Search

Background: Complement activation may play a pathogenic role in patients with severe coronavirus disease 2019 (COVID-19) by contributing to tissue inflammation and microvascular thrombosis., Methods: Serial samples were collected from patients receiving maintenance haemodialysis (HD). Thirty-nine patients had confirmed COVID-19 and 10 patients had no evidence of COVID-19. Plasma C5a and C3a levels were measured using enzyme-linked immunosorbent assay., Results: We identified elevated levels of plasma C3a and C5a in HD patients with severe COVID-19 compared with controls. Serial sampling identified that C5a levels were elevated prior to clinical deterioration in patients who developed severe disease. C3a more closely mirrored both clinical and biochemical disease severity., Conclusions: Our findings suggest that activation of complement plays a role in the pathogenesis of COVID-19, leading to endothelial injury and lung damage. C5a may be an earlier biomarker of disease severity than conventional parameters such as C-reactive protein and this warrants further investigation in dedicated biomarker studies. Our data support the testing of complement inhibition as a therapeutic strategy for patients with severe COVID-19., (© The Author(s) 2020. Published by Oxford University Press on behalf of ERA-EDTA.)

Chronic granulomatous disease (CGD) is an inherited primary immunodeficiency disorder characterised by recurrent and often life-threatening infections and hyperinflammation. It is caused by defects of the phagocytic NADPH oxidase, a multicomponent enzyme system responsible for effective pathogen killing. A phase I/II clinical trial of lentiviral gene therapy is underway for the most common form of CGD, X-linked, caused by mutations in the gp91 phox subunit of the NADPH oxidase. We propose to use a similar strategy to tackle p47 phox -deficient CGD, caused by mutations in NCF1, which encodes the p47 phox cytosolic component of the enzymatic complex. We generated a pCCLCHIM-p47 phox lentiviral vector, containing the chimeric Cathepsin G/FES myeloid promoter and a codon-optimised version of the human NCF1 cDNA. Here we show that transduction with the pCCLCHIM-p47 phox vector efficiently restores p47 phox expression and biochemical NADPH oxidase function in p47 phox -deficient human and murine cells. We also tested the ability of our gene therapy approach to control infection by challenging p47 phox -null mice with Salmonella Typhimurium, a leading cause of sepsis in CGD patients, and found that mice reconstituted with lentivirus-transduced hematopoietic stem cells had a reduced bacterial load compared with untreated mice. Overall, our results potentially support the clinical development of a gene therapy approach using the pCCLCHIM-p47 phox vector.

Dispersal syndromes are often defined by reference to fruit traits that are associated with distinct frugivore guilds. Studies rarely examine the relationship between seed traits and frugivores or test the alternative hypothesis that traits are shaped by climatic variables. We assess whether the evolution of seed size and physical defense are correlated with dispersal-related traits and climatic variables in Artabotrys, a fleshy-fruited tropical lineage. Diaspore traits and WorldClim bioclimatic variables were compiled for 43 species. Correlated evolution was evaluated using phylogenetic regression and model-fitting approaches. The best-fitting multioptima Ornstein-Uhlenbeck model suggests that lineages with smooth testa and thin pericarp (SP) have evolved toward smaller seeds with a thinner testa, whereas lineages with rough testa and/or thick pericarp have evolved toward larger seeds with a thicker testa. A smooth testa facilitates spitting and/or swallowing of intact seeds while fruits with thin pericarp may be preferentially consumed by frugivores with less destructive oral processing, enabling lower investment in seed physical defense in SP lineages. Moreover, small seeds are more likely to be swallowed intact with a food bolus. The effect of climate on seed size and physical defense is equivocal and warrants further investigation., (© 2020 The Authors. Evolution © 2020 The Society for the Study of Evolution.)

Newborn screening (NBS) aims toward early detection of treatable congenital disorders. From January 2008 through December 2017, 13,376 newborns were screened for congenital hypothyroidism (CH), congenital adrenal hyperplasia (CAH), and glucose-6-phosphate dehydrogenase (G6PD) deficiency at Sir Ganga Ram Hospital, India, by measuring G6PD activity, thyroid-stimulating hormone, and 17-hydroxyprogesterone on dried blood specimens. The birth prevalence of 1:2,000 for CH, 1:2,500 for CAH, and 1:125 for G6PD deficiency indicates the latter as the most prevalent. Performance evaluation of testing reveals a robust screening program with 100% sensitivity and >99% specificity. Hence, we recommend NBS for early diagnosis and treatment to prevent adverse outcomes., Competing Interests: Conflict of Interest None declared., (© Thieme Medical Publishers.)

Student-run, physician-supervised free clinics (SRFCs) provide essential healthcare services for many uninsured and underinsured patients in the USA. While SRFCs serve diverse populations and offer distinct services, they face many similar barriers to successful clinic operation. Historically, the sharing of best practices and development strategies across SRFCs has been limited and insufficient for both new and emerging free clinics. To address these challenges, in 2015, the East Harlem Health Outreach Program (EHHOP) at the Icahn School of Medicine at Mount Sinai formed the EHHOP Consulting Group (ECG), with the goal of providing client SRFCs individualized support from medical students. ECG draws from the experience of EHHOP and other veteran SRFCs to provide customized solutions to best address client SRFC needs. Here, we describe ECG's inception, structure, and consulting work with client SRFCs. We propose that this interactive, longitudinal model can be adapted to other healthcare trainee initiatives where cross-institutional collaboration could prove beneficial., Competing Interests: Conflict of InterestDr. Yasmin Meah is a Board member of the Society of Student Run Free Clinics (SSRFC)., (© International Association of Medical Science Educators 2020.)

Loss of IL-10 signaling in macrophages (Mφs) leads to inflammatory bowel disease (IBD). Induced pluripotent stem cells (iPSCs) were generated from an infantile-onset IBD patient lacking a functional IL10RB gene. Mφs differentiated from IL-10RB-/- iPSCs lacked IL-10RB mRNA expression, were unable to phosphorylate STAT3, and failed to reduce LPS induced inflammatory cytokines in the presence of exogenous IL-10. IL-10RB-/- Mφs exhibited a striking defect in their ability to kill Salmonella enterica serovar Typhimurium, which was rescuable after experimentally introducing functional copies of the IL10RB gene. Genes involved in synthesis and receptor pathways for eicosanoid prostaglandin E2 (PGE2) were more highly induced in IL-10RB-/- Mφs, and these Mφs produced higher amounts of PGE2 after LPS stimulation compared with controls. Furthermore, pharmacological inhibition of PGE2 synthesis and PGE2 receptor blockade enhanced bacterial killing in Mφs. These results identify a regulatory interaction between IL-10 and PGE2, dysregulation of which may drive aberrant Mφ activation and impaired host defense contributing to IBD pathogenesis., (© 2019 Mukhopadhyay et al.)

Motivation: Epidemiologic, clinical and translational studies are increasingly generating multiplatform omics data. Methods that can integrate across multiple high-dimensional data types while accounting for differential patterns are critical for uncovering novel associations and underlying relevant subgroups., Results: We propose an integrative model to estimate latent unknown clusters (LUCID) aiming to both distinguish unique genomic, exposure and informative biomarkers/omic effects while jointly estimating subgroups relevant to the outcome of interest. Simulation studies indicate that we can obtain consistent estimates reflective of the true simulated values, accurately estimate subgroups and recapitulate subgroup-specific effects. We also demonstrate the use of the integrated model for future prediction of risk subgroups and phenotypes. We apply this approach to two real data applications to highlight the integration of genomic, exposure and metabolomic data., Availability and Implementation: The LUCID method is implemented through the LUCIDus R package available on CRAN (https://CRAN.R-project.org/package=LUCIDus)., Supplementary Information: Supplementary materials are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Alveolar epithelial type II cells (AEC2s) are the facultative progenitors of lung alveoli and serve as the surfactant-producing cells of air-breathing organisms. Although primary human AEC2s are difficult to maintain stably in cell cultures, recent advances have facilitated the derivation of AEC2-like cells from human pluripotent stem cells (hPSCs) in vitro. Here, we provide a detailed protocol for the directed differentiation of hPSCs into self-renewing AEC2-like cells that can be maintained for up to 1 year in culture as epithelial-only spheres without the need for supporting mesenchymal feeder cells. The month-long protocol requires recapitulation of the sequence of milestones associated with in vivo development of the distal lung, beginning with differentiation of cells into anterior foregut endoderm, which is followed by their lineage specification into NKX2-1 + lung progenitors and then distal/alveolar differentiation to produce progeny that express transcripts and possess functional properties associated with AEC2s.

Borrelia are microaerophilic spirochetes capable of causing multisystemic diseases such as Lyme disease and Relapsing Fever. The ubiquitous Fe/Mn-dependent superoxide dismutase (SOD) provides essential protection from oxidative damage by the superoxide anion. Borrelia possess a single SOD enzyme - SodA that is essential for virulence, providing protection against host-derived reactive oxygen species (ROS). Here we present a method for recombinant expression and purification of Borrelia burgdorferi SodA in E. coli. Metal exchange or insertion into the Fe/Mn-SOD is inhibited in the folded state. We therefore present a method whereby the recombinant Borrelia SodA binds to Mn under denaturing conditions and is subsequently refolded by a reduction in denaturant. SodA purified by metal affinity chromatography and size exclusion chromatography reveals a single band on SDS-PAGE. Protein folding is confirmed by circular dichroism. A coupled enzyme assay demonstrates SOD activity in the presence of Mn, but not Fe. The apparent molecular weight determined by size exclusion corresponds to a dimer of SodA; a homology model of dimeric SodA is presented revealing a surface Cys distal to the dimer interface. The method presented of acquiring a target metal under denaturing conditions may be applicable to the refolding of other metal-binding proteins., (Copyright © 2019 Elsevier Inc. All rights reserved.)

B cells are important in the pathogenesis of many, and perhaps all, immune-mediated diseases. Each B cell expresses a single B cell receptor (BCR) 1 , and the diverse range of BCRs expressed by the total B cell population of an individual is termed the 'BCR repertoire'. Our understanding of the BCR repertoire in the context of immune-mediated diseases is incomplete, and defining this could provide new insights into pathogenesis and therapy. Here, we compared the BCR repertoire in systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, Crohn's disease, Behçet's disease, eosinophilic granulomatosis with polyangiitis, and immunoglobulin A (IgA) vasculitis by analysing BCR clonality, use of immunoglobulin heavy-chain variable region (IGHV) genes and-in particular-isotype use. An increase in clonality in systemic lupus erythematosus and Crohn's disease that was dominated by the IgA isotype, together with skewed use of the IGHV genes in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatments had specific and distinct effects on the repertoire; B cells that persisted after treatment with rituximab were predominately isotype-switched and clonally expanded, whereas the inverse was true for B cells that persisted after treatment with mycophenolate mofetil. Our comparative analysis of the BCR repertoire in immune-mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.

Importance: Radiation therapy for breast cancer is associated with increased risk of a second primary contralateral breast cancer, but the genetic factors modifying this association are not well understood., Objective: To determine whether a genetic risk score comprising single nucleotide polymorphisms in the nonhomologous end-joining DNA repair pathway is associated with radiation-associated contralateral breast cancer., Design, Setting, and Participants: This case-control study included a case group of women with contralateral breast cancer that was diagnosed at least 1 year after a first primary breast cancer who were individually matched to a control group of women with unilateral breast cancer. Inclusion criteria were receiving a first invasive breast cancer diagnosis prior to age 55 years between 1985 and 2008. Women were recruited through 8 population-based cancer registries in the United States, Canada, and Denmark as part of the Women's Environment, Cancer, and Radiation Epidemiology Studies I (November 2000 to August 2004) and II (March 2010 to December 2012). Data analysis was conducted from July 2017 to August 2019., Exposures: Stray radiation dose to the contralateral breast during radiation therapy for the first breast cancer. A novel genetic risk score comprised of genetic variants in the nonhomologous end-joining DNA repair pathway was considered the potential effect modifier, dichotomized as high risk if the score was above the median of 74 and low risk if the score was at or below the median., Main Outcomes and Measures: The main outcome was risk of contralateral breast cancer associated with stray radiation dose stratified by genetic risk score, age, and latency., Results: A total of 5953 women were approached for study participation, and 3732 women (62.7%) agreed to participate. The median (range) age at first diagnosis was 46 (23-54) years. After 5 years of latency or more, among women who received the first diagnosis when they were younger than 40 years, exposure to 1.0 Gy (to convert to rad, multiply by 100) or more of stray radiation was associated with a 2-fold increased risk of contralateral breast cancer compared with women who were not exposed (rate ratio, 2.0 [95% CI, 1.1-3.6]). The risk was higher among women with a genetic risk score above the median (rate ratio, 3.0 [95% CI, 1.1-8.1]), and there was no association among women with a genetic risk score below the median (rate ratio, 1.3 [95% CI, 0.5-3.7]). Among younger women with a high genetic risk score, the attributable increased risk for contralateral breast cancer associated with stray radiation dose was 28%., Conclusions and Relevance: This study found an increased risk of contralateral breast cancer that was attributable to stray radiation exposure among women with a high genetic risk score and who received a first breast cancer diagnosis when they were younger than 40 years after 5 years or more of latency. This genetic risk score may help guide treatment and surveillance for women with breast cancer.

Background: Air pollution exposure has been shown to increase the risk of obesity and metabolic dysfunction in animal models and human studies. However, the metabolic pathways altered by air pollution exposure are unclear, especially in adolescents and young adults who are at a critical period in the development of cardio-metabolic diseases., Objectives: The aim of this study was to examine the associations between air pollution exposure and indices of fatty acid and amino acid metabolism., Methods: A total of 173 young adults (18-23 years) from eight Children's Health Study (CHS) Southern California communities were examined from 2014 to 2018. Near-roadway air pollution (NRAP) exposure (freeway and non-freeway) and regional air pollution exposure (nitrogen dioxide, ozone and particulate matter) during one year before the study visit were estimated based on participants' residential addresses. Serum concentrations of 64 targeted metabolites including amino acids, acylcarnitines, non-esterified fatty acid (NEFA) and glycerol were measured in fasting serum samples. Principal component analysis of metabolites was performed to identify metabolite clusters that represent key metabolic pathways. Mixed effects models were used to analyze the associations of air pollution exposure with metabolomic principal component (PC) scores and individual metabolite concentrations adjusting for potential confounders., Results: Higher lagged one-year averaged non-freeway NRAP exposure was associated with higher concentrations of NEFA oxidation byproducts and higher NEFA-related PC score (all p's ≤ 0.038). The effect sizes were larger among obese individuals (interaction p = 0.047). Among females, higher freeway NRAP exposure was also associated with a higher NEFA-related PC score (p = 0.042). Among all participants, higher freeway NRAP exposure was associated with a lower PC score for lower concentrations of short- and median-chain acylcarnitines (p = 0.044)., Conclusions: Results of this study indicate that NRAP exposure is associated with altered fatty acid metabolism, which could contribute to the metabolic perturbation in obese youth., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Factors that predict melanoma recurrence after a negative sentinel lymph node biopsy (SLNB) are not well-defined. We evaluated melanoma recurrence patterns, factors prognostic for recurrence, and the impact of recurrence on outcomes after a negative SLNB., Methods: The Sentinel Lymph Node Working Group database was evaluated from 1996 to 2016 for negative SLNB melanoma patients. Clinicopathologic characteristics were correlated with recurrence, overall survival (OS), and melanoma-specific survival (MSS)., Results: Median follow-up was 32.1 months. Recurrences developed in 558 of 5351 negative SLN patients (10.4%). First-site of recurrence included a local or in-transit recurrence (LITR) in 221 cases (4.1%), nodal recurrence (NR) in 109 cases (2%), and distant recurrence (DR) in 220 cases (4.1%). On multivariable analysis, age, thickness, head/neck or lower extremity primary, and microsatellitosis significantly predicted for an LITR as first-site. Having an LITR as first-site significantly predicted for a subsequent NR and DR, and significantly predicted for worse OS and MSS. Furthermore, thickness and head/neck or lower extremity primary significantly predicted for an NR as first-site, while a prior LITR significantly predicted for a subsequent NR. Factors significantly predictive for a DR included thickness, head/neck or trunk primary, ulceration, and lymphovascular invasion. Patients with any type of locoregional recurrence were at higher risk for a DR., Conclusions: Recurrences occur in 10.4% of negative SLN patients, with LITR and DR being the most common types. Importantly, having an LITR significantly predicts for a subsequent NR and DR, and is prognostic for worse survival after a negative SLNB.

Environmental stresses dramatically impact the balance between the production of photosynthetically derived energetic electrons and Calvin-Benson-Bassham cycle (CBBC) activity; an imbalance promotes accumulation of reactive oxygen species and causes cell damage. Hence, photosynthetic organisms have developed several strategies to route electrons toward alternative outlets that allow for storage or harmless dissipation of their energy. In this work, we explore the activities of three essential outlets associated with Chlamydomonas reinhardtii photosynthetic electron transport: ( i ) reduction of O 2 to H 2 O through flavodiiron proteins (FLVs) and ( ii ) plastid terminal oxidases (PTOX) and ( iii ) the synthesis of starch. Real-time measurements of O 2 exchange have demonstrated that FLVs immediately engage during dark-to-light transitions, allowing electron transport when the CBBC is not fully activated. Under these conditions, we quantified maximal FLV activity and its overall capacity to direct photosynthetic electrons toward O 2 reduction. However, when starch synthesis is compromised, a greater proportion of the electrons is directed toward O 2 reduction through both the FLVs and PTOX, suggesting an important role for starch synthesis in priming/regulating CBBC and electron transport. Moreover, partitioning energized electrons between sustainable (starch; energetic electrons are recaptured) and nonsustainable (H 2 O; energetic electrons are not recaptured) outlets is part of the energy management strategy of photosynthetic organisms that allows them to cope with the fluctuating conditions encountered in nature. Finally, unmasking the repertoire and control of such energetic reactions offers new directions for rational redesign and optimization of photosynthesis to satisfy global demands for food and other resources., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Gene-environment (G × E) interaction is important for many complex traits. In a case-control study of a disease trait, logistic regression is the standard approach used to model disease as a function of a gene (G), an environmental factor (E), G × E interaction, and adjustment covariates. We propose an alternative model with G as the outcome and show how it provides a unified framework for obtaining results from all of the common G × E tests. These include the 1-degree-of-freedom (df) test of G × E interaction, the 2-df joint test of G and G × E, the case-only and empirical Bayes tests, and several 2-step tests. In the context of this unified model, we propose a novel 3-df test and demonstrate that it provides robust power across a wide range of underlying G × E interaction models. We demonstrate the 3-df test in a genome-wide scan of G × sex interaction for childhood asthma using data from the Children's Health Study (Southern California, 1993-2001). This scan identified a strong G × sex interaction at the phosphodiesterase gene 4D locus (PDE4D), a known asthma-related locus, with a strong effect in males (per-allele odds ratio = 1.70; P = 3.8 × 10-8) and virtually no effect in females. We describe a software program, G×EScan (University of Southern California, Los Angeles, California), which can be used to fit standard and unified models for genome-wide G × E studies., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Ambulatory training in internal medicine residency programs has historically been considered less robust than inpatient-focused training, which prompted a 2009 revision of the Accreditation Council for Graduate Medical Education (ACGME) Program Requirements in Internal Medicine. This revision was intended to create a balance between inpatient and outpatient training standards and to spur innovation in the ambulatory setting., Objective: We explored innovations in ambulatory education in internal medicine residency programs since the 2009 revision of the ACGME Program Requirements in Internal Medicine., Methods: The authors conducted a scoping review of the literature from 2008 to 2017, searching PubMed, ERIC, and Scopus databases. Articles related to improving educational quality of ambulatory components of US-based internal medicine residency programs were eligible for inclusion. Articles were screened for relevance and theme categorization and then divided into 6 themes: clinic redesign, curriculum development, evaluating resident practice/performance, teaching methods, program evaluation, and faculty development. Once a theme was assigned, data extraction and quality assessment using the Medical Education Research Study Quality Instrument (MERSQI) score were completed., Results: A total of 967 potentially relevant articles were discovered; of those, 182 were deemed relevant and underwent full review. Most articles fell into curriculum development and clinic redesign themes. The majority of included studies were from a single institution, used nonstandardized tools, and assessed outcomes at the satisfaction or knowledge/attitude/skills levels. Few studies showed behavioral changes or patient-level outcomes., Conclusions: While a rich diversity of educational innovations have occurred since the 2009 revision of the ACGME Program Requirements in Internal Medicine, there is a significant need for multi-institution studies and higher-level assessment., Competing Interests: Conflict of interest: The authors declare they have no competing interests.

Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk., Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided., Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0., Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening., (© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: Robot-assisted thoracoscopic lobectomy has been shown to be a safe approach to pulmonary lobectomy. This study sought to define, mathematically, the learning curve for RATS lobectomy., Methods: Patients undergoing robot-assisted thoracoscopic lobectomy at a single institution from 2010 through 2016 were considered. Covariates included patient demographics, comorbidities, operating time, length of stay, estimated blood loss, and postoperative complications. A cumulative sum analysis of operating time was performed to define the learning curve., Results: A total of 101 patients were included. Three distinct phases of the learning curve were identified: cases 1-22, cases 23-63, and cases 64-101. There was a statistically significant difference in operating time and estimated blood loss between phases 1 and 2 (P < .05, P = .016, respectively) and between phases 1 and 3 (P < .05, P = .006, respectively). There was no statistically significant difference in comorbidities, chest tube duration, length of stay, postoperative complications, or conversion rate across the learning curve., Conclusion: Based on operating time, the learning curve for robot-assisted thoracoscopic lobectomy is 22 cases, with mastery achieved after 63 cases. No differences in length of stay, chest tube duration, conversion rate, or complication rate were observed in the learning curve. Other factors not measured in this study may play a role in the learning process and warrant further study., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Minority groups experience higher depression but lower treatment rates. Student-run free mental health (MH) clinics, such as the East Harlem Health Outreach Partnership (EHHOP) MH clinic, address this disparity. This study scrutinized EHHOP MH's depression treatment by measuring adherence to antidepressants. Pharmacy data from seventy-nine patients were reviewed according to HEDIS criteria. Results compare EHHOP MH to New York State (NYS) Medicaid and NYS commercial insurance providers. In the acute treatment phase, EHHOP MH performed similarly to NYS Medicaid. In all other comparisons, EHHOP MH had lower adherence rates. Physician notes were reviewed to identify reasons for low adherence.

To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10 -8 , bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.

We designed a curriculum to help sustain pre-clinical knowledge for MD/PhD trainees in their graduate training phase while securing regular providers for our student-run free clinic. MD/PhD involvement increased from 1.91 to 2.45 students-per-clinic-day following implementation, and participants affirmed increased preparedness and comfort entering medical school clinical clerkships., Competing Interests: Conflict of InterestThe authors declare that they have no conflict of interest., (© International Association of Medical Science Educators 2018.)

Purpose: Although speech-language pathologists use parent-delivered home-practice, little is known about the quality of this practice and its relation to treatment efficacy. This study reports both treatment outcomes and fidelity following combined clinician-parent delivery of Rapid Syllable Transition (ReST) treatment., Method: Five children aged 5:1-11:7 with childhood apraxia of speech received 12 treatment sessions; six clinic-based and six at home, using multiple baselines across participants design. We investigated the children's acquisition of treated pseudo words, generalisation to untreated pseudo and real words, and maintenance of gains. We also assessed parent and clinician treatment fidelity and reliability of perceptual judgements., Result: Two children improved on all treated behaviours; two showed treatment effect on one of their two treated behaviours, and one child had no treatment effect. Only two children generalised to the majority of untreated items. Variable treatment fidelity was found across parents and aspects of treatment. Child outcome was likely influenced by multiple factors, including treatment fidelity, reliability of perceptual judgements and child factors., Conclusion: Combined clinician-parent delivery of ReST was less efficacious than previously reported clinician-only delivered ReST. Further investigation of the factors affecting outcome is recommended prior to clinical application of the combined model of service delivery.

The pursuit of dedicated research time during surgical residency prolongs training and delays entry into practice. Currently, there is a lack of research quantifying the financial implication of this delay and trainees' understanding of its impact on career earnings. An opportunity cost analysis was performed regarding the impact of delay due to training within general surgery and selected subspecialties. An anonymous survey was distributed to general surgery categorical junior trainees in 2017 at a large academic hospital in the Northeast to determine understanding and beliefs regarding dedicated training on career earnings. For all specialties analyzed, dedicated research time was shown to negatively affect career earnings. The net cost was highest among those intending to pursue cardiothoracic surgery and lowest for those intending to pursue surgical oncology. A total of 26 of 35 (74%) present research residents and clinical residents intending to perform dedicated research time responded to an anonymous survey. On average, survey respondents underestimated the impact of dedicated research time on career earnings by $1.4 million. Dedicated research time during general surgery residency carries a substantial opportunity cost to overall career earnings. General surgery residents lack understanding of both the direction and the magnitude of this opportunity cost.

Although hybridisation between closely related species is common and known to be important in plant evolution, hybridisation at the generic level or above is comparatively rare. We address ancient intergeneric hybridisation in the early-divergent angiosperm family Annonaceae by phylogenetic reconstruction, divergence time estimation and coalescent simulation of the genus Dasymaschalon using a multi-locus approach based on molecular data from five chloroplast (matK, psbA-trnH, ndhF, rbcL, and trnL-F) and five nuclear (ITS, ETS, AP3, PhyA, and PhyC) DNA markers. We demonstrate incongruence among different gene trees: Dasymaschalon is retrieved as monophyletic in the nuclear ribosomal tree (based on ITS and ETS), but is non-monophyletic in the chloroplast and Phy-gene trees (with poor resolution in the AP3 tree), with the majority of species assigned to a strongly supported clade but three species (D. filipes, D. longiflorum and D. tibetense) more closely related to the sister genus Friesodielsia. Three contrasting approaches-a coalescent method based on molecular dating, incongruence pattern comparison, and a multi-accession phylogenetic reconstruction-are used to assess the patterns of this gene tree incongruence and test hypotheses of ancient hybridisation and incomplete lineage sorting. Our results support a late Miocene intergeneric hybridisation between members of the Dasymaschalon and Friesodielsia lineages in continental Asia-west Malesia., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The phagocyte NADPH oxidase is a multi subunit protein complex that generates reactive oxygen species at cell membranes and within phagosomes. It is essential for host defence as evidenced by the severe immunodeficiency syndrome caused by a loss of one of the subunits. This is known as chronic granulomatous disease (CGD). However, the phagocyte NADPH oxidase also has a key role to play in regulating immunity and it is notable that chronic granulomatous disease is also characterised by autoimmune and autoinflammatory manifestations. This is because reactive oxygen species play a role in regulating signalling through their ability to post-translationally modify amino acid residues such as cysteine and methionine. In this review, I will outline the major aspects of innate immunity that are regulated by the phagocyte NADPH oxidase, including control of transcription, autophagy, the inflammasome and type 1 interferon signalling., (Copyright © 2018. Published by Elsevier Inc.)

High-throughput sequencing of the DNA/RNA encoding antibody heavy- and light-chains is rapidly transforming the field of adaptive immunity. It can address key questions, including: (i) how the B-cell repertoire differs in health and disease; and (ii) if it does differ, the point(s) in B-cell development at which this occurs. The advent of technologies, such as whole-genome sequencing, offers the chance to link abnormalities in the B-cell antibody repertoire to specific genomic variants and polymorphisms. Here, we discuss the current research using B-cell antibody repertoire sequencing in three polygenic autoimmune diseases where there is good evidence for a pathological role for B-cells, namely systemic lupus erythematosus, multiple sclerosis and rheumatoid arthritis. These autoimmune diseases exhibit significantly skewed B-cell receptor repertoires compared with healthy controls. Interestingly, some common repertoire defects are shared between diseases, such as elevated IGHV4-34 gene usage. B-cell clones have effectively been characterized and tracked between different tissues and blood in autoimmune disease. It has been hypothesized that these differences may signify differences in B-cell tolerance; however, the mechanisms and implications of these defects are not clear., (© 2018 The Authors. Immunology Published by John Wiley & Sons Ltd.)

Purpose: To understand parents' perceptions of Rapid Syllable Transition (ReST) treatment and their experience of either telehealth or combined parent-clinician delivery of speech-language pathology., Method: Thematic analyses of semi-structured interviews were conducted with 10 parents (5 telehealth, 5 parent-clinician) after their child completed 12 sessions of ReST treatment., Results: Three themes were unique to telehealth: "telehealth was a million times easier," "technical problems weren't deal breakers," and "telehealth therapy has different boundaries." Three themes were unique to parent-clinician delivery: "therapy is something to get over and done with," "I wasn't very good at doing therapy," and "my child doesn't like me as his therapist." Both groups had themes related to the significance of childhood apraxia of speech, the importance of specialist treatment, and ReST being a "different way forward.", Conclusions: Speech-language pathologists should carefully consider the suitability of caregiver-provided ReST treatment, and increase telehealth delivery of ReST treatment.

Background: Studies using metabolomic data have identified metabolites from several compound classes that are associated with disease-related lifestyle factors., Objective: In this study, we identified metabolic signatures reflecting lifestyle patterns and related them to the risk of hepatocellular carcinoma (HCC) in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort., Design: Within a nested case-control study of 147 incident HCC cases and 147 matched controls, partial least squares (PLS) analysis related 7 modified healthy lifestyle index (HLI) variables (diet, BMI, physical activity, lifetime alcohol, smoking, diabetes, and hepatitis) to 132 targeted serum-measured metabolites and a liver function score. The association between the resulting PLS scores and HCC risk was examined in multivariable conditional logistic regression models, where ORs and 95% CIs were computed., Results: The lifestyle component's PLS score was negatively associated with lifetime alcohol, BMI, smoking, and diabetes, and positively associated with physical activity. Its metabolic counterpart was positively related to the metabolites sphingomyelin (SM) (OH) C14:1, C16:1, and C22:2, and negatively related to glutamate, hexoses, and the diacyl-phosphatidylcholine PC aaC32:1. The lifestyle and metabolomics components were inversely associated with HCC risk, with the ORs for a 1-SD increase in scores equal to 0.53 (95% CI: 0.38, 0.74) and 0.28 (0.18, 0.43), and the associated AUCs equal to 0.64 (0.57, 0.70) and 0.74 (0.69, 0.80), respectively., Conclusions: This study identified a metabolic signature reflecting a healthy lifestyle pattern which was inversely associated with HCC risk. The metabolic profile displayed a stronger association with HCC than did the modified HLI derived from questionnaire data. Measuring a specific panel of metabolites may identify strata of the population at higher risk for HCC and can add substantial discrimination compared with questionnaire data. This trial was registered at clinicaltrials.gov as NCT03356535.

Consolidation of the lung is a common pathology which is sometimes life threatening. One of the primary causes is the infection of lung tissue (pneumonia). Vocal resonance and vocal fremitus are part of the routine clinical examination of the respiratory system by physicians, which although time consuming, helps in the diagnosis of consolidation of the lung. In this paper, we suggest a possible automatic lung consolidation detection system that can be used by health workers with basic training. Analysis is performed on the vocal resonance sound signals recorded using an electronic stethoscope from the chest walls of normal subjects and patients. We show that for the detection system, use of signal loudness, which is generally considered by physicians, would be infeasible and propose that signal power spectral density computed using our system be considered. Certain frequency regions in the power spectral density (periodogram) are proved to be significant indicators of lung consolidation using t-tests. These findings are then applied to design the detection system using Gaussian naive Bayes classifiers.

Background: Robotic-assisted thoracoscopic surgery (RobATS) lobectomy is becoming more common for the treatment of lung cancer. As with any relatively new technology, there is the assumption that greater experience leads to greater proficiency. The objective of this study was to analyze outcomes of patients undergoing RobATS lobectomy as hospitals gain experience, and to describe outcomes after conversion to open procedures., Study Design: The National Cancer Database (NCDB) was used to analyze robotic lobectomies for lung cancer from 2010 to 2014. Individual hospitals were categorized by the year they began reporting robotic lobectomies to the NCDB. Primary outcomes were perioperative morbidity and mortality and rate of conversion to open lobectomy., Results: There were 7,645 robotic lobectomies identified from 465 hospitals. The overall conversion rate was 9.2% (n = 702). A propensity-matched analysis showed no significant difference between experienced and inexperienced hospitals with respect to 30-day mortality (1.07% vs 2.03%, p = 0.092) or 90-day mortality (2.35% vs 3.63%, p = 0.104). Conversion to open was a predictor of 30-day mortality (odds ratio [OR] 2.54, CI 1.56 to 4.14) and 90-day mortality (OR 2.68, CI 1.83 to 3.91). Patients who underwent conversion had higher 90-day mortality compared with patients not undergoing conversion, in years of experience: 2 (p = 0.043), 3 (p = 0.002), and 4 (p = 0.003)., Conclusions: Mortality after RobATS lobectomy at experienced hospitals is not significantly different than at inexperienced hospitals. Though conversion rates decrease with experience, patients who undergo conversion have higher mortality than those who do not, particularly in hospitals with more experience. This suggests that a deliberate effort to increase experience with and improve patient selection for RobATS lobectomies may ameliorate the conversions and their attendant sequelae., (Copyright © 2018. Published by Elsevier Inc.)

Background & Aims: Guidelines for initiating colorectal cancer (CRC) screening are based on family history but do not consider lifestyle, environmental, or genetic risk factors. We developed models to determine risk of CRC, based on lifestyle and environmental factors and genetic variants, and to identify an optimal age to begin screening., Methods: We collected data from 9748 CRC cases and 10,590 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colorectal Transdisciplinary study, from 1992 through 2005. Half of the participants were used to develop the risk determination model and the other half were used to evaluate the discriminatory accuracy (validation set). Models of CRC risk were created based on family history, 19 lifestyle and environmental factors (E-score), and 63 CRC-associated single-nucleotide polymorphisms identified in genome-wide association studies (G-score). We evaluated the discriminatory accuracy of the models by calculating area under the receiver operating characteristic curve values, adjusting for study, age, and endoscopy history for the validation set. We used the models to project the 10-year absolute risk of CRC for a given risk profile and recommend ages to begin screening in comparison to CRC risk for an average individual at 50 years of age, using external population incidence rates for non-Hispanic whites from the Surveillance, Epidemiology, and End Results program registry., Results: In our models, E-score and G-score each determined risk of CRC with greater accuracy than family history. A model that combined both scores and family history estimated CRC risk with an area under the receiver operating characteristic curve value of 0.63 (95% confidence interval, 0.62-0.64) for men and 0.62 (95% confidence interval, 0.61-0.63) for women; area under the receiver operating characteristic curve values based on only family history ranged from 0.53 to 0.54 and those based only E-score or G-score ranged from 0.59 to 0.60. Although screening is recommended to begin at age 50 years for individuals with no family history of CRC, starting ages calculated based on combined E-score and G-score differed by 12 years for men and 14 for women, for individuals with the highest vs the lowest 10% of risk., Conclusions: We used data from 2 large international consortia to develop CRC risk calculation models that included genetic and environmental factors along with family history. These determine risk of CRC and starting ages for screening with greater accuracy than the family history only model, which is based on the current screening guideline. These scoring systems might serve as a first step toward developing individualized CRC prevention strategies., (Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Purpose The Women's Environmental Cancer and Radiation Epidemiology (WECARE) study demonstrated the importance of breast cancer family history on contralateral breast cancer (CBC) risk, even for noncarriers of deleterious BRCA1/2 mutations. With the completion of WECARE II, updated risk estimates are reported. Additional analyses that exclude women negative for deleterious mutations in ATM, CHEK2*1100delC, and PALB2 were performed. Patients and Methods The WECARE Study is a population-based case-control study that compared 1,521 CBC cases with 2,212 individually matched unilateral breast cancer (UBC) controls. Participants were younger than age 55 years when diagnosed with a first invasive breast cancer between 1985 and 2008. Women were interviewed about breast cancer risk factors, including family history. A subset of women was screened for deleterious mutations in BRCA1/2, ATM, CHEK2*1100delC, and PALB2. Rate ratios (RRs) were estimated using multivariable conditional logistic regression. Cumulative absolute risks (ARs) were estimated by combining RRs from the WECARE Study and population-based SEER*Stat cancer incidence data. Results Women with any first-degree relative with breast cancer had a 10-year AR of 8.1% for CBC (95% CI, 6.7% to 9.8%). Risks also were increased if the relative was diagnosed at an age younger than 40 years (10-year AR, 13.5%; 95% CI, 8.8% to 20.8%) or with CBC (10-year AR, 14.1%; 95% CI, 9.5% to 20.7%). These risks are comparable with those seen in BRCA1/2 deleterious mutation carriers (10-year AR, 18.4%; 95% CI, 16.0% to 21.3%). In the subset of women who tested negative for deleterious mutations in BRCA1/2, ATM, CHEK2*1100delC, and PALB2, estimates were unchanged. Adjustment for known breast cancer single-nucleotide polymorphisms did not affect estimates. Conclusion Breast cancer family history confers a high CBC risk, even after excluding women with deleterious mutations. Clinicians are urged to use detailed family histories to guide treatment and future screening decisions for young women with breast cancer.

Background: The "meeting-in-the-middle" (MITM) is a principle to identify exposure biomarkers that are also predictors of disease. The MITM statistical framework was applied in a nested case-control study of hepatocellular carcinoma (HCC) within European Prospective Investigation into Cancer and Nutrition (EPIC), where healthy lifestyle index (HLI) variables were related to targeted serum metabolites. Methods: Lifestyle and targeted metabolomic data were available from 147 incident HCC cases and 147 matched controls. Partial least squares analysis related 7 lifestyle variables from a modified HLI to a set of 132 serum-measured metabolites and a liver function score. Mediation analysis evaluated whether metabolic profiles mediated the relationship between each lifestyle exposure and HCC risk. Results: Exposure-related metabolic signatures were identified. Particularly, the body mass index (BMI)-associated metabolic component was positively related to glutamic acid, tyrosine, PC aaC38:3, and liver function score and negatively to lysoPC aC17:0 and aC18:2. The lifetime alcohol-specific signature had negative loadings on sphingomyelins (SM C16:1, C18:1, SM(OH) C14:1, C16:1 and C22:2). Both exposures were associated with increased HCC with total effects (TE) = 1.23 (95% confidence interval = 0.93-1.62) and 1.40 (1.14-1.72), respectively, for BMI and alcohol consumption. Both metabolic signatures mediated the association between BMI and lifetime alcohol consumption and HCC with natural indirect effects, respectively, equal to 1.56 (1.24-1.96) and 1.09 (1.03-1.15), accounting for a proportion mediated of 100% and 24%. Conclusions: In a refined MITM framework, relevant metabolic signatures were identified as mediators in the relationship between lifestyle exposures and HCC risk. Impact: The understanding of the biological basis for the relationship between modifiable exposures and cancer would pave avenues for clinical and public health interventions on metabolic mediators. Cancer Epidemiol Biomarkers Prev; 27(5); 531-40. ©2018 AACR ., (©2018 American Association for Cancer Research.)

Background: Few studies have examined the risk factors for and timing of venous thromboembolism (VTE) in patients undergoing surgical procedures for lung cancer, and there are limited data to formulate guidelines for extended VTE prophylaxis after hospital discharge. This study sought to identify risk factors for postdischarge VTE after lung resection., Methods: Patients undergoing anatomic resection for lung cancer were identified in the National Surgical Quality Improvement Program database from 2005 to 2015. Patients' demographic and clinical characteristics were evaluated for any association with postdischarge VTE. Predictors of postdischarge VTE were identified using multivariable analysis., Results: VTE occurred in 1.6% (234) of the 14,308 patients identified; 44% (102) VTE events occurred after hospital discharge. Undergoing pneumonectomy was associated with a threefold increased risk for postdischarge VTE compared with lobectomy (2.0% versus 0.6%, p < 0.01), as was open resection compared with minimally invasive resection (0.8% versus 0.6%, p < 0.01). Prolonged operative time (>75th percentile) was also associated with an increased risk for postdischarge VTE compared with shorter operative time. Multivariable analysis identified older age, obesity, pneumonectomy, and prolonged operative time as independent predictors of postdischarge VTE., Conclusions: Significant proportions of VTE events occur after hospital discharge. Although there are data to suggest that the risk for VTE extends beyond this period, few patients are managed with postdischarge prophylaxis. These data suggest that postdischarge prophylaxis should be considered for those patients at high risk for VTE, particularly for older patients, those who are obese, and after extended or lengthy resections., (Copyright © 2018 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)

The Dasymaschalon alliance within the early divergent angiosperm family Annonaceae comprises c. 180 species in four genera ( Dasymaschalon, Desmos, Friesodielsia , and Monanthotaxis ). The alliance offers an excellent opportunity for investigating perianth evolution and functional adaptations because of the presence of different numbers of petal whorls and contrasting floral chamber morphologies. The absence of the inner petal whorl in Dasymaschalon renders it distinctive in the family: previous studies have suggested that its three outermost stamens might be homologous with the inner petals of the sister genus, Friesodielsia , reflecting a homeotic shift of floral organ identify from inner petals to stamens. To investigate this hypothesis and general perianth evolution in the alliance, we (i) compared the floral vascularization of selected Dasymaschalon and Friesodielsia species using paraffin serial sectioning, and (ii) mapped selected perianth characters of inferred functional significance onto a molecular phylogenetic framework of the Dasymaschalon alliance (46 accessions; five cpDNA, and two nrDNA markers). The results indicate that the vasculature of the outermost stamen whorl of Dasymaschalon does not fuse with the perianth cortical vascular system, but instead splits from the basal traces of the free stamen bundles, contradicting previous inferences of homology with the inner corolla whorl of other Annonaceae. The loss of the inner petal whorl in Dasymaschalon is less likely to be due to a homeotic mutation, and instead possibly involved either the loss of genes that are responsible for determining inner petals or else the expression failure of these genes. Optimizations of perianth characters indicate that the absence of the inner petal whorl and the connivence of outer petals during anthesis are synapomorphic for Dasymaschalon . Circadian trapping of pollinators is inferred either to be derived in the stem lineage of the Dasymaschalon-Friesodielsia clade, or else to have evolved in parallel in the Dasymaschalon and Friesodielsia lineages. Subsequent changes in the remaining petals of Dasymaschalon flowers (which do not fully separate during anthesis) are likely to have enabled perpetuation of the circadian trapping mechanism, lessening the adverse impacts of inner petal loss.

Background: Previous literature suggests that patients with non-small cell lung cancer (NSCLC) and unsuspected N2 disease (cN0, pN2) represent a distinct subgroup associated with improved overall survival compared to patients with N2 disease identified prior to resection (cN2, pN2)., Methods: Retrospective analysis of the National Cancer Database of patients from 2004 to 2011 with cN0 and cN2 status found to be pathologic stage III-N2 NSCLC after surgical resection. Comparison of 5-year survival of patients with unsuspected N2 disease versus those with known N2 disease after surgical resection using Kaplan-Meier analysis was made. The independent effect of unsuspected N2 disease on mortality was analyzed using multivariate analysis., Results: A total of 3271 patients with pathologic stage III-N2 NSCLC underwent curative intent surgical resection with or without adjuvant chemotherapy or chemotherapy and radiation. Unsuspected N2 disease was identified in 48% of patients. Patients with unsuspected N2 disease were more likely to have T1 tumors (37 vs. 32%, p < 0.001). Unsuspected N2 disease did not impact 5-year overall survival compared with known N2 when adjuvant therapy was utilized (40 vs. 37%, p = 0.167). Multivariate analysis identified older age, higher comorbidity score, and treatment with surgery alone as independent risk factors for mortality. The presence of unsuspected N2 disease was not significant in this model., Conclusions: The findings of this study suggest that unsuspected N2 disease is associated with equivalent 5-year survival compared to cN2 disease when adjuvant therapy is employed. These results support the use of adjuvant chemotherapy and radiation therapy when confronted with unsuspected N2 disease after surgical resection for stage IIIA-NSCLC.

When exposed to certain stimuli, phagocytes (including neutrophils, macrophages and eosinophils) undergo marked changes in the way they handle oxygen. Firstly, their rate of oxygen uptake increases greatly. This is accompanied by (i) the production of large amounts of superoxide and hydrogen peroxide and (ii) the metabolism of large quantities of glucose through the hexose monophosphate shunt. We now know that the oxygen used is not for respiration but for the production of powerful microbiocidal agents downstream of the initial production of superoxide. Concomitantly, glucose is oxidised through the hexose monophosphate shunt to re-generate the NADPH that has been consumed through the reduction of molecular oxygen to generate superoxide. This phagocyte respiratory burst is generated by an NADPH oxidase multi-protein complex that has a catalytic core consisting of membrane-bound gp91phox (CYBB) and p22phox (CYBA) sub-units and cytosolic components p47phox (NCF1), p67phox (NCF2) and p40phox (NCF4). Finally, another cytosolic component, the small G-protein Rac (Rac2 in neutrophils and Rac1 in macrophages) is also required for full activation. The importance of the complex in host defence is underlined by chronic granulomatous disease, a severe life-limiting immunodeficiency caused by mutations in the genes encoding the individual subunits. In this review, I will discuss the experimental evidence that underlies our knowledge of the respiratory burst, outlining how elegant biochemical analysis, coupled with study of patients deficient in the various subunits has helped elucidate the function of this essential part of innate immunity. I will also discuss some exciting recent studies that shed new light on how the abundance of the various components is controlled. Finally, I will explore the emerging role of reactive oxygen species such as superoxide and hydrogen peroxide in the pathogenesis of major human diseases including auto-inflammatory diseases., (Copyright © 2017. Published by Elsevier B.V.)

Recently, many new approaches, study designs, and statistical and analytical methods have emerged for studying gene-environment interactions (G×Es) in large-scale studies of human populations. There are opportunities in this field, particularly with respect to the incorporation of -omics and next-generation sequencing data and continual improvement in measures of environmental exposures implicated in complex disease outcomes. In a workshop called "Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases," held October 17-18, 2014, by the National Institute of Environmental Health Sciences and the National Cancer Institute in conjunction with the annual American Society of Human Genetics meeting, participants explored new approaches and tools that have been developed in recent years for G×E discovery. This paper highlights current and critical issues and themes in G×E research that need additional consideration, including the improved data analytical methods, environmental exposure assessment, and incorporation of functional data and annotations., (Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health 2017.)

A growing knowledge base of genetic and environmental information has greatly enabled the study of disease risk factors. However, the computational complexity and statistical burden of testing all variants by all environments has required novel study designs and hypothesis-driven approaches. We discuss how incorporating biological knowledge from model organisms, functional genomics, and integrative approaches can empower the discovery of novel gene-environment interactions and discuss specific methodological considerations with each approach. We consider specific examples where the application of these approaches has uncovered effects of gene-environment interactions relevant to drug response and immunity, and we highlight how such improvements enable a greater understanding of the pathogenesis of disease and the realization of precision medicine., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.)

Background: Women with unilateral breast cancer (UBC) are at risk of developing a subsequent contralateral breast cancer (CBC). Common variants are associated with breast cancer risk. Whether these influence CBC risk is unknown., Methods: Participants were breast cancer cases from the population-based Women's Environmental Cancer and Radiation Epidemiology (WECARE) Study. Sixty-seven established breast cancer risk loci were genotyped directly or by imputation in 1459 case subjects with CBC and 2126 UBC control subjects. An unweighted polygenic risk score (PRS) was created by summing the number of risk alleles for each directly genotyped single nucleotide polymorphism (SNP), or for imputed loci, the imputed dosage. A weighted PRS was calculated similarly, but where each SNP's contribution was weighted by the published per-allele log odds ratio. Unweighted and weighted polygenic risk scores and CBC risk were modeled using conditional logistic regression. Cumulative CBC risk was estimated and benchmarked using Surveillance, Epidemiology, and End Results population incidence rates., Results: Both unweighted and weighted PRS were statistically significantly associated with CBC risk. The adjusted risk ratio of CBC in women in the upper quartile of unweighted PRS compared with the lowest quartile was 1.63 (95% confidence interval [CI] = 1.33 to 2.00). The estimated 10-year cumulative risk for women in the upper quartile of the unweighted PRS was 7.4% (95% CI = 6.0% to 9.1%). For women in the upper quartile of the weighted PRS, the risk ratio for CBC was 1.75 (95% CI = 1.41 to 2.18) compared with women in the lowest quartile. There was no statistically significant heterogeneity by age, treatment (radiation therapy dose, tamoxifen, chemotherapy), estrogen receptor status of the first primary, histology of the first primary, length of at-risk period for CBC, or breast cancer family history., Conclusions: Common genomic variants associated with the development of first primary breast cancer are also associated with the development of CBC; the risk is strongest among those who carry more risk alleles., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Mutations in the human NBEAL2 gene cause gray platelet syndrome (GPS), a bleeding diathesis characterized by a lack of α granules in platelets. The functions of the NBEAL2 protein have not been explored outside platelet biology, but there are reports of increased frequency of infection and abnormal neutrophil morphology in patients with GPS. We therefore investigated the role of NBEAL2 in immunity by analyzing the phenotype of Nbeal2-deficient mice. We found profound abnormalities in the Nbeal2-deficient immune system, particularly in the function of neutrophils and NK cells. Phenotyping of Nbeal2-deficient neutrophils showed a severe reduction in granule contents across all granule subsets. Despite this, Nbeal2-deficient neutrophils had an enhanced phagocyte respiratory burst relative to Nbeal2-expressing neutrophils. This respiratory burst was associated with increased expression of cytosolic components of the NADPH oxidase complex. Nbeal2-deficient NK cells were also dysfunctional and showed reduced degranulation. These abnormalities were associated with increased susceptibility to both bacterial (Staphylococcus aureus) and viral (murine CMV) infection in vivo. These results define an essential role for NBEAL2 in mammalian immunity.

Background: Stage I non-small-cell lung cancer is potentially curable, yet older patients undergo treatment at lower rates than younger patients. This analysis sought to describe the treatment outcomes of nonagenarians with stage I non-small-cell lung cancer to better guide treatment decisions in this population., Methods: The National Cancer DataBase was queried for patients age ≥90 years old with stage I non-small-cell lung cancer (tumors ≤4 cm). Patients were divided into 3 groups: local therapy, other therapy, or no treatment. The primary outcomes were 5-year overall and relative survival., Results: Of the 616 patients identified, 33% (202) were treated with local therapy, 34% (207) were treated with other therapy, and 34% (207) underwent no treatment. Compared with local therapy, overall mortality was significantly higher with no treatment (hazard ratio 2.50, 95% confidence interval, 1.95-3.21) and other therapy (hazard ratio 1.43, 95% confidence interval, 1.11-1.83). The 5-year relative survival was 81% for local therapy, 49% for other therapy, and 32% for no treatment (P < .0001)., Conclusion: Nonagenarians managed with local therapy for stage I non-small-cell lung cancer (tumors ≤4 cm) have better overall survival than those receiving other therapy or no treatment and should be considered for treatment with either operation or stereotactic body radiation therapy if able to tolerate treatment., (Copyright © 2017 Elsevier Inc. All rights reserved.)

A growing number and increasing diversity of factors are available for epidemiological studies. These measures provide new avenues for discovery and prevention, yet they also raise many challenges for adoption in epidemiological investigations. Here, we evaluate 1) designs to investigate diseases that consider heterogeneous and multidimensional indicators of exposure and behavior, 2) the implementation of numerous methods to capture indicators of exposure, and 3) the analytical methods required for discovery and validation. We find that case-control studies have provided insights into genetic susceptibility but are insufficient for characterizing complex effects of environmental factors on disease development. Prospective and two-phase designs are required but must balance extended data collection with follow-up of study participants. We discuss innovations in assessments including the microbiome; mass spectrometry and metabolomics; behavioral assessment; dietary, physical activity, and occupational exposure assessment; air pollution monitoring; and global positioning and individual sensors. We claim the the availability of extensive correlated data raises new challenges in disentangling specific exposures that influence cancer risk from among extensive and often correlated exposures. In conclusion, new high-dimensional exposure assessments offer many new opportunities for environmental assessment in cancer development. Cancer Epidemiol Biomarkers Prev; 26(9); 1370-80. ©2017 AACR ., (©2017 American Association for Cancer Research.)

Background: The Asimina-Disepalum clade (Annonaceae subfam. Annonoideae tribe Annoneae) includes a major Neotropical-Asian biogeographical disjunction. We evaluate whether this disjunction can be explained by the Eocene boreotropics hypothesis, which relies on the existence of extensive boreotropical forests during the Late Palaeocene-Early Eocene thermal maximum (52-50 Ma), followed by disruption of boreotropical vegetation during post-Eocene cooling. Molecular dating using an uncorrelated relaxed molecular clock (UCLD) model with two fossil calibrations, ancestral range estimation, and ecological niche modelling across evolutionary time were performed. Our focus was the geographical origin of Disepalum and general biogeographic patterns within this genus. Comparison of ecological tolerance among extant species and niche reconstructions at ancestral nodes within the clade enabled insights in likely migration routes of lineages, as well as evaluating the role of bioclimatic ecological differentiation in the diversification of Disepalum within Southeast Asia., Results: The inferred vicariance event associated with the Asimina-Disepalum disjunction is estimated to have originated ca. 40 Mya [95% highest posterior density (HPD): 44.3-35.5 Mya]. The Disepalum crown lineage is estimated to have originated ca. 9 Mya (95% HPD: 10.6-7.6), either in western Malesia and continental Southeast Asia, or exclusively in western Malesia. Ecological niche modelling shows that seasonality of temperature and precipitation are major contributors determining the geographical range of species. Ancestral niche modelling furthermore indicates that the ancestor of the Asimina-Disepalum clade likely had bioclimatic preferences close to conditions found in current tropical and subtropical climates across Asia, whereas the ancestors of the Asimina and Disepalum crown groups are projected onto the more subtropical and tropical regions, respectively., Conclusions: The vicariance event associated with the Neotropical-Asian disjunction within the Asimina-Disepalum clade likely coincided with climatic deterioration at the Eocene-Oligocene boundary. Although detrended component analyses (DCA) indicate that altitude and seasonality of temperature and precipitation have the greatest influence in determining the geographical range of species, isolation due to palaeogeographic and palaeoclimatic events appears to be of greater significance than climate niche differentiation in driving diversification in Disepalum.