosis-related genes, DIABLO, TRAPPC4 and FADD, in the context of smallpox vaccination. We also use an integrative network approach to characterize these iQTL interactions in a posterior network of known prior functional interactions. iQTL is an efficient, open-source tool to analyze variant interactions in eQTL studies, providing better understanding of the function of epistasis in immune response and other complex phenotypes.

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with the allergen-specific modulation of immune reactivity.

BACKGROUND: Timothy grass (TG) pollen is a common seasonal airborne allergen associated with symptoms ranging from mild rhinitis to severe asthma. OBJECTIVE: The aim of this study was to characterize changes in TG-specific T cell responses as a function of seasonality. METHODS: Peripheral blood mononuclear cells (PBMCs) obtained from allergic individuals and non-allergic controls, either during the pollen season or out of season, were stimulated with either TG extract or a pool of previously identified immunodominant antigenic regions. RESULTS: PBMCs from allergic subjects exhibit higher IL-5 and IL-10 responses in season than when collected out of season. In the case of non-allergic subjects, as expected we observed lower IL-5 responses and robust production of IFN-γ compared to allergic individuals. Strikingly, non-allergic donors exhibited an opposing pattern, with decreased immune reactivity in season. The broad down-regulation in non-allergic donors indicates that healthy individuals are not oblivious to allergen exposure, but rather react with an active modulation of responses following the antigenic stimulus provided during the pollen season. Transcriptomic analysis of allergen-specific T cells defined genes modulated in concomitance with the allergen exposure and inhibition of responses in non-allergic donors. CONCLUSION AND CLINICAL RELEVANCE: Magnitude and functionality of T helper cell responses differ substantially in season vs. out of season in allergic and non-allergic subjects. The results indicate the specific and opposing modulation of immune responses following the antigenic stimulation during the pollen season. This seasonal modulation reflects the enactment of specific molecular programmes associated with health and allergic disease.