DNA glycosylases provide antiviral defence in prokaryotes.

Bacteria have adapted to phage predation by evolving a vast assortment of defence systems1. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data2. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library3 with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.

Pharmacokinetic-Pharmacodynamic Evidence From a Phase 3 Trial to Support Flat-Dosing of Rifampicin for Tuberculosis.

BACKGROUND: The optimal dosing strategy for rifampicin in treating drug-susceptible tuberculosis (TB) is still highly debated. In the phase 3 clinical trial Study 31/ACTG 5349 (NCT02410772), all participants in the control regimen arm received 600 mg rifampicin daily as a flat dose. Here, we evaluated relationships between rifampicin exposure and efficacy and safety outcomes. METHODS: We analyzed rifampicin concentration time profiles using population nonlinear mixed-effects models. We compared simulated rifampicin exposure from flat- and weight-banded dosing. We evaluated the effect of rifampicin exposure on stable culture conversion at 6 months; TB-related unfavorable outcomes at 9, 12, and 18 months using Cox proportional hazard models; and all trial-defined safety outcomes using logistic regression. RESULTS: Our model-derived rifampicin exposure ranged from 4.57 mg · h/L to 140.0 mg · h/L with a median of 41.8 mg · h/L. Pharmacokinetic simulations demonstrated that flat-dosed rifampicin provided exposure coverage similar to the weight-banded dose. Exposure-efficacy analysis (n = 680) showed that participants with rifampicin exposure below the median experienced similar hazards of stable culture conversion and TB-related unfavorable outcomes compared with those with exposure above the median. Exposure-safety analysis (n = 722) showed that increased rifampicin exposure was not associated with increased grade 3 or higher adverse events or serious adverse events. CONCLUSIONS: Flat-dosing of rifampicin at 600 mg daily may be a reasonable alternative to the incumbent weight-banded dosing strategy for the standard-of-care 6-month regimen. Future research should assess the optimal dosing strategy for rifampicin, at doses higher than the current recommendation.

Trends in epidemiology and primary treatment of anal squamous cell carcinoma in the Netherlands (1990-2021).

A rapid increase in the incidence of anal squamous cell carcinoma (SCC) was reported in several countries over the past decades. This study assessed trends in epidemiology and primary treatment over a 32-year period (1990-2021) using the Netherlands Cancer Registry. The study population included 4273 patients, 44.2% male and 55.8% female (median age 63 years). The age-standardised incidence rate (European Standardised Rate, ESR) increased from 0.5 to 1.6 per 100,000, which entailed an average annual percentage change (AAPC) of 5.0% (95% confidence interval [CI]: 4.5%-5.8%). While incidence among females increased continuously over the total period (AAPC 4.9%; 95%CI: 4.4%-5.6%), to 1.8 per 100,000 ESR in 2021, incidence among males increased until 2016 (annual percentage change [APC] of 6.3%; 95%CI: 5.6%-10.7%), after which it seemed to stabilise (APC -2.1%; 95%CI: -16.8%-4.5%). Significant trends were also observed in distribution of age, tumour stage and primary treatment modalities. Five-year relative survival (RS) was estimated using the Pohar-Perme estimator, and this improved from 56.1% in 1990-1997 (95%CI: 49.3%-62.4%) to 67.9% in 2014-2021 (95%CI: 64.7%-70.9%), but remained poor for stage IV disease. Evaluation through a multivariable Poisson regression model demonstrated diagnosis in the most recent period to be independently associated with better RS, in addition to female sex, younger age, early disease stage and any treatment. In conclusion, the rising incidence of anal SCC seems to decline in males, but not in females, and advances in diagnostics and therapeutic management have likely contributed to improved prognosis.

Uptake of intermittent preventive treatment of malaria in pregnancy and risk factors for maternal anaemia and low birthweight among HIV-negative mothers in Dschang, West region of Cameroon: a cross sectional study.

BACKGROUND: Approximately 32 million pregnant women are at risk of malaria with up to 10,000 maternal deaths and 200,000 neonates at risk annually. Intermittent Preventive Treatment (IPT) with sulfadoxine-pyrimethamine (SP) is recommended by the World Health Organization (WHO) to reduce disease in pregnancy and adverse maternal and newborn outcomes. At least three doses of SP should be taken by pregnant women during antenatal consultation (ANC) beginning from the thirteenth week of pregnancy till parturition. The aim of this study was to assess uptake of IPT during pregnancy and risk factors for maternal anaemia and infant birth weight in Dschang, West region of Cameroon. METHODS: A total of 380 consenting pregnant women at delivery were recruited in a cross- sectional prospective survey between January to December 2021. Data on ANC attendance, total dose of IPT and history of malaria were abstracted from hospital ANC records while socio-demographic characteristics, bed net use and obstetrics history of each participant were also recorded through an interview. Further, blood samples were collected from the intervillous space for assessment of maternal anaemia and microscopic parasitology. Nested PCR based on amplification of the Plasmodium 18S sRNA was carried out to detect submicroscopic infection. IPTp coverage was calculated per WHO recommendation and the prevalence of anaemia and low birth weight were estimated as proportions in the total sample of pregnant women and live births, respectively. Crude and adjusted odds ratios and their 95% confidence intervals were used to estimate associations between pregnancy outcomes considered and risk factors in specific and general models. A p < 0.05 was considered significant. The R software (V4.1.4) was used for all analyses. RESULTS: A majority of pregnant women was aged between 24 and 34 years old (59.2%) and had secondary education (58.8%). Uptake of ≥ 3 IPTp was 64.99% with 77.20% of all who received at least one IPTp doses taking a mix of SP and DP or DP alone in successive ANC contacts. Those with four or more ANC contacts (73.42%) were more likely to have received at least one IPTp. Furthermore, 13.9% of live births had low birthweights (BW < 2500 g) and one in four parturient women with moderate anaemia by WHO criteria. Microscopy (blood smear examination) and PCR-based diagnosis revealed between 0% and 1.57% of parasite-infected placental samples, respectively. Reported malaria in pregnancy predicted maternal anaemia at birth but not birth weight. Only gestational age (< 37 weeks) and bed net use (< 5 months) significantly predicted infant birth weight at delivery. CONCLUSION: The uptake of WHO recommended IPT doses during pregnancy was moderately high. Reported malaria in pregnancy, poor bed net coverage, gestational age less than 37 weeks adversely affect maternal haemoglobin levels at birth and infant birth weight. Asymptomatic and submicroscopic placental parasite infections was found at low prevalence. Together these results highlight the importance of maintaining aggressive measures to prevent malaria in pregnancy and protect the health of mother and baby.

Referral patterns of GIST patients: data from a nationwide study.

BACKGROUND: This study compares the characteristics, referral and treatment patterns and overall survival (OS) of gastrointestinal stromal tumor (GIST) patients treated in reference and non-reference centers in the Netherlands. PATIENTS AND METHODS: This retrospective cohort study on patients diagnosed between 2016 and 2019, utilises data from the Netherlands Cancer Registry and the Dutch Nationwide Pathology Database. Patients were categorized into two groups: patients diagnosed in or referred to reference centers and patients diagnosed in non-reference centers without referral. RESULTS: This study included 1,550 GIST patients with a median age of 67.0 in reference and 68.0 years in non-reference centers. Eighty-seven per cent of patients were diagnosed in non-reference centers, of which 36.5% (493/1,352) were referred to a reference center. Referral rates were higher for high-risk (62.2% [74/119]) and metastatic patients (67.2% [90/134]). Mutation analysis was performed in 96.9% and 87.6% of these cases in reference and in non-reference centers (p < 0.01), respectively. Systemic therapy was given in reference centers versus non-reference in 89.5% versus 82.0% (p < 0.01) of high-risk and in 94.1% versus 65.9% (p < 0.01) of metastatic patients, respectively. The proportion of positive resection margins and tumor rupture did not differ between reference and non-reference centers. Median OS was not reached. CONCLUSION: A substantial amount of metastatic GIST patients in non-reference centers did not receive systemic treatment. This might be due to valid reasons. However, optimisation of the referral strategy of GIST patients in the Netherlands could benefit patients. Further research is needed to explore reasons for not starting systemic treatment in metastatic GIST patients.

Proton pump inhibitors associated with severe COVID-19 among two-dose but not three-dose vaccine recipients.

BACKGROUND AND AIM: Proton pump inhibitors (PPIs) may increase the risk of COVID-19 among non-vaccinated subjects via various mechanisms, including gut dysbiosis. We aimed to investigate whether PPIs also affect the clinical outcomes of COVID-19 among vaccine recipients. METHODS: This was a territory-wide cohort study of 3 272 286 vaccine recipients (aged ≥ 18 years) of ≥ 2 doses of either BNT162b2 or CoronaVac. Exclusion criteria included prior gastrointestinal surgery, immunocompromised status, and prior COVID-19. The primary outcome was COVID-19, and secondary outcomes included COVID-19-related hospitalization and severe infection (composite of intensive care unit admission, ventilatory support, and/or death). Covariates include age, sex, the Charlson Comorbidity Index, comorbidities, and concomitant medication use. Subjects were followed from index date (first dose of vaccination) until outcome occurrence, death, additional dose of vaccination, or March 31, 2022. Exposure was pre-vaccination PPI use (any prescription within 90 days before the index date). Propensity score (PS) matching and a Poisson regression model were used to estimate the adjusted incidence rate ratio (aIRR) of outcomes with PPI use. RESULTS: Among 439 154 PS-matched two-dose vaccine recipients (mean age: 65.3 years; male: 45.7%) with a median follow-up of 6.8 months (interquartile range: 2.6-7.9), PPI exposure was associated with a higher risk of COVID-19 (aIRR: 1.08; 95% confidence interval [95% CI]: 1.05-1.10), hospitalization (aIRR: 1.20; 95% CI: 1.08-1.33), and severe infection (aIRR: 1.57; 95% CI: 1.24-1.98). Among 188 360 PS-matched three-dose vaccine recipients (mean age: 62.5 years; male: 49.0%; median follow-up: 9.1 months [interquartile range: 8.0-10.9]), PPIs were associated with higher infection risk (aIRR: 1.11; 95% CI: 1.08-1.15) but not other outcomes. CONCLUSIONS: Although PPI use was associated with a higher COVID-19 risk, severe infection was limited to two-dose but not three-dose vaccine recipients.

Increasing access to pediatric surgical care: Assessing district hospital readiness in rural Rwanda.

Introduction/Background: Safe and quality surgery is crucial for child health. In Rwanda, district hospitals serve as primary entry points for pediatric patients needing surgical care. This paper reports on the organizational readiness and facility capacity to provide pediatric surgery in three district hospitals in rural Rwanda. Methods: We administered the Children's Surgical Assessment Tool (CSAT), adapted for a Rwandan district hospital, to assess facility readiness across 5 domains (infrastructure, workforce, service delivery, financing, and training) at three Partners in Health supported district hospitals (Kirehe, Rwinkwavu, and Butaro District Hospitals). We used the Safe Surgery Organizational Readiness Tool (SSORT) to measure perceived individual and team readiness to implement surgical quality improvement interventions across 14 domains. Results: None of the facilities had a dedicated pediatric surgeon, and the most common barriers to pediatric surgery were lack of surgeon (68%), lack of physician anesthesiologists (19%), and inadequate infrastructure (17%). There were gaps in operating and recovery room infrastructure, and information management for pediatric outpatients and referrals. In SSORT interviews (n=47), the highest barriers to increasing pediatric surgery capacity were facility capacity (mean score=2.6 out of 5), psychological safety (median score=3.0 out of 5), and resistance to change (mean score=1.5 out of 5 with 5=no resistance). Conclusions: This study highlights challenges in providing safe and high-quality surgical care to pediatric patients in three rural district hospitals in Rwanda. It underscores the need for targeted interventions to address facility and organizational barriers prior to implementing interventions to expand pediatric surgical capacity.

Primary immunoprevention of adult onset cancers by vaccinating against retired tissue-specific self-proteins.

Despite the enormous success of childhood prophylactic vaccination against diseases caused by pathogens, there is currently no similar preventive vaccine program against diseases confronted with age like breast cancer and ovarian cancer. With the exception of the annual influenza vaccine, current recommendations for adult vaccination are for either primary vaccines not received during childhood or for booster vaccinations to maintain the immunity against pathogens already induced during childhood. Here we describe a strategy to provide prophylactic pre-emptive immunity against the development of adult onset cancers not associated with any definitive etiopathogenic agent. We propose that safe and effective pre-emptive immunity may be induced in cancer-free subjects by vaccination against immunodominant tissue-specific self-proteins that are 'retired' from expression in normal tissues as part of the normal aging process but are expressed in tumors that emerge with age. Primary immunoprevention of adult onset cancers like breast cancer and ovarian cancer represents a great challenge and an even greater unmet need for our current healthcare.

Ethical dilemmas in prioritizing patients for scarce radiotherapy resources.

BACKGROUND: Radiotherapy is an essential component of cancer treatment, yet many countries do not have adequate capacity to serve all patients who would benefit from it. Allocation systems are needed to guide patient prioritization for radiotherapy in resource-limited contexts. These systems should be informed by allocation principles deemed relevant to stakeholders. This study explores the ethical dilemmas and views of decision-makers engaged in real-world prioritization of scarce radiotherapy resources at a cancer center in Rwanda in order to identify relevant principles. METHODS: Semi-structured interviews were conducted with a purposive sample of 22 oncology clinicians, program leaders, and clinical advisors. Interviews explored the factors considered by decision-makers when prioritizing patients for radiotherapy. The framework method of thematic analysis was used to characterize these factors. Bioethical analysis was then applied to determine their underlying normative principles. RESULTS: Participants considered both clinical and non-clinical factors relevant to patient prioritization for radiotherapy. They widely agreed that disease curability should be the primary overarching driver of prioritization, with the goal of saving the most lives. However, they described tension between curability and competing factors including age, palliative benefit, and waiting time. They were divided about the role that non-clinical factors such as social value should play, and agreed that poverty should not be a barrier. CONCLUSIONS: Multiple competing principles create tension with the agreed upon overarching goal of maximizing lives saved, including another utilitarian approach of maximizing life-years saved as well as non-utilitarian principles, such as egalitarianism, prioritarianism, and deontology. Clinical guidelines for patient prioritization for radiotherapy can combine multiple principles into a single allocation system to a significant extent. However, conflicting views about the role that social factors should play, and the dynamic nature of resource availability, highlight the need for ongoing work to evaluate and refine priority setting systems based on stakeholder views.

Stability, change, and reliable individual differences in electroencephalography measures: A lifespan perspective on progress and opportunities.

Electroencephalographic (EEG) methods have great potential to serve both basic and clinical science approaches to understand individual differences in human neural function. Importantly, the psychometric properties of EEG data, such as internal consistency and test-retest reliability, constrain their ability to differentiate individuals successfully. Rapid and recent technological and computational advancements in EEG research make it timely to revisit the topic of psychometric reliability in the context of individual difference analyses. Moreover, pediatric and clinical samples provide some of the most salient and urgent opportunities to apply individual difference approaches, but the changes these populations experience over time also provide unique challenges from a psychometric perspective. Here we take a developmental neuroscience perspective to consider progress and new opportunities for parsing the reliability and stability of individual differences in EEG measurements across the lifespan. We first conceptually map the different profiles of measurement reliability expected for different types of individual difference analyses over the lifespan. Next, we summarize and evaluate the state of the field's empirical knowledge and need for testing measurement reliability, both internal consistency and test-retest reliability, across EEG measures of power, event-related potentials, nonlinearity, and functional connectivity across ages. Finally, we highlight how standardized pre-processing software for EEG denoising and empirical metrics of individual data quality may be used to further improve EEG-based individual differences research moving forward. We also include recommendations and resources throughout that individual researchers can implement to improve the utility and reproducibility of individual differences analyses with EEG across the lifespan.

Patients' experiences undergoing breast evaluation in Rwanda's Women's Cancer Early Detection Program.

PURPOSE: There is urgent need for interventions to facilitate earlier diagnosis of breast cancer in low- and middle-income countries where mammography screening is not widely available. Understanding patients' experiences with early detection efforts, whether they are ultimately diagnosed with cancer or benign disease, is critical to optimize interventions and maximize community engagement. We sought to understand the experiences of patients undergoing breast evaluation in Rwanda's Women's Cancer Early Detection Program (WCEDP). METHODS: We conducted in-person semi-structured interviews with 30 patients in two districts of Rwanda participating in the WCEDP. Patients represented a range of ages and both benign and malignant diagnoses. Interviews were recorded, transcribed, translated, and thematically analyzed. RESULTS: Participants identified facilitators and barriers of timely care along the breast evaluation pathway. Community awareness initiatives were facilitators to care-seeking, while persistent myths and stigma about cancer were barriers. Participants valued clear clinician-patient communication and emotional support from clinicians and peers. Poverty was a major barrier for participants who described difficulty paying for transport, insurance premiums, and other direct and indirect costs of hospital referrals in particular. COVID-19 lockdowns caused delays for referred patients. Although false-positive clinical breast exams conferred financial and emotional burdens, participants nonetheless voiced appreciation for their experience and felt empowered to monitor their own breast health and share knowledge with others. CONCLUSION: Rwandan women experienced both benefits and burdens as they underwent breast evaluation. Enthusiasm for participation was not reduced by the experience of a false-positive result. Reducing financial, logistical and emotional burdens of the breast diagnostic pathway through patient navigation, peer support and decentralization of diagnostic services could improve patients' experience.

Low-dose aspirin does not lower the risk of colorectal cancer in patients with type 2 diabetes taking metformin.

BACKGROUND: Low-dose aspirin and metformin have been individually associated with a reduced risk of cancer. Whether their concurrent use in adults with type 2 diabetes mellitus (T2DM) is associated with a reduced risk of colorectal cancer (CRC) is unclear. OBJECTIVE: Among individuals with T2DM taking metformin, we sought to evaluate the association between low-dose aspirin versus no aspirin and the risk of CRC. METHODS: A multiple-database new-user cohort study of patients with T2DM taking metformin was conducted between 2007 and 2010 (Clinical Data Analysis and Reporting System [CDARS], Hong Kong) and 2007-2016 (The Health Improvement Network [THIN], UK). The primary outcome was incident CRC. Patients were followed from index date of prescription until the earliest occurrence of an outcome of interest, an incident diagnosis of any cancer, death, or until 31 December 2019. Cox proportional hazards regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CI). Estimates were pooled using an inverse variance random effects model, and heterogeneity was assessed using I2 . RESULTS: After one-to-one propensity-score matching, 57,534 patients were included (CDARS = 16,276; THIN = 41,258). The median (IQR) follow-up was 9.3 (6.5-10.7) years in CDARS and 3.2 (1.1-5.8) years in THIN. The concurrent use of low-dose aspirin and metformin was not associated with a lower risk of CRC compared to metformin only (HR = 0.89, 95% CI 0.75-1.05, I2  = 0%). CONCLUSION: Low-dose aspirin was not associated with a lower risk of CRC in patients with T2DM taking metformin. Our study does not support the routine use of low-dose aspirin in this population.

Epidemiology of adult meningioma: Report from the Dutch Brain Tumour Registry (2000-2019).

BACKGROUND AND PURPOSE: Meningiomas are the most common primary tumours of the central nervous system. This study aimed to provide comprehensive nationwide estimates on the incidence, prevalence and prognostic impact of meningioma diagnosis in the Netherlands. METHODS: Adult patients diagnosed with meningioma in 2000-2019 were selected from the Dutch Brain Tumour Registry (DBTR), part of the Netherlands Cancer Registry (NCR). Time trends in age-adjusted incidence and prevalence rates were evaluated using the estimated annual percentage change (EAPC). Relative survival rates were calculated using the Pohar Perme estimator. Case completeness of the DBTR/NCR was estimated through record linkage with one of the Dutch neuro-oncology centres. RESULTS: From a total of 23,454 cases of meningioma, 11,306 (48.2%) were histologically confirmed and 12,148 (51.8%) were radiological diagnoses. Over time, the incidence of diagnosis increased from 46.9 per 1,000,000 inhabitants (European Standardized Rate [ESR]) to 107.3 (EAPC 4.7%, p < 0.01), with an increase in the incidence of radiological diagnoses from 14.0 to 70.2 per 1,000,000 ESR (EAPC 9.1%, p < 0.01). The prevalence of meningioma was estimated at 1012/1,000,000 on 1 January 2020, with almost 17,800 individuals having had a diagnosis of meningioma. Relative survival rate at 10 years for grade 1 meningiomas was 91.0% (95% confidence interval [CI] 89.4%-92.3%), 71.3% (95% CI 66.8%-75.2%) for grade 2 meningiomas and 36.4% (95% CI 27.3%-45.6%) for grade 3 meningiomas. Local case completeness was estimated at 97.6% for histologically confirmed meningiomas and 84.5% for radiological diagnoses. CONCLUSION: With a near-complete registry, meningioma prevalence was estimated at over 1000 per 1,000,000 inhabitants.

Leveraging uncertainty estimates and derivative information in Gaussian process regression for efficient collection and use of molecular simulation data.

We introduce Gaussian Process Regression (GPR) as an enhanced method of thermodynamic extrapolation and interpolation. The heteroscedastic GPR models that we introduce automatically weight provided information by its estimated uncertainty, allowing for the incorporation of highly uncertain, high-order derivative information. By the linearity of the derivative operator, GPR models naturally handle derivative information and, with appropriate likelihood models that incorporate heterogeneous uncertainties, are able to identify estimates of functions for which the provided observations and derivatives are inconsistent due to the sampling bias that is common in molecular simulations. Since we utilize kernels that form complete bases on the function space to be learned, the estimated uncertainty in the model takes into account that of the functional form itself, in contrast to polynomial interpolation, which explicitly assumes the functional form to be fixed. We apply GPR models to a variety of data sources and assess various active learning strategies, identifying when specific options will be most useful. Our active-learning data collection based on GPR models incorporating derivative information is finally applied to tracing vapor-liquid equilibrium for a single-component Lennard-Jones fluid, which we show represents a powerful generalization to previous extrapolation strategies and Gibbs-Duhem integration. A suite of tools implementing these methods is provided at https://github.com/usnistgov/thermo-extrap.

Clinical Features, Survival, and Burden of Toxicities in Survivors More Than One Year After Lung Cancer Immunotherapy.

INTRODUCTION: Anti-PD-(L)1 immune checkpoint inhibitors (ICI) improve survival in patients with advanced non-small cell lung cancer (aNSCLC). The clinical features, survival, and burden of toxicities of patients with aNSCLC alive >1 year from ICI initiation are poorly understood. MATERIALS AND METHODS: We defined ICI survivors as patients alive >1 year after ICI start and retrospectively reviewed demographics, treatment, and immune-related adverse events (irAEs). Long-term irAEs were defined as ongoing irAEs lasting >1 year; burden of toxicity measures were based on percentage of days a patient experienced toxicity. Using linear and logistic regression, we evaluated association between demographics and disease characteristics with burden of toxicity. RESULTS: We identified 114 ICI survivors from 317 patients with aNSCLC. Half (52%) experienced an irAE of any grade, and 23.7% developed long-term irAEs. More ICI survivors with irAES in the first year had never smoked (P = .018) or received ICIs as frontline therapy (P = .015). The burden of toxicity in the first year significantly correlated with the burden of toxicity afterward (ρ = 0.72; P < .001). No patients with progressive disease had a high burden of toxicity, and they experienced 30.6% fewer days with toxicity than those with stable disease. Increased duration of therapy was associated with higher odds of experiencing toxicity. Half of ICI survivors with irAEs were still receiving treatment for unresolved irAEs at time of death or last follow-up. CONCLUSION: Significant proportions of ICI survivors have unresolved long-term toxicities. These data support a growing need to understand long-term toxicity to optimize management of those treated with ICIs.

Cost-Effectiveness of Midazolam Versus Haloperidol Versus Olanzapine for the Management of Acute Agitation in the Accident and Emergency Department.

OBJECTIVES: A multicenter randomized clinical trial in Hong Kong Accident and Emergency (A&E) departments concluded that intramuscular (IM) olanzapine is noninferior to haloperidol and midazolam, in terms of efficacy and safety, for the management of acutely agitated patients in A&E setting. Determining their comparative cost-effectiveness will further provide an economic perspective to inform the choice of sedative in this setting. METHODS: This analysis used data from a randomized clinical trial conducted in Hong Kong A&E departments between December 2014 and September 2019. A within-trial cost-effectiveness analysis comparing the 3 sedatives was conducted, from the A&E perspective and a within-trial time horizon, using a decision-analytic model. Sensitivity analyses were also undertaken. RESULTS: In the base-case analysis, median total management costs associated with IM midazolam, haloperidol, and olanzapine were Hong Kong dollar (HKD) 1958.9 (US dollar [USD] 251.1), HKD 2504.5 (USD 321.1), and HKD 2467.6 (USD 316.4), respectively. Agitation management labor cost was the main cost driver, whereas drug costs contributed the least. Midazolam dominated over haloperidol and olanzapine. Probabilistic sensitivity analyses supported that midazolam remains dominant > 95% of the time and revealed no clear difference in the cost-effectiveness of IM olanzapine versus haloperidol (incremental cost-effectiveness ratio 667.16; 95% confidence interval -770.89, 685.90). CONCLUSIONS: IM midazolam is the dominant cost-effective treatment for the management of acute agitation in the A&E setting. IM olanzapine could be considered as an alternative to IM haloperidol given that there is no clear difference in cost-effectiveness, and their adverse effect profile should be considered when choosing between them.

Building Interpretable Machine Learning Models to Identify Chemometric Trends in Seabirds of the North Pacific Ocean.

Marine environmental monitoring efforts often rely on the bioaccumulation of persistent anthropogenic contaminants in organisms to create a spatiotemporal record of the ecosystem. Intercorrelation results from the origin, uptake, and transport of these contaminants throughout the ecosystem and may be affected by organism-specific processes such as biotransformation. Here, we explore trends that machine learning tools reveal about a large, recently released environmental chemistry data set of common anthropogenic pollutants measured in the eggs of five seabird species from the North Pacific Ocean. We modeled these data with a variety of machine learning approaches and found models that could accurately determine a range of taxonomic and spatiotemporal trends. We illustrate a general workflow and set of analysis tools that can be used to identify interpretable models which perform nearly as well as state-of-the-art "black boxes." For example, we found shallow decision trees that could resolve genus with greater than 96% accuracy using as few as two analytes and a k-nearest neighbor classifier that could resolve species differences with more than 94% accuracy using only five analytes. The benefits of interpretability outweighed the marginally improved accuracy of more complex models. This demonstrates how machine learning may be used to discover rational, quantitative trends in these systems.

Systematic control of collective variables learned from variational autoencoders.

Variational autoencoders (VAEs) are rapidly gaining popularity within molecular simulation for discovering low-dimensional, or latent, representations, which are critical for both analyzing and accelerating simulations. However, it remains unclear how the information a VAE learns is connected to its probabilistic structure and, in turn, its loss function. Previous studies have focused on feature engineering, ad hoc modifications to loss functions, or adjustment of the prior to enforce desirable latent space properties. By applying effectively arbitrarily flexible priors via normalizing flows, we focus instead on how adjusting the structure of the decoding model impacts the learned latent coordinate. We systematically adjust the power and flexibility of the decoding distribution, observing that this has a significant impact on the structure of the latent space as measured by a suite of metrics developed in this work. By also varying weights on separate terms within each VAE loss function, we show that the level of detail encoded can be further tuned. This provides practical guidance for utilizing VAEs to extract varying resolutions of low-dimensional information from molecular dynamics and Monte Carlo simulations.

Derivable genetic programming for two-dimensional colloidal materials.

We describe a method for deriving surface functionalization patterns for colloidal systems that can induce self-assembly into any chosen periodic symmetry at a planar interface. The result is a sequence of letters, s ∈ {A,T,C,G}, or a gene, that describes the perimeter of the colloidal object and programs its self-assembly. This represents a genome that is finite and can be exhaustively enumerated. These genes derive from symmetry, which may be topologically represented by two-dimensional parabolic orbifolds; since these orbifolds are surfaces that may be derived from first principles, this represents an ab initio route to colloid functionality. The genes are human readable and can be employed to easily design colloidal units. We employ a biological (genetic) analogy to demonstrate this and illustrate their connection to the designs of Maurits Cornelis (M. C.) Escher.

Umbilical metastases: Real-world data shows abysmal outcome.

Umbilical metastases form a clinical challenge, especially when they represent the first sign of malignant disease and the primary tumor is unknown. Our study aims to generate insight into the origin and timing of umbilical metastasis, as well as patient survival, using population-based data. A nationwide review of pathology records of patients diagnosed with an umbilical metastasis between 1979 and 2015 was performed. Data was collected from the Nationwide Network and Registry of Histopathology and Cytopathology (PALGA) and the Netherlands Cancer Registry. Kaplan-Meier analyses and log-rank testing were used to estimate overall survival and a Cox proportional hazard model was used to determine multivariable hazard ratios. A total of 806 patients with an umbilical metastasis were included. There were 210 male (26.1%) and 596 female (73.9%) patients. Distribution of umbilical metastases was different between male and female patients due to the high incidence of umbilical metastases originating from the ovaries in females. They most frequently originated from the ovaries in female patients (38.8%) and from the colon in male patients (43.8%). In 18% of cases no primary tumor could be identified. Prognosis after diagnosis of an umbilical metastasis was dismal with a median survival of 7.9 months (95% confidence interval 6.7-9.1). The origin of the primary tumor was an independent prognostic factor for overall survival. In conclusion, umbilical metastases relatively rare, mainly originating from intraabdominal primary tumors. Survival is dependent on the origin of the primary tumor and poor overall survival rates warrant early recognition.