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Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

Nitrification is a major issue that utilities must address if they utilize chloramines as a secondary disinfectant. Nitrification is the oxidation of free ammonia to nitrite which is then further oxidized to nitrate. Free ammonia is found in drinking water systems as a result of overfeeding at the water treatment plant (WTP) or as a result of the decomposition of monochloramine. Premise plumbing systems (i.e., the plumbing systems within buildings and homes) are characterized by irregular usage patterns, high water age, high temperature, and high surface-to-volume ratios. These characteristics create ideal conditions for increased chloramine decay, bacterial growth, and nitrification. This review discusses factors within premise plumbing that are likely to influence nitrification, and vice versa. Factors influencing, or influenced by, nitrification include the rate at which chloramine residual decays, microbial regrowth, corrosion of pipe materials, and water conservation practices. From a regulatory standpoint, the greatest impact of nitrification within premise plumbing is likely to be a result of increased lead levels during Lead and Copper Rule (LCR) sampling. Other drinking water regulations related to nitrifying parameters are monitored in a manner to reduce premise plumbing impacts. One way to potentially control nitrification in premise plumbing systems is through the development of building management plans.

The UK's Trade Remedies Authority (TRA) conducts economic assessments of the ramifications of trade remedies, the Economic Interest Test (EIT). Such assessments are not mandated by the World Trade Organization but are conducted by certain trade remedy investigating authorities, including those of Brazil, Canada, the European Union, and New Zealand. The EIT is a mandatory part of the UK trade remedy system and is arguably more transparent than similar interest tests conducted by other trade remedy investigating authorities. However, stakeholder participation remains a challenge and the TRA is working on ways to improve participation. To date, the TRA has completed 11 EITs in its trade remedy cases, with a further ten live cases. These cases cover different products, markets, and countries, across which the likely positive and negative impacts of trade remedy differ. This paper invites experts to review the TRA's EIT methodology.

Nucleoporins have been reported to regulate pluripotent biology, but how they do so remains partially characterized. This study examined the effects of nup155 gene disruption on mouse embryonic stem cells to gain insights into possible mechanisms by which nucleoporins regulate pluripotency in a pro-arrhythmogenic stem cell line. Embryonic stem cells with gene-trapped nup155 exhibited aberrant colony morphology underscored by abnormal transcriptome remodeling. Bioinformatic analysis of whole transcriptome data from nup155 +/− embryonic stem cells revealed changes in a variety of non-coding RNA elements, with significant under expression of miR291a , miR291b , miR293 , and miR294 . These miRNAs are members of the larger regulatory miR290–295 cluster that regulates pluripotency and are controlled by the canonical stem cell-related factors SOX2, OCT4, and NANOG. Expression analysis of these factors revealed downregulation in all three, supported by biochemical profiling and image analysis. These data implicate disruption of the miR -SOX2/OCT4/NANOG regulatory circuit occurs downstream of nup155 gene lesion.

Historical Lead and Copper Rule (LCR) regulatory sampling data from the Philadelphia Water Department were examined to explore their potential value for guiding a water utility's progress with regard to optimal corrosion control treatment (OCCT). If a system has established a stable water treatment process with consistent corrosion control treatment (CCT) and has achieved continued decreases in lead levels during regulatory sampling, then the information collected during LCR monitoring can be used as an important data set of a broader OCCT evaluation and will help inform the benefit of additional changes in CCT. Since water utilities have LCR data dating back to 1992, these data should be used to make informed decisions. This research also showed that the addition of orthophosphate has resulted in a significant decrease in lead levels at the customer tap. Additionally, profile sampling was performed to show that first‐draw 1 L samples following a 6 h stagnation period provide a good representation of the lead concentrations measured from lead service line and home plumbing samples at the same sites and may be used to indicate overall changes in lead concentrations at the tap resulting from CCT for this system.

Providing safe drinking water is the core mission of drinking water providers and requires balancing numerous potential challenges to accomplish this mission successfully. A key challenge in maintaining high quality drinking water in chloraminated water systems is nitrification. Nitrification is a biochemical process where bacteria in the water and biofilms of a system, primarily ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), oxidize ammonia to nitrite and then further to nitrate. In chloraminated drinking water systems, nitrification is a detrimental process that can cause rapid loss of disinfectant residual and potentially result in increased bacterial regrowth and regulatory violations. The goal of this dissertation is to increase understanding and improve the effectiveness of water systems’ responses to nitrification events.One of the most important elements in effectively managing nitrification in a drinking water system is how quickly the water system recognizes that nitrification is on-going and can respond. To that end, a novel data-driven method is proposed for developing site-specific action levels for total chlorine within a drinking water system. This method utilizes historical total chlorine data, which is readily available for all chloraminated systems, to isolate the “falling limb” of the curve and then calculate action levels based on only this portion of the total chlorine trend. Isolating the falling limb of the curve allows the action levels to be based solely on the portion of the curve where nitrification is beginning and proliferating. In this research, we demonstrate that this method helps provide action levels that can alert water systems to the initial start of nitrification and to the onset of severe nitrification more effectively than previously proposed methods.While nitrification effects the chemistry of the bulk water in drinking water systems, the process is largely taking place and being seeded by the biofilms that grow within these systems. One of the challenges of studying biofilms within drinking water systems is that most coupon designs don’t simulate the position and curvature of a pipe wall. In this dissertation, we utilize two in-situ biofilm samplers, one installed directly into the main in the street and the other installed into the building plumbing of a dedicated sampling shed within the Philadelphia Water Department’s system. Using these biofilm samplers, the spatiotemporal heterogeneity was assessed within a single sampler, between samplers small distances apart (in the street vs in an adjacent building), and in different buildings within the same service area. This research demonstrates that there are significant differences between biofilms that grow in different samplers and in different buildings, but there are minimal differences between biofilm samples that are collected from within a single sampler. This research acts as a springboard for the use of the samplers for testing of varying conditions to assess the impacts of a controlled variable without the concern of any differences potentially being caused by natural variation within the samplers.A common mitigation strategy for nitrification within a water system is the use of conventional flushing, specifically point flushing and continuous flushing. Using the biofilm samplers, the impacts of these two flushing techniques on the biofilms that seed the nitrification process was assessed. Results show that neither of these flushing methods resulted in significant changes in the biofilm’s microbial community. Furthermore, this research confirms that the use of these conventional flushing methods should be used primarily as an early response to nitrification rather than as a method to address severe nitrification.

ObjectiveEstimates of the prevalence of rheumatic heart disease (RHD) in many endemic countries are limited to samples of children attending schools, which generate an incomplete picture of disease burden in communities. The present study conducted household-based RHD screening in a representative community in Gulu district, Uganda.MethodsMembers of households identified through a two-stage cluster-sampling approach between the ages of 5 years and 50 years were invited to undergo limited cardiac testing with a handheld echocardiogram to assess for the presence of RHD. Suspicious cases underwent confirmatory echocardiogram with a fully functional machine.ResultsOf the 2453 community members screened, 2.45% (95% CI 1.87% to 3.14%) showed echocardiographic evidence of RHD with 1.26% (95% CI 0.860% to 1.79%) having definite RHD. The overall prevalence of RHD among participants <20 years was 2.52% (95% CI 1.78% to 3.45%), with a borderline prevalence of 1.97% (95% CI 1.33% to 2.82%) and a definite prevalence of 0.544% (95% CI 0.235% to 1.07%). Prevalence rates among youth increased with age and peaked in the age group of 16–20 years. The overall adult prevalence (>20 years) of RHD was 2.34% (95% CI 1.49% to 3.49%). The majority of definite cases were mild (81%) and marked by mitral regurgitation and associated morphological valve changes (71%).ConclusionOur data reveal a high prevalence of undiagnosed RHD within an endemic community and fill a critical gap in RHD epidemiology in African adults.

Rheumatic fever, an immune sequela of untreated streptococcal infections, is an important contributor to global cardiovascular disease. The goal of this study was to describe trends, characteristics, and cost burden of children discharged from hospitals with a diagnosis of RF from 2000 to 2012 within the United States. Using the Kids' Inpatient Database, we examined characteristics of children discharged from hospitals with the diagnosis of rheumatic fever over time including: overall hospitalisation rates, age, gender, race/ethnicity, regional differences, payer type, length of stay, and charges. The estimated national cumulative incidence of rheumatic fever in the United States between 2000 and 2012 was 0.61 cases per 100,000 children. The median age was 10 years, with hospitalisations significantly more common among children aged 6-11 years. Rheumatic fever hospitalisations among Asian/Pacific Islanders were significantly over-represented. The proportion of rheumatic fever hospitalisations was greater in the Northeast and less in the South, although the highest number of rheumatic fever admissions occurred in the South. Expected payer type was more likely to be private insurance, and the median total hospital charges (adjusted for inflation to 2012 dollars) were $16,000 (interquartile range: $8900-31,200). Median length of stay was 3 days, and the case fatality ratio for RF in the United States was 0.4%. Rheumatic fever persists in the United States with an overall downwards trend between 2003 and 2012. Rheumatic fever admissions varied considerably based on age group, region, and origin.

Introduction Rheumatic heart disease causes substantial morbidity in children in low-income countries. School-based echocardiographic screening has been suggested as a means to identify children with latent disease; however, little is known about the experience of children and teachers participating in screenings. The aim of our study was to assess students' and teachers' experience of school-based echocardiographic screening and identify areas for improvement. Materials and methods A school-based echocardiographic screening programme was conducted in five schools in Northern Uganda in 2013. After 8 months, an age- and gender-stratified population that included 5% of the participating students and teachers completed a questionnaire via an in-person interview. Responses were reviewed by question and coded to identify key themes. A total of 255 students (mean 10.7 years; 48% male) and 35 teachers participated in our study. In total, 95% of the students and 100% of the teachers were happy to have participated in the screening; however, students reported feeling scared (35%) and nervous (48%) during the screening process. Programmatic strengths included the following: knowing one's health status, opportunity to receive treatment, and staff interactions. Although 43% of the patients did not suggest a change with open-ended questioning, concerns regarding privacy, fear of the screening process, and a desire to include others in the community were noted. Discussion School-based echocardiographic rheumatic heart disease screening was well received by students and teachers. Future programmes would likely benefit from improved pre-screening education regarding the screening process and diagnosis of rheumatic heart disease. Furthermore, education of teachers and students could improve screening perception and establish realistic expectations regarding the scope of screening.