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Summary: Background: Paediatric hepatocellular carcinomas (HCC) traditionally arise in the context of a normal structural and functional liver and carry a dismal prognosis. While chemotherapy is the frontline standard, there is emerging interest in the study of immunotherapies for paediatric patients with relapsed/refractory disease. There is limited data to support whether immunotherapies will be of utility in this patient population. Methods: Six paediatric patients (median age:16 years, range: 12–17 at the time of treatment) with advanced hepatocellular neosplams, either conventional hepatocellular or fibrolamellar carcinoma, were treated with immunotherapy. Patients were consented to institutional genomic profiling and biobanking protocols. Baseline samples and serial tissue samples, when available, were evaluated for somatic mutation rate, actionable gene mutations, and pan-immune bulk RNA expression profiling. Results were correlated with clinical course. Findings: Three patients responded to checkpoint inhibition: one achieved a complete, durable response and the other two, prolonged stable disease. Three additional patients progressed. Diagnostic tissue from the complete responder demonstrated a higher relative mutational burden and robust immune infiltrate. Pre-treatment samples from the three responders demonstrated decreased expression of genes associated with T-cell dysfunction. Interpretation: A subset of patients with primary paediatric hepatocellular tumours will respond to immunotherapy. Immunotherapies are currently under prospective study for relapsed/refractory liver tumours in paediatric patients. Results from this report support the prospective collection of serial serum and tissue samples which may further identify genomic and immunophenotypic patterns predictive of response. Funding: This work was supported by Philanthropic funds (Pan Mass Challenge, Team Angus and Team Perspective).

Abstract We provide a formulation of quantum mechanics based on the cohomology of the Batalin-Vilkovisky (BV) algebra. Focusing on quantum-mechanical systems without gauge symmetry we introduce a homotopy retract from the chain complex of the harmonic oscillator to finite-dimensional phase space. This induces a homotopy transfer from the BV algebra to the algebra of functions on phase space. Quantum expectation values for a given operator or functional are computed by the function whose pullback gives a functional in the same cohomology class. This statement is proved in perturbation theory by relating the perturbation lemma to Wick’s theorem. We test this method by computing two-point functions for the harmonic oscillator for position eigenstates and coherent states. Finally, we derive the Unruh effect, illustrating that these methods are applicable to quantum field theory.

Abstract Background Immune checkpoint inhibitors (ICI) have improved outcomes in a variety of adult cancers and are prescribed with increasing frequency across oncology. However, patterns of off‐label use of ICI in pediatrics remain unclear. Methods This is a single‐institution, retrospective cohort study evaluating off‐label ICI use in pediatric and young adult patients with cancer treated at our institution from 2014 to 2022. Response was based on clinician assessment derived from clinical records. Immune‐related adverse events (iRAEs) were classified according to CTCAE v5.0. Results We identified 50 unique patients treated with off‐label ICI (28 with solid tumors, 20 with central nervous system (CNS) tumors, 2 with hematologic malignancies). At time of ICI initiation, only five patients (10%) had localized disease, and all but one patient was treated in the relapsed/refractory setting. All patients were treated with the FDA‐approved weight‐based dosing recommendations. Overall, there was disease control in 21 patients (42%), with best response including one complete response (melanoma), two partial responses (high‐grade glioma, CNS nongerminomatous germ cell tumor), and 18 patients with stable disease. Forty‐four patients (88%) eventually experienced disease progression. Among 22 patients (44%) experiencing iRAEs, 10 (20%) had a grade ≥3 irAE, 12 (24%) required corticosteroids, and 14 (28%) required ICI discontinuation. irAE occurrence was associated with significantly improved progression‐free survival (HR 0.35; 95% CI: 0.18 to 0.68; p = 0.002) and overall survival (HR 0.33; 95% CI: 0.17 to 0.66; p = 0.002). Conclusions At our institution, ICI was most commonly prescribed in the relapsed/refractory setting to patients with metastatic disease. The treatment was generally well‐tolerated in the pediatric population. The overall response rate was low, and the majority of patients eventually experienced disease progression. A few patients, however, had durable treatment responses. Further studies are needed to identify which pediatric patients are most likely to benefit from ICI.

IntroductionPrior studies have investigated the diagnostic potential of microRNA (miRNA) expression profiles for endometriosis. However, the vast majority of previous studies have only included adult women. Therefore, we sought to investigate differential expression of miRNAs among adolescents and young adults with endometriosis.MethodsThe Women's Health Study: from Adolescence to Adulthood (A2A) is an ongoing WERF EPHect compliant longitudinal cohort. Our analysis included 64 patients with surgically-confirmed endometriosis (96% rASRM stage I/II) and 118 females never diagnosed with endometriosis frequency matched on age (median = 21 years) and hormone use at blood draw. MicroRNA measurement was separated into discovery (10 cases and 10 controls) and internal replication (54 cases and 108 controls) phases. The levels of 754 plasma miRNAs were assayed in the discovery phase using PCR with rigorous internal control measures, with the relative expression of miRNA among cases vs. controls calculated using the 2−ΔΔCt method. miRNAs that were significant in univariate analyses stratified by hormone use were included in the internal replication phase. The internal replication phase was split 2:1 into a training and testing set and utilized FirePlex miRNA assay to assess 63 miRNAs in neural network analyses. The testing set of the validation phase was utilized to calculate the area under the curve (AUC) of the best fit models from the training set including hormone use as a covariate.ResultsIn the discovery phase, 49 miRNAs were differentially expressed between endometriosis cases and controls. The associations of the 49 miRNAs differed by hormone use at the time of blood draw. Neural network analysis in the testing set of the internal replication phase determined a final model comprising 5 miRNAs (miR-542-3p, let-7b-3p, miR-548i, miR-769-5p, miR-30c-1-3p), yielding AUC = 0.77 (95% CI: 0.67–0.87, p

Summary: Liver tumors account for approximately 2% of all pediatric malignancies. Children with advanced stages of hepatoblastoma (HB) are cured only 50–70% of the time while children with advanced hepatocellular carcinoma (HCC) have a

Abstract Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) comprise a spectrum of neurodegenerative diseases linked to TDP-43 proteinopathy, which at the cellular level, is characterized by loss of nuclear TDP-43 and accumulation of cytoplasmic TDP-43 inclusions that ultimately cause RNA processing defects including dysregulation of splicing, mRNA transport and translation. Complementing our previous work in motor neurons, here we report a novel model of TDP-43 proteinopathy based on overexpression of TDP-43 in a subset of Drosophila Kenyon cells of the mushroom body (MB), a circuit with structural characteristics reminiscent of vertebrate cortical networks. This model recapitulates several aspects of dementia-relevant pathological features including age-dependent neuronal loss, nuclear depletion and cytoplasmic accumulation of TDP-43, and behavioral deficits in working memory and sleep that occur prior to axonal degeneration. RNA immunoprecipitations identify several candidate mRNA targets of TDP-43 in MBs, some of which are unique to the MB circuit and others that are shared with motor neurons. Among the latter is the glypican Dally-like-protein (Dlp), which exhibits significant TDP-43 associated reduction in expression during aging. Using genetic interactions we show that overexpression of Dlp in MBs mitigates TDP-43 dependent working memory deficits, conistent with Dlp acting as a mediator of TDP-43 toxicity. Substantiating our findings in the fly model, we find that the expression of GPC6 mRNA, a human ortholog of dlp, is specifically altered in neurons exhibiting the molecular signature of TDP-43 pathology in FTD patient brains. These findings suggest that circuit-specific Drosophila models provide a platform for uncovering shared or disease-specific molecular mechanisms and vulnerabilities across the spectrum of TDP-43 proteinopathies.

Abstract Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.

Abstract Background Unintentional injuries, including traumatic brain injuries (TBI), are the leading cause of pediatric morbidity and mortality in the USA. Helmet usage can reduce TBI incidence and severity; however, the epidemiology of pediatric TBI and helmet use is ever evolving. With lifestyle changes potentially accelerated by the pandemic, we predicted a decrease in helmet utilization with an associated increase in TBI during the pandemic compared to the pre-pandemic period. Results There were 1093 patients that presented with AWHUR injuries from 2018 to 2020 with an annual increase from 263 patients in 2018 up to 492 in 2020. The most frequently implicated mechanisms included bicycles (35.9%), ATVs (20.3%), skateboards (11.6%), scooters (8.3%), and dirt bikes (7.4%). Unhelmeted patients increased from 111 (58.7%) in 2018 to 258 (64.8%) in 2020. There was not a significant difference in the proportion of injuries that were unhelmeted from 38.9% in 2018–2019 to 35.2% in 2020 (p = 0.30), as well as the proportion of head injuries from 2018 to 2019 (24.3%) to 2020 (29.3%) (p = 0.07). A significant increase was seen in neurosurgical consultation from 17 (6.5%) in 2018 to 87 (17.7%) in 2020 (p = 0.02). Notably, there was an increase in the percentage of publicly insured patients presenting with injuries from AWHUR during 2020 (p

Abstract Background Pediatric interventional oncology (PIO) is a growing field intended to provide additional or alternative treatment options for pediatric patients with benign or malignant tumors. Large series of patients treated uniformly and subjected to rigorous endpoints for efficacy are not available. Methods We designed a collaborative initiative to capture data from pediatric patients with benign and malignant tumors who underwent a therapeutic interventional radiology procedure. Modified Response Evaluation Criteria in Solid Tumors (mRECIST) was utilized as a measure of radiologic response and data were collected regarding improvement in pain and functional endpoints. Cumulative incidence of progressive disease was calculated using both the treated site and the patient as the analytic unit. Findings Forty patients, 16 with malignant tumors and 24 with benign tumors, underwent a total of 88 procedures. Cryo‐ and radiofrequency ablation were the most frequently utilized techniques for both cohorts of patients. A complete or partial response, or prolonged disease stability, were achieved in approximately 40% of patients with malignant tumors and 60% of patients with benign tumors. No patients had progressive disease as their best response. Resolution of pain and improved mobility with return‐to‐baseline activity were demonstrated across patients from both cohorts. Only minor complications were experienced. Interpretation Interventional radiology‐guided interventions can serve as an alternative or complementary approach to the treatment of benign and malignant tumors in pediatric patients. Prospective, multi‐institutional trials are required to adequately study utility, treatment endpoints, and durability of response.

Background: While the majority of reproductive-aged females will experience pelvic pain during their lives, biological mechanisms underlying pelvic pain are not well understood. We investigated associations between pelvic pain symptoms and oxidative stress among people with and without surgically-confirmed endometriosis. Methods: Using an enzyme-linked immunosorbent assay, we measured 8-Hydroxy-2’-deoxyguanosine (8-OHdG) in urine samples and corrected for creatinine levels in 434 surgically-confirmed endometriosis participants compared to 605 participants never diagnosed with endometriosis. At enrollment, participants reported details of their pelvic pain symptoms. Linear regression was used to compute geometric mean (GM) creatinine-corrected 8-OHdG levels with 95% confidence intervals (CI) among all participants and those with and without endometriosis separately, adjusting for potential confounders. Interactions by surgically-confirmed endometriosis status were tested by Wald statistics. Results: No trends in 8-OHdG were observed among those with or without endometriosis for severity or frequency of dysmenorrhea, acyclic pelvic pain, dyspareunia or pain with bowel movements. Among endometriosis participants, lower 8-OHdG levels were observed for participants with any white, blue/black, or brown lesions (GM=76.7 versus 82.9 ng/mg; p=0.10), which was primarily driven by lower levels of 8-OHdG for any blue/black lesions (GM=72.8 versus 81.6 ng/mg; p=0.05). Conclusion: While no associations were observed between 8-OHdG and pelvic pain symptoms, future research is needed to assess how other pathways of oxidative damage, e.g. through proteins or lipids, may affect endometriosis-associated symptoms. Additionally, further research is needed to understand differences in oxidative stress among endometriosis lesion sub-phenotypes.

IntroductionOver four million women in the US alone have been diagnosed with endometriosis. For those living with this disease, surgery and hormonal treatment reduce associated pelvic pain in some, while others continue to experience life impacting pain. Therefore, identification of accessible and cost-effective methods of pain reduction to compliment current treatment is urgently needed. Our objective was to quantify the prevalence of complementary and alternative methods used to manage acyclic pelvic pain and their reported benefit among women of different age groups living with endometriosis.MethodsWe used baseline questionnaire data from laparoscopically-confirmed endometriosis cases who completed a WERF EPHect compliant questionnaire in the longitudinal cohort of The Women's Health Study: From Adolescence to Adulthood (A2A). Participants with acyclic pelvic pain were asked to indicate specific methods or activities that either helped or worsened their pelvic/lower abdominal pain. Differences among age groups [adolescent (25 years)] were assessed using Fisher's exact test.ResultsOf the 357 participants included in analysis, sleep for coping was reported more frequently among adolescents (n = 59, 57.3%) compared to young adults (n = 40, 44.0%) and adults (n = 19, 31.1%; p = 0.004). Adolescents also reported more frequent use of music (n = 29, 21.2%) than young adults (n = 10, 7.0%) and adults (n = 7, 9.1%; p = 0.001). Exercise worsened pain most commonly among adolescents (n = 82, 59.9%), followed by younger adults (n = 67, 46.9%), and adults (n = 27, 35.1%; p = 0.002).DiscussionOur analysis of participants in the A2A cohort showed that the prevalence of complementary and alternative methods used for coping with endometriosis-associated acyclic pelvic pain varied by age group. Future studies should aim to provide information that will further inform decisions in making care plans for managing endometriosis-associated pain that is effective, accessible, and tailored to the preferences of the patient.

While all childhood cancers are rare, tumors that are particularly infrequent or underrepresented within pediatrics are studied under the umbrella of the Children’s Oncology Group Rare Tumor committee, divided into the Retinoblastoma and Infrequent Tumor subcommittees. The Infrequent Tumor subcommittee has traditionally included an emphasis on globally rare tumors such as adrenocortical carcinoma, nasopharyngeal carcinoma, or those tumors that are rare in young children, despite being common in adolescents and young adults, such as colorectal carcinoma, thyroid carcinoma, and melanoma. Pleuropulmonary blastoma, gonadal stromal tumors, pancreatic tumors including pancreatoblastoma, gastrointestinal stromal tumor, nonmelanoma skin cancers, neuroendocrine tumors, and desmoplastic small round cell tumors, as well as other carcinomas are also included under the heading of the Children’s Oncology Group Rare Tumor committee. While substantial challenges exist in rare cancers, inclusion and global collaboration remain key priorities to ensure high quality research to advance care.

BackgroundPeritoneal fluid is a medium for endometriosis-associated biomarker discovery from which the local peritoneal environment and pathophysiologic pathways are often inferred. Therefore, we evaluated the associations between peritoneal fluid color and volume at time of endometriosis-related laparoscopic surgery with patient characteristics, endometriosis type and lesion location in adolescents and young adults with endometriosis.MethodsWe conducted a cross-sectional analysis among 545 patients undergoing surgery for endometriosis who enrolled in the Women's Health Study: from Adolescence to Adulthood cohort study. Patient characteristics, surgically visualized endometriosis phenotypes, and gross characteristics of peritoneal fluid were collected in compliance with World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project (EPHect) tools. Chi-square or Fisher's exact tests were applied to test for differences across categories.ResultsMost of the patients were adolescents or young adults (86% age

Abstract We explore perturbative double field theory about time-dependent (cosmological) backgrounds to cubic order. To this order the theory is consistent in a weakly constrained sense, so that for a toroidal geometry it encodes both momentum and genuine winding modes. We give a self-contained discussion of the consistency problems and their resolution, including the role of cocycle factors and the O(d, d, ℤ) duality. Finally, as a first step toward the computation of cosmological correlation functions, we propose a generalized scalar-vector-tensor decomposition and use it to construct gauge invariant generalized Bardeen variables. Compared to standard cosmology there are fewer tensor modes but more vector and scalar modes.

Abstract The incidence and biochemical consequences of rare tumor subtypes are often hard to study. Fibrolamellar liver cancer (FLC) is a rare malignancy affecting adolescents and young adults. To better characterize the incidence and biochemical consequences of this disease, we combined a comprehensive analysis of the electronic medical record and national payer data and found that FLC incidence is likely five to eight times higher than previous estimates. By employing unsupervised learning on clinical laboratory data from patients with hyperammonemia, we find that FLC-associated hyperammonemia mirrors metabolic dysregulation in urea cycle disorders. Our findings demonstrate that advanced computational analysis of rich clinical datasets can provide key clinical and biochemical insights into rare cancers.

This study aimed to evaluate the influence of films based on chitosan and rosemary extract on the physicochemical, microbiological, and oxidative characteristics of beef. Refrigerated steaks of Longissimus dorsi were distributed in a factorial arrangement (4 × 4) into four treatments consisting of four edible films (control; chitosan; chitosan + 4% rosemary extract; and chitosan + 8% rosemary extract) and four days of aging (0, 2, 4, and 8 days). Incorporating 4% or 8% rosemary extract into the chitosan film improved the characteristics of the films in terms of moisture absorption and elasticity. The edible coatings with chitosan and rosemary extract and the different days of aging increased the tenderness and decreased the lipid oxidation of beef. In addition, the chitosan films containing rosemary extract increased the water-holding capacity and decreased the cooking losses of beef. The films containing 4% and 8% rosemary extract decreased the development of mesophilic and psychrotrophic bacteria and Staphylococcus ssp. in beef. We recommend incorporating 4% rosemary extract into chitosan-based coatings to preserve the quality of refrigerated beef.

Background: Ewing sarcoma is a rare tumor of the bone or soft tissues characterized by diffuse membranous staining for CD99. As this tumor remains incurable in the metastatic, relapsed, and refractory settings, we explored the downstream immune implications of targeting CD99. Methods: We discovered a human anti-CD99 antibody (NOA2) by phagemid panning and investigated NOA2 immune cell-mediated cytotoxicity in vitro and in vivo focusing on the myeloid cell compartment, given that M2 macrophages are present in human tumors and associated with a poor prognosis. Results: NOA2 is capable of inducing immune effector cell-mediated Ewing death in vitro via engagement of macrophages. Mice with metastatic Ewing tumors, treated with NOA2, experience tumor growth arrest and an associated increase in intratumoral macrophages. Further, incubation of macrophages and Ewing cells with NOA2, in conjunction with anti-PILRα antibody blockade in vitro, results in the reactivation of previously dormant macrophages possibly due to interrupted binding of Ewing CD99 to macrophage PILRα. Conclusions: These studies are the first to demonstrate the role of human immune effector cells in anti-CD99-mediated Ewing tumor death. We propose that the engagement of CD99 by NOA2 results in the recruitment of intratumoral macrophages. In addition, interruption of the CD99:PILRα checkpoint axis may be a relevant therapeutic approach to activate tumor-associated macrophages.

Abstract The urban environment influences human health, safety and wellbeing. Cities in Africa are growing faster than other regions but have limited data to guide urban planning and policies. Our aim was to use smart sensing and analytics to characterise the spatial patterns and temporal dynamics of features of the urban environment relevant for health, liveability, safety and sustainability. We collected a novel dataset of 2.1 million time-lapsed day and night images at 145 representative locations throughout the Metropolis of Accra, Ghana. We manually labelled a subset of 1,250 images for 20 contextually relevant objects and used transfer learning with data augmentation to retrain a convolutional neural network to detect them in the remaining images. We identified 23.5 million instances of these objects including 9.66 million instances of persons (41% of all objects), followed by cars (4.19 million, 18%), umbrellas (3.00 million, 13%), and informally operated minibuses known as tro tros (2.94 million, 13%). People, large vehicles and market-related objects were most common in the commercial core and densely populated informal neighbourhoods, while refuse and animals were most observed in the peripheries. The daily variability of objects was smallest in densely populated settlements and largest in the commercial centre. Our novel data and methodology shows that smart sensing and analytics can inform planning and policy decisions for making cities more liveable, equitable, sustainable and healthy.

Road traffic has become the leading source of air pollution in fast-growing sub-Saharan African cities. Yet, there is a dearth of robust city-wide data for understanding space-time variations and inequalities in combustion related emissions and exposures. We combined nitrogen dioxide (NO _2 ) and nitric oxide (NO) measurement data from 134 locations in the Greater Accra Metropolitan Area (GAMA), with geographical, meteorological, and population factors in spatio-temporal mixed effects models to predict NO _2 and NO concentrations at fine spatial (50 m) and temporal (weekly) resolution over the entire GAMA. Model performance was evaluated with 10-fold cross-validation (CV), and predictions were summarized as annual and seasonal (dusty [Harmattan] and rainy [non-Harmattan]) mean concentrations. The predictions were used to examine population distributions of, and socioeconomic inequalities in, exposure at the census enumeration area (EA) level. The models explained 88% and 79% of the spatiotemporal variability in NO _2 and NO concentrations, respectively. The mean predicted annual, non-Harmattan and Harmattan NO _2 levels were 37 (range: 1–189), 28 (range: 1–170) and 50 (range: 1–195) µ g m ^−3 , respectively. Unlike NO _2 , NO concentrations were highest in the non-Harmattan season (41 [range: 31–521] µ g m ^−3 ). Road traffic was the dominant factor for both pollutants, but NO _2 had higher spatial heterogeneity than NO. For both pollutants, the levels were substantially higher in the city core, where the entire population (100%) was exposed to annual NO _2 levels exceeding the World Health Organization (WHO) guideline of 10 µ g m ^−3 . Significant disparities in NO _2 concentrations existed across socioeconomic gradients, with residents in the poorest communities exposed to levels about 15 µ g m ^−3 higher compared with the wealthiest ( p < 0.001). The results showed the important role of road traffic emissions in air pollution concentrations in the GAMA, which has major implications for the health of the city’s poorest residents. These data could support climate and health impact assessments as well as policy evaluations in the city.

We aimed to assess whether object play can be used as a positive emotional state indicator for farmed spotted pacas (Cuniculus paca) by examining its association with other positive welfare markers including affiliative behavior and low-amplitude vocalizations. We submitted six groups of spotted pacas (one male/two females per group) (N = 18) to an ABA experimental design (A1/A2: without ball; B: with three boomer balls). Object play behavior occurred only during phase B (mean = 35.5 s, SE = 6.4). The spotted pacas spent more time in affiliative and exploratory behaviors and less time engaging in agonistic interactions during phase B than in both control phases (A1 and A2) (p < 0.05). Moreover, the spotted pacas emitted more low-amplitude bark vocalizations during phase B than during either control phase (p < 0.05), and such vocalizations have previously been shown to indicate a positive affective state and low arousal level. Because the expression of object play was associated with a decrease in aggression, an increase in affiliative behavior, and an increase in low-amplitude barking, we suggest that object play can be used as a non-invasive indicator of positive emotional state in this species.

IntroductionChronic pelvic pain (CPP) is a common condition affecting up to 26.6% of women, with many suffering for several years before diagnosis and/or treatment. Its clinical presentation is varied and there are frequently comorbid conditions both within and outside the pelvis. We aim to explore whether specific subgroups of women with CPP report different clinical symptoms and differing impact of pain on their quality of life (QoL).MethodsThe study is part of the Translational Research in Pelvic Pain (TRiPP) project which is a cross-sectional observational cohort study. The study includes 769 female participants of reproductive age who completed an extensive set of questions derived from standardised WERF EPHect questionnaires. Within this population we defined a control group (reporting no pelvic pain, no bladder pain syndrome, and no endometriosis diagnosis, N = 230) and four pain groups: endometriosis-associated pain (EAP, N = 237), interstitial cystitis/bladder pain syndrome (BPS, N = 72), comorbid endometriosis-associated pain and BPS (EABP, N = 120), and pelvic pain only (PP, N = 127).ResultsClinical profiles of women with CPP (13–50 years old) show variability of clinical symptoms. The EAP and EABP groups scored higher than the PP group (p

IntroductionPositive social comparative feedback indicates to the learner that they are performing better than others. While this type feedback supports motor skill learning in some tasks, the effect of social comparative feedback on implicit motor sequence learning remains unknown. The aim of this study was to determine the effect of positive social comparative feedback on the learning of and expectancies for a motor sequence task.MethodsForty-eight individuals practiced a joystick-based sequence task and were divided into three feedback groups: CONTROL (no performance feedback), RT ONLY (response time only feedback), and RT+POS (response time plus positive social comparison). Participants attended sessions on two consecutive days: Day 1 for repetitive motor practice/skill acquisition and Day 2 for retention testing. Performance related expectancies, like perceived competence, were measured before and after motor practice on Day 1 and at retention on Day 2.ResultsWhile all groups improved with practice, the CONTROL group showed better overall performance/learning (faster response times) compared with the RT ONLY group. Despite similar response times, the RT+POS showed higher peak velocities than the RT ONLY group. Overall, the RT+POS and CONTROL demonstrated increases in perceived competence while the RT ONLY group did not.DiscussionThe results of this study suggest that feedback content is an important consideration during motor practice sessions since feedback without context (RT ONLY) may be detrimental to motor sequence learning. The results also suggest that, if providing performance related feedback during practice of a skill that relies on implicit sequence learning processes, comparative context may be necessary for enhancing expectancies and supporting.

ObjectiveOptimal debulking with no macroscopic residual disease strongly predicts ovarian cancer survival. The ability to predict likelihood of optimal debulking, which may be partially dependent on tumor biology, could inform clinical decision-making regarding use of neoadjuvant chemotherapy. Thus, we developed a prediction model including epidemiological factors and tumor markers of residual disease after primary debulking surgery.MethodsUnivariate analyses examined associations of 11 pre-diagnosis epidemiologic factors (n=593) and 24 tumor markers (n=204) with debulking status among incident, high-stage, epithelial ovarian cancer cases from the Nurses’ Health Studies and New England Case Control study. We used Bayesian model averaging (BMA) to develop prediction models of optimal debulking with 5x5-fold cross-validation and calculated the area under the curve (AUC).ResultsCurrent aspirin use was associated with lower odds of optimal debulking compared to never use (OR=0.52, 95%CI=0.31-0.86) and two tissue markers, ADRB2 (OR=2.21, 95%CI=1.23-4.41) and FAP (OR=1.91, 95%CI=1.24-3.05) were associated with increased odds of optimal debulking. The BMA selected aspirin, parity, and menopausal status as the epidemiologic/clinical predictors with the posterior effect probability ≥20%. While the prediction model with epidemiologic/clinical predictors had low performance (average AUC=0.49), the model adding tissue biomarkers showed improved, but weak, performance (average AUC=0.62).ConclusionsAddition of ovarian tumor tissue markers to our multivariable prediction models based on epidemiologic/clinical data slightly improved the model performance, suggesting debulking status may be in part driven by tumor characteristics. Larger studies are warranted to identify those at high risk of poor surgical outcomes informing personalized treatment.

Abstract Background Prior studies have documented limited use of medications to treat opioid use disorders (OUD) for people incarcerated within state prisons in the United States. Using the framework of the criminal justice OUD service cascade, this study interviewed representatives of prison systems in states most heavily impacted by opioid overdose regarding the provision of medications for OUD (MOUD). Methods A stratified sampling strategy included states with high indicators of opioid-overdose deaths. Two sampling strata targeted states with: 1) OUD overdose rates significantly higher than the per capita national average; or 2) high absolute number of OUD overdose fatalities. Interviews were completed with representatives from 21 of the 23 (91%) targeted states in 2019, representing 583 prisons across these states. Interviews assessed service provision across the criminal justice OUD service cascade, including OUD screening, withdrawal management, MOUD availability and provision, overdose prevention, re-entry services, barriers, and needs for training and technical assistance. Results MOUD (buprenorphine, methadone, or naltrexone) was available in at least one prison in approximately 90% of the state prison systems and all three medications were available in at least one prison in 62% of systems. However, MOUD provision was limited to subsets of prisons within these systems: 15% provided buprenorphine, 9% provided methadone, 36% provided naltrexone, and only 7% provided all three. Buprenorphine and methadone were most frequently provided to pregnant women or individuals already receiving these at admission, whereas naltrexone was primarily used at release. Funding was the most frequently cited barrier for all medications. Conclusion Study findings yield a complex picture of how, when, and to whom MOUD is provided across prisons within prison systems in states most heavily impacted by opioid overdose in the United States and have implications for expanding availability.

Abstract Many of the > 3.5 million breast cancer survivors in the US have undergone breast reconstruction following mastectomy. Patients report that nipple-areolar complex (NAC) reconstruction is psychologically important, yet current reconstruction techniques commonly result in inadequate shape, symmetry, and nipple projection. Our team has developed an allogeneic acellular graft for NAC reconstruction (dcl-NAC) designed to be easy to engraft, lasting, and aesthetically pleasing. Here, dcl-NAC safety and host-mediated re-cellularization was assessed in a 6-week study in rhesus macaque non-human primates (NHPs). Human-derived dcl-NACs (n = 30) were engrafted on the dorsum of two adult male NHPs with each animal’s own nipples as controls (n = 4). Weight, complete blood counts, and metabolites were collected weekly. Grafts were removed at weeks 1, 3, or 6 post-engraftment for histology. The primary analysis evaluated health, re-epithelialization, and re-vascularization. Secondary analysis evaluated re-innervation. Weight, complete blood counts, and metabolites remained mostly within normal ranges. A new epidermal layer was observed to completely cover the dcl-NAC surface at week 6 (13–100% coverage, median 93.3%) with new vasculature comparable to controls at week 3 (p = 0.10). Nerves were identified in 75% of dcl-NACs (n = 9/12) at week 6. These data suggest that dcl-NAC is safe and supports host-mediated re-cellularization.

ABSTRACT There is growing evidence that genetic diversity in Mycobacterium tuberculosis, the causative agent of tuberculosis, contributes to the outcomes of infection and public health interventions, such as vaccination. Epidemiological studies suggest that among the phylogeographic lineages of M. tuberculosis, strains belonging to a sublineage of Lineage 2 (mL2) are associated with concerning clinical features, including hypervirulence, treatment failure, and vaccine escape. The global expansion and increasing prevalence of this sublineage has been attributed to the selective advantage conferred by these characteristics, yet confounding host and environmental factors make it difficult to identify the bacterial determinants driving these associations in human studies. Here, we developed a molecular barcoding strategy to facilitate high-throughput, experimental phenotyping of M. tuberculosis clinical isolates. This approach allowed us to characterize growth dynamics for a panel of genetically diverse M. tuberculosis strains during infection and after vaccination in the mouse model. We found that mL2 strains exhibit distinct growth dynamics in vivo and are resistant to the immune protection conferred by Bacillus Calmette-Guerin (BCG) vaccination. The latter finding corroborates epidemiological observations and demonstrates that mycobacterial features contribute to vaccine efficacy. To investigate the genetic and biological basis of mL2 strains’ distinctive phenotypes, we performed variant analysis, transcriptional studies, and genome-wide transposon sequencing. We identified functional genetic changes across multiple stress and host response pathways in a representative mL2 strain that are associated with variants in regulatory genes. These adaptive changes may underlie the distinct clinical characteristics and epidemiological success of this lineage. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a remarkably heterogeneous disease, a feature that complicates clinical care and public health interventions. The contributions of pathogen genetic diversity to this heterogeneity are uncertain, in part due to the challenges of experimentally manipulating M. tuberculosis, a slow-growing, biosafety level 3 organism. To overcome these challenges, we applied a molecular barcoding strategy to a panel of M. tuberculosis clinical isolates. This novel application of barcoding permitted the high-throughput characterization of M. tuberculosis strain growth dynamics and vaccine resistance in the mouse model of infection. Integrating these results with genomic analyses, we uncover bacterial pathways that contribute to infection outcomes, suggesting targets for improved therapeutics and vaccines.

Little is known about the quality of the special educators who move schools, switch to general education, or leave teaching. In this study, the author examined if turnover (moving schools within a district, moving schools between districts, switching to general education, or leaving teaching in the state) was associated with two common indicators of teacher quality: value-added scores or teaching observation scores. On average, special educators' probability of leaving teaching in the state declined as their value-added score increased, after accounting for the characteristics of teachers, their students, and their schools. Observation scores were similarly negatively associated with leaving and with moving within or between districts. Eight percent of special educators switched to general education positions, and the probability of switching was not associated with teachers' value-added or observation scores. The author discusses the implications for ensuring schools retain effective special educators while noting the limitations of current measures of special educator quality used in practice.

Abstract We show that the perturbative expansion of general gauge theories can be expressed in terms of gauge invariant variables to all orders in perturbations. In this we generalize techniques developed in gauge invariant cosmological perturbation theory, using Bardeen variables, by interpreting the passing over to gauge invariant fields as a homotopy transfer of the strongly homotopy Lie algebras encoding the gauge theory. This is illustrated for Yang-Mills theory, gravity on flat and cosmological backgrounds and for the massless sector of closed string theory. The perturbation lemma yields an algorithmic procedure to determine the higher corrections of the gauge invariant variables and the action in terms of these.

Abstract Background Single patient Investigational New Drug (IND) applications are one mechanism through which experimental therapies are accessed for children with cancer. The landscape of use, outcomes, and toxicity from single patient INDs remains unknown in pediatric oncology. Methods We performed a retrospective analysis of all single patient INDs requested and prescribed at a single institution between 1/1/2007 and 5/1/2019. We report aggregate data from the US Food and Drug Administration (FDA) on single patient IND applications over the final two years of the study (2017–2019). We report an overview of all IND applications, as well as clinical descriptions of patients, treatments, outcomes, and toxicity. Results Over the 2‐year period, the FDA approved all 171 submitted single patient IND requests for pediatric oncology. We identified 56 requests from our center during the 12‐year study period, and all were approved (median time from FDA submission to approval: 1 day (range 0–12)). 71% of requests were based on disease histology. Lack of pediatric clinical trial (65%) was the most common reason for use. 48 approved requests were ultimately administered. The median duration of treatment was 84 days (range: 4–1590), with 3 patients remaining on treatment at time of analysis. Only 7% discontinued treatment due to toxicity. Three‐year overall survival was 50% (95% CI, 35–64). Conclusions Single patient INDs in pediatric oncology were universally approved in our national and single‐center analysis. In our cohort, single patient INDs were primarily utilized based on disease histology, rather than genomics, for agents that lacked a clinical trial.

Costimulation pathways play an essential role in T cell activation, differentiation, and regulation. CD155 expressed on antigen-presenting cells (APCs) interacts with TIGIT, an inhibitory costimulatory molecule, and CD226, an activating costimulatory molecule, on T cells. TIGIT and CD226 are expressed at varying levels depending on the T cell subset and activation state. T follicular helper cells in germinal centers (GC-Tfh) in human tonsils express high TIGIT and low CD226. However, the biological role of the CD155/TIGIT/CD226 axis in human Tfh cell biology has not been elucidated. To address this, we analyzed tonsillar CD4+ T cell subsets cultured with artificial APCs constitutively expressing CD155. Here we show that CD226 signals promote the early phase of Tfh cell differentiation in humans. CD155 signals promoted the proliferation of naïve CD4+ T cells and Tfh precursors (pre-Tfh) isolated from human tonsils and upregulated multiple Tfh molecules and decreased IL-2, a cytokine detrimental for Tfh cell differentiation. Blocking CD226 potently inhibited their proliferation and expression of Tfh markers. By contrast, while CD155 signals promoted the proliferation of tonsillar GC-Tfh cells, their proliferation required only weak CD226 signals. Furthermore, attenuating CD226 signals rather increased the expression of CXCR5, ICOS, and IL-21 by CD155-stimulated GC-Tfh cells. Thus, the importance of CD226 signals changes according to the differentiation stage of human Tfh cells and wanes in mature GC-Tfh cells. High TIGIT expression on GC-Tfh may play a role in attenuating the detrimental CD226 signals post GC-Tfh cell maturation.

Endometriosis affects reproductive-aged females and varies considerably in terms of symptom presentation, morphologic features, and treatment response. Most studies investigating symptom recurrence after an endometriosis-related surgery have been conducted among adults. The Endometriosis pain QUality aftEr Surgical Treatment (EndoQUEST) Study was established to assess characteristics and biomarkers that are associated with pain remediation and improved quality of life after an endometriosis-related surgery among adolescents and young adults. This paper describes the EndoQUEST methodology, summarizes baseline descriptive factors, and compares characteristics by participant retention status. We enrolled 100 surgically-confirmed endometriosis participants aged 12-23 years who provided questionnaire data on reproductive and behavioral factors, pain characteristics and quality of life at three time points; before surgery, 6 weeks to 26 weeks after surgery, and 1 year after surgery. Among these 100 participants, 88 provided blood and/or saliva at all three time points, while 12 provided blood and/or saliva samples only before surgery and 6 to 26 weeks after surgery. There was little evidence of lost to follow-up at 1 year after surgery due to pain symptoms, as pain and quality of life characteristics were similar between participants who completed the questionnaire 1 year after surgery and those who did not. Analyses utilizing these longitudinal data will advance personalized treatment decision making for adolescents and young adults with endometriosis.

The skin functions as a protective barrier to inhibit the entry of foreign pathogens, all the while hosting a diverse milieu of microorganisms. Over time, skin cells, immune cells, cytokines, and microbes interact to integrate the processes of maintaining the skin’s physical and immune barrier. In the present study, the basal expression of two immunologically divergent mouse strains C57BL/6 and BALB/c, as well as a strain on the C57 background lacking IL-6, was characterized. Additionally, cutaneous antimicrobial gene expression profiles and skin bacterial microbiome were assessed between strains. Total RNA sequencing was performed on untreated C57BL/6 (control), BALB/c, and IL-6-deficient skin samples and found over 3,400 genes differentially modulated between strains. It was found that each strain modulated its own transcriptional “profile” associated with skin homeostasis and also influenced the overall bacterial colonization as indicated by the differential phyla present on each strain. Together, these data not only provide a comprehensive view of the transcriptional changes in homeostatic skin of different mouse strains but also highlight the possible influence of the strain differences (e.g., Th1/Th2 balance) as well as a role for IL-6 in overall skin immunity and resident microbial populations.

Drawing on eight waves of the Schools and Staffing Survey and the National Teacher and Principal Survey, we used a difference-in-differences research design to examine special education teachers' (SETs) responses to No Child Left Behind (NCLB) and the subsequent reauthorization of the Individuals with Disabilities Education Act (IDEA). IDEA was associated with decreases in the proportion of SETs with special education as a field of study and graduate degrees, an increase in co-teaching, and a decrease in the proportion of SETs working in a resource delivery model, with no evidence that NCLB influenced these outcomes. Little consistent evidence was found to indicate these federal policies influenced SETs' job attitudes (e.g., job satisfaction). We identified differences in these associations based on school poverty status and grade level. These findings help to better understand the status and challenges of the current SET workforce and the unintended consequences of federal reform policies.

Abstract Background Cancer Antigen 125 (CA125) is currently the best available ovarian cancer screening biomarker. However, CA125 has been limited by low sensitivity and specificity in part due to normal variation between individuals. Personal characteristics that influence CA125 could be used to improve its performance as screening biomarker. Methods We developed and validated linear and dichotomous (≥35 U/mL) circulating CA125 prediction models in postmenopausal women without ovarian cancer who participated in one of five large population-based studies: Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO, n = 26,981), European Prospective Investigation into Cancer and Nutrition (EPIC, n = 861), the Nurses’ Health Studies (NHS/NHSII, n = 81), and the New England Case Control Study (NEC, n = 923). The prediction models were developed using stepwise regression in PLCO and validated in EPIC, NHS/NHSII and NEC. Result The linear CA125 prediction model, which included age, race, body mass index (BMI), smoking status and duration, parity, hysterectomy, age at menopause, and duration of hormone therapy (HT), explained 5% of the total variance of CA125. The correlation between measured and predicted CA125 was comparable in PLCO testing dataset (r = 0.18) and external validation datasets (r = 0.14). The dichotomous CA125 prediction model included age, race, BMI, smoking status and duration, hysterectomy, time since menopause, and duration of HT with AUC of 0.64 in PLCO and 0.80 in validation dataset. Conclusions The linear prediction model explained a small portion of the total variability of CA125, suggesting the need to identify novel predictors of CA125. The dichotomous prediction model showed moderate discriminatory performance which validated well in independent dataset. Our dichotomous model could be valuable in identifying healthy women who may have elevated CA125 levels, which may contribute to reducing false positive tests using CA125 as screening biomarker.

Background: We present the first reported case of heterotopic gastric mucosa (HGM) with pyloric type metaplasia obstructing the bile duct, with a literature review of bile duct obstruction from other types of HGM in children and adults. Case presentation: A 10-year old boy presented with severe, episodic, post-prandial, epigastric pain. An extensive work-up found a partially obstructing lesion of the common bile duct adjacent to the cystic duct. He underwent surgical resection of the lesion with restoration of the biliary drainage via choledocho-duodenostomy. Pathology revealed heterotopic gastric mucosa with pyloric metaplasia. Recovery was uneventful and he remains symptom-free 36 months later. Conclusions: Obstructing lesions of the biliary tree are exceedingly rare in children. In contrast with adults, there is minimal concern that such a lesion represents a malignancy. This may lead to prolonged diagnostic work-up as opposed to early surgical exploration. While it can be difficult to differentiate between benign and high-risk bile duct lesions in adults, malignant transformation of HGM of the bile duct has only been reported in an adult. In every pediatric and adult case reviewed, surgical exploration was required to establish the diagnosis. Our patient's pathology revealed pyloric type metaplasia as a component of HGM. This is the first report of pyloric type metaplasia in the literature. Previously reports have only shown HGM of fundic origin. We advocate early resection of these lesions for both diagnostic purposes, and due to the potential for malignant transformation.

Introduction Air and noise pollution are emerging environmental health hazards in African cities, with potentially complex spatial and temporal patterns. Limited local data are a barrier to the formulation and evaluation of policies to reduce air and noise pollution.Methods and analysis We designed a year-long measurement campaign to characterise air and noise pollution and their sources at high-resolution within the Greater Accra Metropolitan Area (GAMA), Ghana. Our design uses a combination of fixed (year-long, n=10) and rotating (week-long, n =~130) sites, selected to represent a range of land uses and source influences (eg, background, road traffic, commercial, industrial and residential areas, and various neighbourhood socioeconomic classes). We will collect data on fine particulate matter (PM2.5), nitrogen oxides (NOx), weather variables, sound (noise level and audio) along with street-level time-lapse images. We deploy low-cost, low-power, lightweight monitoring devices that are robust, socially unobtrusive, and able to function in Sub-Saharan African (SSA) climate. We will use state-of-the-art methods, including spatial statistics, deep/machine learning, and processed-based emissions modelling, to capture highly resolved temporal and spatial variations in pollution levels across the GAMA and to identify their potential sources. This protocol can serve as a prototype for other SSA cities.Ethics and dissemination This environmental study was deemed exempt from full ethics review at Imperial College London and the University of Massachusetts Amherst; it was approved by the University of Ghana Ethics Committee (ECH 149/18-19). This protocol is designed to be implementable in SSA cities to map environmental pollution to inform urban planning decisions to reduce health harming exposures to air and noise pollution. It will be disseminated through local stakeholder engagement (public and private sectors), peer-reviewed publications, contribution to policy documents, media, and conference presentations.

Background: Caregiver strain is recognized globally with Parkinson's disease (PD). Comparatively little is understood about caregiver burden and strain in Asia.Objective: To investigate caregiver strain for families living with PD in Singapore, in light of international data.Methods: Ninety-four caregivers were recruited via people living with idiopathic PD in Singapore. Caregiver strain was assessed using the Zarit Burden Interview (ZBI); health status was assessing using the Cumulative Illness Rating Scale for Geriatrics (CIRS-G). PD disability measures were the Unified Parkinson's Disease Rating Scale (UPDRS) and modified Hoehn and Yahr (1967) Scale.Results: Primary caregivers of people living with PD in Singapore were mostly cohabiting spouses, partners or offspring. Around half employed foreign domestic helpers. Mean caregiving duration was 5.9 years with an average of eight hours per day spent in caregiving roles. Most care providers were comparatively healthy. Caregivers reported significant levels of strain which increased with greater level of disability (r = 0.36, n = 94, p < 0.001). Associations were significant between caregiver strain and scores on the UPDRS mentation, behavior, and mood subscales [r = 0.46, n = 94, p < 0.001, 95% CI (0.28, 0.60)]. High scores on the UPDRS activities of daily living subscale were associated with caregiver strain [r = 0.50, n = 94, p < 0.001, CI (0.33, 0.64)].Conclusion: Most caregivers in this Singapore sample reported high levels of strain, despite comparatively good physical function. Caregiver strain in PD spans geopolitical and cultural boundaries and correlates with disease severity. These results support the need for better early recognition, education, and support for caregivers of people living with PD.

Endometriosis is a painful gynecologic disease affecting one in ten reproductive aged women worldwide. Few studies have correlated this symptomatology with biomarker levels among women with and without endometriosis, and no studies correlating pain with biomarker levels have been performed in young patient populations. The purpose of this study was to examine whether CA125 correlates with different types and severity of pain among adolescents and young women with and without endometriosis and assess its performance as an endometriosis biomarker among those presenting with dysmenorrhea in this young population. Reproductive-aged women with laparoscopically-confirmed endometriosis (n = 282) and controls (n = 293) who participated in The Women's Health Study: From Adolescence to Adulthood (A2A), a cohort of adolescents and young women enrolled from 2012-2018, were included in this cross-sectional analysis. Plasma CA125 values were measured using WERF EPHect compliant blood samples collected at enrollment. Average CA125 were calculated by self-reported pain type (i.e. dysmenorrhea, non-cyclic/general pelvic pain, dyspareunia), severity, and frequency in endometriosis cases and controls. Median age at blood draw was 24 years in controls and 17 years in cases, with 68% and 89% non-Hispanic white, respectively. Most endometriosis cases (95%) were rASRM stage I/II. Average CA125 values were 12.5 U/mL in controls and 12.1 U/mL in cases adjusted for age. CA125 did not differ by pain type, its severity, or frequency in endometriosis cases or controls. Among participants who reported dysmenorrhea, CA125 did not discriminate endometriosis cases from controls using cutoff of 35 U/mL (AUC = 0.51, 95%CI = 0.50-0.53). Among adolescents and young adult women, CA125 did not correlate with pain type. CA125 did not efficiently discriminate endometriosis cases from controls even when accounting for pain symptomatology. Average CA125 values were low in adolescents and young women in both endometriosis cases and controls, suggesting cautious interpretation may be needed when measuring CA125 in this population.

Response to intervention (RTI) is a method for providing academic support to students and for identifying specific learning disabilities (SLDs). Using interrupted time series and hazard models, we examined if statewide RTI adoption in the U.S. state of Tennessee was associated with changes in rates of SLD and first-time SLD identification in elementary schools, and if these associations varied across student groups. Response to intervention was associated with an initial decline in the percentage of students with SLD in the state that continued over time, with larger decreases for students who were Black or economically disadvantaged. Response to intervention was associated with a 61% average decrease in the odds of first-time SLD identification by third grade (about a 0.006 change in the predicted probability), with greater declines for students who were Black or economically disadvantaged. We discuss these results in the context of disproportionality in special education and the need for research examining whether declines in SLD were due to improved academic outcomes, as opposed to delays in identification.

[This corrects the article DOI: 10.1371/journal.ppat.1006939.].

ABSTRACT In Mycobacterium tuberculosis, recent genome-wide association studies have identified a novel constellation of mutations that are correlated with high-level drug resistances. Interpreting the functional importance of the new resistance-associated mutations has been complicated, however, by a lack of experimental validation and a poor understanding of the epistatic factors influencing these correlations, including strain background and programmatic variation in treatment regimens. Here we perform a genome-wide association analysis in a panel of Mycobacterium tuberculosis strains from China to identify variants correlated with resistance to the second-line prodrug ethionamide (ETH). Mutations in a bacterial monooxygenase, Rv0565c, are significantly associated with ETH resistance. We demonstrate that Rv0565c is a novel activator of ETH, independent of the two known activators, EthA and MymA. Clinically prevalent mutations abrogate Rv0565c function, and deletion of Rv0565c confers a consistent fitness benefit on M. tuberculosis in the presence of partially inhibitory doses of ETH. Interestingly, Rv0565c activity affects susceptibility to prothionamide (PTH), the ETH analog used in China, to a greater degree. Further, clinical isolates vary in their susceptibility to both ETH and PTH, to an extent that correlates with the total expression of ETH/PTH activators (EthA, MymA, and Rv0565c). These results suggest that clinical strains considered susceptible to ETH/PTH are not equally fit during treatment due to both Rv0565c mutations and more global variation in the expression of the prodrug activators. IMPORTANCE Phenotypic antibiotic susceptibility testing in Mycobacterium tuberculosis is slow and cumbersome. Rapid molecular diagnostics promise to help guide therapy, but such assays rely on complete knowledge of the molecular determinants of altered antibiotic susceptibility. Recent genomic studies of antibiotic-resistant M. tuberculosis have identified several candidate loci beyond those already known to contribute to antibiotic resistance; however, efforts to provide experimental validation have lagged. Our study identifies a gene (Rv0565c) that is associated with resistance to the second-line antibiotic ethionamide at a population level. We then use bacterial genetics to show that the variants found in clinical strains of M. tuberculosis improve bacterial survival after ethionamide exposure.

Multitiered systems for supporting students' behavior in schools rely on teachers using generally effective classroom management strategies, such as Tier 1 practices. However, few tools exist to easily assess classwide Tier 1 practices. In this brief report, we describe one potential tool, the Classroom Atmosphere Rating Scale--Brief (CARS-B) and assess the properties of the tool using item response theory and multilevel models. We found that most items on the CARS-B had acceptable discriminations and difficulty estimates. Teachers' CARS-B latent scores were positively associated with student group on-task. We discuss potential changes to the CARS-B and its use in research and practice.

Visualization of infection and the associated host response has been challenging in adult vertebrates. Owing to their transparency, zebrafish larvae have been used to directly observe infection in vivo; however, such larvae have not yet developed a functional adaptive immune system. Cells involved in adaptive immunity mature later and have therefore been difficult to access optically in intact animals. Thus, the study of many aspects of vertebrate infection requires dissection of adult organs or ex vivo isolation of immune cells. Recently, CLARITY and PACT (passive clarity technique) methodologies have enabled clearing and direct visualization of dissected organs. Here, we show that these techniques can be applied to image host-pathogen interactions directly in whole animals. CLARITY and PACT-based clearing of whole adult zebrafish and Mycobacterium tuberculosis-infected mouse lungs enables imaging of mycobacterial granulomas deep within tissue to a depth of more than 1 mm. Using established transgenic lines, we were able to image normal and pathogenic structures and their surrounding host context at high resolution. We identified the three-dimensional organization of granuloma-associated angiogenesis, an important feature of mycobacterial infection, and characterized the induction of the cytokine tumor necrosis factor (TNF) within the granuloma using an established fluorescent reporter line. We observed heterogeneity in TNF induction within granuloma macrophages, consistent with an evolving view of the tuberculous granuloma as a non-uniform, heterogeneous structure. Broad application of this technique will enable new understanding of host-pathogen interactions in situ.

CFTR modulators have revolutionized the treatment of individuals with cystic fibrosis (CF) by improving the function of existing protein. Unfortunately, almost half of the disease-causing variants in CFTR are predicted to introduce premature termination codons (PTC) thereby causing absence of full-length CFTR protein. We hypothesized that a subset of nonsense and frameshift variants in CFTR allow expression of truncated protein that might respond to FDA-approved CFTR modulators. To address this concept, we selected 26 PTC-generating variants from four regions of CFTR and determined their consequences on CFTR mRNA, protein and function using intron-containing minigenes expressed in 3 cell lines (HEK293, MDCK and CFBE41o-) and patient-derived conditionally reprogrammed primary nasal epithelial cells. The PTC-generating variants fell into five groups based on RNA and protein effects. Group A (reduced mRNA, immature (core glycosylated) protein, function 1% (n = 5)), Group D (reduced mRNA, mature protein, function >1% (n = 5)) and Group E (aberrant RNA splicing, mature protein, function > 1% (n = 1)) variants responded to modulators. Increasing mRNA level by inhibition of NMD led to a significant amplification of modulator effect upon a Group D variant while response of a Group A variant was unaltered. Our work shows that PTC-generating variants should not be generalized as genetic 'nulls' as some may allow generation of protein that can be targeted to achieve clinical benefit.

For many pathogens, including most targets of effective vaccines, infection elicits an immune response that confers significant protection against reinfection. There has been significant debate as to whether natural Mycobacterium tuberculosis (Mtb) infection confers protection against reinfection. Here we experimentally assessed the protection conferred by concurrent Mtb infection in macaques, a robust experimental model of human tuberculosis (TB), using a combination of serial imaging and Mtb challenge strains differentiated by DNA identifiers. Strikingly, ongoing Mtb infection provided complete protection against establishment of secondary infection in over half of the macaques and allowed near sterilizing bacterial control for those in which a secondary infection was established. By contrast, boosted BCG vaccination reduced granuloma inflammation but had no impact on early granuloma bacterial burden. These findings are evidence of highly effective concomitant mycobacterial immunity in the lung, which may inform TB vaccine design and development.

Once considered a phenotypically monomorphic bacterium, there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis (Mtb) strains in clinically relevant characteristics, including virulence and response to antibiotics. However, the genetic and molecular basis for most phenotypic differences among Mtb strains remains unknown. To investigate the basis of strain variation in Mtb, we performed genome-wide transposon mutagenesis coupled with next-generation sequencing (TnSeq) for a panel of Mtb clinical isolates and the reference strain H37Rv to compare genetic requirements for in vitro growth across these strains. We developed an analytic approach to identify quantitative differences in genetic requirements between these genetically diverse strains, which vary in genomic structure and gene content. Using this methodology, we found differences between strains in their requirements for genes involved in fundamental cellular processes, including redox homeostasis and central carbon metabolism. Among the genes with differential requirements were katG, which encodes the activator of the first-line antitubercular agent isoniazid, and glcB, which encodes malate synthase, the target of a novel small-molecule inhibitor. Differences among strains in their requirement for katG and glcB predicted differences in their response to these antimicrobial agents. Importantly, these strain-specific differences in antibiotic response could not be predicted by genetic variants identified through whole genome sequencing or by gene expression analysis. Our results provide novel insight into the basis of variation among Mtb strains and demonstrate that TnSeq is a scalable method to predict clinically important phenotypic differences among Mtb strains.

BackgroundLiver tumors are rare in children with histologic heterogeneity that makes diagnosis challenging. Systematic histopathological review, performed as part of collaborative therapeutic protocols, identified relevant histologic subtypes that are important to distinguish. The Children's Hepatic tumors International Collaboration (CHIC) was established to study pediatric liver tumors on a global scale and led to establishment of a provisional consensus classification for use in international clinical trials. The current study is the validation of this initial classification and first large-scale application by international expert reviewers.ProcedureThe CHIC initiative includes data from 1605 children treated on eight multicenter hepatoblastoma (HB) trials. Review of 605 available tumors was performed by seven expert pathologists from three consortia (US, EU, Japan). Cases with discordant diagnoses were collectively reviewed to reach a final consensus diagnosis.ResultsOf 599 cases with sufficient material for review, 570 (95.2%) were classified as HB by all consortia, and 29 (4.8%) as non-HB, which included "hepatocellular neoplasm, NOS" and malignant rhabdoid tumors. 453 of 570 HBs were classified as epithelial by final consensus. Some patterns (i.e., small cell undifferentiated, macrotrabecular, cholangioblastic) were selectively identified by reviewers from different consortia. All consortia identified a similar number of mixed epithelial-mesenchymal HB.ConclusionsThis study represents the first large-scale application and validation of the pediatric malignant hepatocellular tumors consensus classification. It is a valuable resource to train future generations of investigators on accurate diagnosis of these rare tumors and provides a framework for further international collaborative studies and refinement of the current classification of pediatric liver tumors.

Recent studies posit a role for non-coding RNAs in epithelial ovarian cancer (EOC). Combining small RNA sequencing from 179 human serum samples with a neural network analysis produced a miRNA algorithm for diagnosis of EOC (AUC 0.90; 95% CI: 0.81–0.99). The model significantly outperformed CA125 and functioned well regardless of patient age, histology, or stage. Among 454 patients with various diagnoses, the miRNA neural network had 100% specificity for ovarian cancer. After using 325 samples to adapt the neural network to qPCR measurements, the model was validated using 51 independent clinical samples, with a positive predictive value of 91.3% (95% CI: 73.3–97.6%) and negative predictive value of 78.6% (95% CI: 64.2–88.2%). Finally, biologic relevance was tested using in situ hybridization on 30 pre-metastatic lesions, showing intratumoral concentration of relevant miRNAs. These data suggest circulating miRNAs have potential to develop a non-invasive diagnostic test for ovarian cancer.

Effective CD8 T cell responses are vital for the control of chronic viral infections. Many factors of the host immune response contribute to the maintenance of effector CD8 T cell responses versus CD8 T cell exhaustion during chronic infection. Specific MHC alleles and the degree of MHC heterogeneity are associated with enhanced CD8 T cell function and viral control during human chronic infection. However, it is currently unclear to what extent host genetics influences the establishment of chronic viral infection. In order to examine the impact of MHC heterogeneity versus non-MHC host genetics on the development of chronic viral infection, an F1 cross of B10.D2 x B6 (D2B6F1) and BALB.B x BALB/c (BCF1) mice were infected with the clone-13 (Cl-13) strain of lymphocytic choriomeningitis virus (LCMV). Following chronic Cl-13 infection both H-2bxd D2B6F1 and BCF1 mice demonstrated increased viral control compared to homozygous mice. Strikingly, H-2bxd D2B6F1 mice on a C57BL genetic background exhibited mortality following Cl-13 infection. CD8 T cell depletion prevented mortality in Cl-13-infected D2B6F1 mice indicating that mortality was CD8 T-cell-dependent. D2B6F1 mice maintained more CD8 T cell effector cytokine production and exhibited reduced expression of the T cell exhaustion marker PD-1. In addition, D2B6F1 mice also induced a larger Th1 response than BCF1 mice and Cl-13-induced mortality in D2B6F1 mice was also dependent on CD4 T-cell-mediated IFN-γ production. Thus, following a chronic viral infection, increased functionality of the CD8 T cell response allowed for more rapid viral clearance at the cost of enhanced immunopathology dependent on both MHC diversity and the genetic background of the host.