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It is generally assumed that larger juveniles are more physiologically mature, hence their overall condition and subsequent performance are higher.Some taxa face extreme workload transitions during development (e.g. nest departure in birds), which may select for non‐linear growth profiles that decouple relationships between body size and physiological state, making the links between metrics of development (e.g. body mass) and juvenile performance uncertain.We manipulated perceived mass in European starlings approaching fledging using 4.0 g weighted backpacks, measuring subsequent growth trajectories (mass, wing length) and physiological state (aerobic capacity, energy state, oxidative status) to test whether body size and physiology are coupled during a non‐linear developmental phase (pre‐fledging mass recession). Nanotag radio transmitters were then used to track post‐fledging performance (activity, activity‐slope, dispersal).Weighted nestlings had greater pre‐fledging mass recession and marginally reduced wing growth when compared to controls. Consequently, weighted birds had lower body mass at fledging, while also displaying markers of oxidative stress (increased reactive oxygen metabolites), yet aerobic capacity and energy state were equal between treatment groups.Previously weighted birds showed no correlation between fledgling state (body size, physiology) and subsequent performance. However, control fledglings that had decreased mass recession and greater wing growth prior to fledging dispersed earlier, while longer wings at fledging were associated with more rapid increases in post‐fledging activity (activity‐slope). In addition, control fledglings with lower haemoglobin also dispersed earlier, while increased reactive oxygen metabolites were associated with decreased activity levels. Body mass and energy state were unrelated to any metric of post‐fledging performance.Our data suggest mass‐independent development of some physiological traits in species with non‐linear growth profiles, potentially with a context‐dependent oxidative cost, and that physiology may predict some measures of post‐fledging performance not captured by body size. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Halogenated disinfection byproducts (DBPs) are an unintended consequence of drinking water disinfection, and can have significant toxicity. XAD resins are commonly used to extract and enrich trace levels of DBPs for comprehensive, nontarget identification of DBPs and also for in vitro toxicity studies. However, XAD resin recoveries for complete classes of halogenated DBPs have not been evaluated, particularly for low, environmentally relevant levels (ng/L to low µg/L). Thus, it is not known whether levels of DBPs or the toxicity of drinking water might be underestimated. In this study, DAX-8/XAD-2 layered resins were evaluated, considering both adsorption and elution from the resins, for extracting 66 DBPs from water. Results demonstrate that among the 7 classes of DBPs investigated, trihalomethanes (THMs), including iodo-THMs, were the most efficiently adsorbed, with recovery of most THMs ranging from 50%-96%, followed by halonitromethanes (40%-90%). The adsorption ability of XAD resins for haloacetonitriles, haloacetamides, and haloacetaldehydes was highly dependent on the individual species. The adsorption capacity of XAD resins for haloacetic acids was lower (5%-48%), even after adjusting to pH 1 before extraction. Recovery efficiency for most DBPs was comparable with their adsorption, as most were eluted effectively from XAD resins by ethyl acetate. DBP polarity and molecular weight were the two most important factors that determine their recovery. Recovery of trichloromethane, iodoacetic acid, chloro- and iodo-acetonitrile, and chloroacetamide were among the lowest, which could lead to underestimation of toxicity, particularly for iodoacetic acid and iodo-acetonitrile, which are highly toxic. [ABSTRACT FROM AUTHOR]

The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance. [ABSTRACT FROM AUTHOR]

Lead contamination in the City of Flint, MI has been well documented over the past two years, with lead levels above the EPA Action Level until summer 2016. This resulted from an ill-fated decision to switch from Detroit water (Lake Huron) with corrosion control, to Flint River water without corrosion control. Although lead levels are now closer to normal, reports of skin rashes have sparked questions surrounding tap water in some Flint homes. This study investigated the presence of contaminants, including disinfection by-products (DBPs), in the hot tap water used for showering in the homes of residents in Flint. Extensive quantitative analysis of 61 regulated and priority unregulated DBPs was conducted in Flint hot and cold tap water, along with the analysis of 50 volatile organic compounds and a nontarget comprehensive, broadscreen analysis, to identify a possible source for the reported skin rashes. For comparison, chlorinated hot and cold waters from three other cities were also sampled, including Detroit, which also uses Lake Huron as its source water. Results showed that hot water samples generally contained elevated levels of regulated and priority unregulated DBPs compared to cold water samples, but trihalomethanes were still within regulatory limits. Overall, hot shower water from Flint was similar to waters sampled from the three other cities and did not have unusually high levels of DBPs or other organic chemicals that could be responsible for the skin rashes observed by residents. It is possible that an inorganic chemical or microbial contaminant may be responsible. [ABSTRACT FROM AUTHOR]

A survey was conducted at eight U.S. drinking water plants, that spanned a wide range of water qualities and treatment/disinfection practices. Plants that treated heavily-wastewater-impacted source waters had lower trihalomethane to dihaloacetonitrile ratios due to the presence of more organic nitrogen and HAN precursors. As the bromide to total organic carbon ratio increased, there was more bromine incorporation into DBPs. This has been shown in other studies for THMs and selected emerging DBPs (HANs), whereas this study examined bromine incorporation for a wider group of emerging DBPs (haloacetaldehydes, halonitromethanes). Moreover, bromine incorporation into the emerging DBPs was, in general, similar to that of the THMs. Epidemiology studies that show an association between adverse health effects and brominated THMs may be due to the formation of brominated emerging DBPs of heath concern. Plants with higher free chlorine contact times before ammonia addition to form chloramines had less iodinated DBP formation in chloraminated distribution systems, where there was more oxidation of the iodide to iodate (a sink for the iodide) by the chlorine. This has been shown in many bench-scale studies (primarily for iodinated THMs), but seldom in full-scale studies (where this study also showed the impact on total organic iodine. Collectively, the THMs, haloacetic acids, and emerging DBPs accounted for a significant portion of the TOCl, TOBr, and TOI; however, ∼50% of the TOCl and TOBr is still unknown. The correlation of the sum of detected DBPs with the TOCl and TOBr suggests that they can be used as reliable surrogates. [ABSTRACT FROM AUTHOR]

Gold nanoparticles having a rod-like morphology are regularly investigated as potential nano-therapeutic materials owing to their interesting optical properties, facile surface modification, tunable aspect ratios, and low cytotoxicity. Gold nanorods are historically prepared starting from HAuCl 4 in the presence of ascorbic acid, silver nitrate, and the growth directing surfactant, cetyltrimethylammonium bromide (CTAB). While CTAB drives a rod-like morphology, it is known to be cytotoxic. This inherent toxicity is often addressed by removing or masking the native CTAB surfactant present on the nanorod surface. In the current study we have investigated a less toxic alternative surfactant, dodecylethyldimethylammonium bromide (C 12 EDMAB), as a possible growth-directing agent. Monodisperse gold nanorods having various lengths have been grown in the presence of C 12 EDMAB. SEM data suggests that the quantity of C 12 EDMAB on the rod’s surface is much higher than that of CTAB. Toxicity assays were performed on HEp-2 and A549 cells showing lower toxicity at select concentrations for C 12 EDMAB coated rods. [ABSTRACT FROM AUTHOR]

Recent urban public water supply contamination events emphasize the importance of screening treated drinking water quality after distribution. In vitro bioassays, when run concurrently with analytical chemistry methods, are effective tools to evaluating the efficacy of water treatment processes and water quality. We tested 49 water samples representing the Chicago Department of Water Management service areas for estrogen, (anti)androgen, glucocorticoid receptor-activating contaminants and cytotoxicity. We present a tiered screening approach suitable to samples with anticipated low-level activity and initially tested all extracts for statistically identifiable endocrine activity; performing a secondary dilution-response analysis to determine sample EC 50 and biological equivalency values (BioEq). Estrogenic activity was detected in untreated Lake Michigan intake water samples using mammalian (5/49; median: 0.21 ng E2Eq/L) and yeast cell (5/49; 1.78 ng E2Eq/L) bioassays. A highly sensitive (anti)androgenic activity bioassay was applied for the first time to water quality screening and androgenic activity was detected in untreated intake and treated pre-distribution samples (4/49; 0.93 ng DHTEq/L). No activity was identified above method detection limits in the yeast androgenic, mammalian anti-androgenic, and both glucocorticoid bioassays. Known estrogen receptor agonists were detected using HPLC/MS-MS (estrone: 0.72–1.4 ng/L; 17α-estradiol: 1.3–1.5 ng/L; 17β-estradiol: 1.4 ng/L; equol: 8.8 ng/L), however occurrence did not correlate with estrogenic bioassay results. Many studies have applied bioassays to water quality monitoring using only relatively small samples sets often collected from surface and/or wastewater effluent. However, to realistically adapt these tools to treated water quality monitoring, water quality managers must have the capacity to screen potentially hundreds of samples in short timeframes. Therefore, we provided a tiered screening model that increased sample screening speed, without sacrificing statistical stringency, and detected estrogenic and androgenic activity only in pre-distribution Chicago area samples. Unlabelled Image • Corresponding pre- and post-distribution treated water samples were assessed. • We applied a screening model for low level biological activity in water samples. • Inaugural use of an (anti)androgenic bioassay for water quality screening • Estrogen and androgen activity were detected in untreated water. • No biological activity detected in tapwater above method detection limits. [ABSTRACT FROM AUTHOR]

Safe drinking water at the point of use (tapwater, TW) is a public-health priority. TW exposures and potential human-health concerns of 540 organics and 35 inorganics were assessed in 45 Chicago-area United States (US) homes in 2017. No US Environmental Protection Agency (EPA) enforceable Maximum Contaminant Level(s) (MCL) were exceeded in any residential or water treatment plant (WTP) pre-distribution TW sample. Ninety percent (90%) of organic analytes were not detected in treated TW, emphasizing the high quality of the Lake Michigan drinking-water source and the efficacy of the drinking-water treatment and monitoring. Sixteen (16) organics were detected in >25% of TW samples, with about 50 detected at least once. Low-level TW exposures to unregulated disinfection byproducts (DBP) of emerging concern, per/polyfluoroalkyl substances (PFAS), and three pesticides were ubiquitous. Common exceedances of non-enforceable EPA MCL Goal(s) (MCLG) of zero for arsenic [As], lead [Pb], uranium [U], bromodichloromethane, and tribromomethane suggest potential human-health concerns and emphasize the continuing need for improved understanding of cumulative effects of low-concentration mixtures on vulnerable sub-populations. Because DBP dominated TW organics, residential-TW concentrations are potentially predictable with expanded pre-distribution DBP monitoring. However, several TW chemicals, notably Pb and several infrequently detected organic compounds, were not readily explained by pre-distribution samples, illustrating the need for continued broad inorganic/organic TW characterization to support consumer assessment of acceptable risk and point-of-use treatment options. Unlabelled Image • Drinking-water contaminants role in human health obscured by point-of-use data gap. • 540 organics/35 inorganics assessed in home and treatment plant tapwater in Chicago. • No enforceable standards exceeded, indicating source quality and treatment efficacy. • Common exceedances of MCLG-zero guidance illustrate perceived human health hazard. • Exceedances highlight improved analytics and critical low-level effects data needs. [ABSTRACT FROM AUTHOR]