Decreases in Epoxide-Driven Secondary Organic Aerosol Production under Highly Acidic Conditions: The Importance of Acid-Base Equilibria.

Isoprene has the highest atmospheric emissions of any nonmethane hydrocarbon, and isoprene epoxydiols (IEPOX) are well-established oxidation products and the primary contributors forming isoprene-derived secondary organic aerosol (SOA). Highly acidic particles (pH 0-3) widespread across the lower troposphere enable acid-driven multiphase chemistry of IEPOX, such as epoxide ring-opening reactions forming methyltetrol sulfates through nucleophilic attack of sulfate (SO42-). Herein, we systematically demonstrate an unexpected decrease in SOA formation from IEPOX on highly acidic particles (pH < 1). While IEPOX-SOA formation is commonly assumed to increase at low pH when more [H+] is available to protonate epoxides, we observe maximum SOA formation at pH 1 and less SOA formation at pH 0.0 and 0.4. This is attributed to limited availability of SO42- at pH values below the acid dissociation constant (pKa) of SO42- and bisulfate (HSO4-). The nucleophilicity of HSO4- is 100× lower than SO42-, decreasing SOA formation and shifting particulate products from low-volatility organosulfates to higher-volatility polyols. Current model parameterizations predicting SOA yields for IEPOX-SOA do not properly account for the SO42-/HSO4- equilibrium, leading to overpredictions of SOA formation at low pH. Accounting for this underexplored acidity-dependent behavior is critical for accurately predicting SOA concentrations and resolving SOA impacts on air quality.

Assessing Bias in Cognitive Testing for Older Adults with Sensory Impairment: An Analysis of Differential Item Functioning in the Baltimore Longitudinal Study on Aging (BLSA) and the Atherosclerosis Risk in Communities Neurocognitive Study (ARIC-NCS).

OBJECTIVES: Vision and hearing impairments affect 55% of people aged 60+ years and are associated with lower cognitive test performance; however, tests rely on vision, hearing, or both. We hypothesized that scores on tests that depend on vision or hearing are different among those with vision or hearing impairments, respectively, controlling for underlying cognition. METHODS: Leveraging cross-sectional data from the Baltimore Longitudinal Study of Aging (BLSA) and the Atherosclerosis Risk in Communities Neurocognitive Study (ARIC-NCS), we used item response theory to test for differential item functioning (DIF) by vision impairment (better eye presenting visual acuity worse than 20/40) and hearing impairment (better ear .5-4 kHz pure-tone average > 25 decibels). RESULTS: We identified DIF by vision impairment for tests whose administrations do not rely on vision [e.g., Delayed Word Recall both in ARIC-NCS: .50 logit difference between impaired and unimpaired (p = .04) and in BLSA: .62 logits (p = .02)] and DIF by hearing impairment for tests whose administrations do not rely on hearing [Digit Symbol Substitution test in BLSA: 1.25 logits (p = .001) and Incidental Learning test in ARIC-NCS: .35 logits (p = .001)]. However, no individuals had differences between unadjusted and DIF-adjusted measures of greater than the standard error of measurement. CONCLUSIONS: DIF by sensory impairment in cognitive tests was independent of administration characteristics, which could indicate that elevated cognitive load among persons with sensory impairment plays a larger role in test performance than previously acknowledged. While these results were unexpected, neither of these samples are nationally representative and each has unique selection factors; thus, replication is critical.

The effect of missing data and imputation on the detection of bias in cognitive testing using differential item functioning methods.

BACKGROUND: Item response theory (IRT) methods for addressing differential item functioning (DIF) can detect group differences in responses to individual items (e.g., bias). IRT and DIF-detection methods have been used increasingly often to identify bias in cognitive test performance by characteristics (DIF grouping variables) such as hearing impairment, race, and educational attainment. Previous analyses have not considered the effect of missing data on inferences, although levels of missing cognitive data can be substantial in epidemiologic studies. METHODS: We used data from Visit 6 (2016-2017) of the Atherosclerosis Risk in Communities Neurocognitive Study (N = 3,580) to explicate the effect of artificially imposed missing data patterns and imputation on DIF detection. RESULTS: When missing data was imposed among individuals in a specific DIF group but was unrelated to cognitive test performance, there was no systematic error. However, when missing data was related to cognitive test performance and DIF group membership, there was systematic error in DIF detection. Given this missing data pattern, the median DIF detection error associated with 10%, 30%, and 50% missingness was -0.03, -0.08, and -0.14 standard deviation (SD) units without imputation, but this decreased to -0.02, -0.04, and -0.08 SD units with multiple imputation. CONCLUSIONS: Incorrect inferences in DIF testing have downstream consequences for the use of cognitive tests in research. It is therefore crucial to consider the effect and reasons behind missing data when evaluating bias in cognitive testing.

Isoprene Epoxydiol-Derived Sulfated and Nonsulfated Oligomers Suppress Particulate Mass Loss during Oxidative Aging of Secondary Organic Aerosol.

Acid-driven multiphase chemistry of isoprene epoxydiols (IEPOX) with inorganic sulfate aerosols contributes substantially to secondary organic aerosol (SOA) formation, which constitutes a large mass fraction of atmospheric fine particulate matter (PM2.5). However, the atmospheric chemical sinks of freshly generated IEPOX-SOA particles remain unclear. We examined the role of heterogeneous oxidation of freshly generated IEPOX-SOA particles by gas-phase hydroxyl radical (•OH) under dark conditions as one potential atmospheric sink. After 4 h of gas-phase •OH exposure (∼3 × 108 molecules cm-3), chemical changes in smog chamber-generated IEPOX-SOA particles were assessed by hydrophilic interaction liquid chromatography coupled with electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (HILIC/ESI-HR-QTOFMS). A comparison of the molecular-level compositional changes in IEPOX-SOA particles during aging with or without •OH revealed that decomposition of oligomers by heterogeneous •OH oxidation acts as a sink for •OH and maintains a reservoir of low-volatility compounds, including monomeric sulfate esters and oligomer fragments. We propose tentative structures and formation mechanisms for previously uncharacterized SOA constituents in PM2.5. Our results suggest that this •OH-driven renewal of low-volatility products may extend the atmospheric lifetimes of particle-phase IEPOX-SOA by slowing the production of low-molecular weight, high-volatility organic fragments and likely contributes to the large quantities of 2-methyltetrols and methyltetrol sulfates reported in PM2.5.

Initial pH Governs Secondary Organic Aerosol Phase State and Morphology after Uptake of Isoprene Epoxydiols (IEPOX).

Aerosol acidity increases secondary organic aerosol (SOA) formed from the reactive uptake of isoprene-derived epoxydiols (IEPOX) by enhancing condensed-phase reactions within sulfate-containing submicron particles, leading to low-volatility organic products. However, the link between the initial aerosol acidity and the resulting physicochemical properties of IEPOX-derived SOA remains uncertain. Herein, we show distinct differences in the morphology, phase state, and chemical composition of individual organic-inorganic mixed particles after IEPOX uptake to ammonium sulfate particles with different initial atmospherically relevant acidities (pH = 1, 3, and 5). Physicochemical properties were characterized via atomic force microscopy coupled with photothermal infrared spectroscopy (AFM-PTIR) and Raman microspectroscopy. Compared to less acidic particles (pH 3 and 5), reactive uptake of IEPOX to the most acidic particles (pH 1) resulted in 50% more organosulfate formation, clearer phase separation (core-shell), and more irregularly shaped morphologies, suggesting that the organic phase transitioned to semisolid or solid. This study highlights that initial aerosol acidity may govern the subsequent aerosol physicochemical properties, such as viscosity and morphology, following the multiphase chemical reactions of IEPOX. These results can be used in future studies to improve model parameterizations of SOA formation from IEPOX and its properties, toward the goal of bridging predictions and atmospheric observations.

Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis.

Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.

An epigenome-wide association study meta-analysis of educational attainment.

The epigenome is associated with biological factors, such as disease status, and environmental factors, such as smoking, alcohol consumption and body mass index. Although there is a widespread perception that environmental influences on the epigenome are pervasive and profound, there has been little evidence to date in humans with respect to environmental factors that are biologically distal. Here we provide evidence on the associations between epigenetic modifications-in our case, CpG methylation-and educational attainment (EA), a biologically distal environmental factor that is arguably among the most important life-shaping experiences for individuals. Specifically, we report the results of an epigenome-wide association study meta-analysis of EA based on data from 27 cohort studies with a total of 10 767 individuals. We find nine CpG probes significantly associated with EA. However, robustness analyses show that all nine probes have previously been found to be associated with smoking. Only two associations remain when we perform a sensitivity analysis in the subset of never-smokers, and these two probes are known to be strongly associated with maternal smoking during pregnancy, and thus their association with EA could be due to correlation between EA and maternal smoking. Moreover, the effect sizes of the associations with EA are far smaller than the known associations with the biologically proximal environmental factors alcohol consumption, body mass index, smoking and maternal smoking during pregnancy. Follow-up analyses that combine the effects of many probes also point to small methylation associations with EA that are highly correlated with the combined effects of smoking. If our findings regarding EA can be generalized to other biologically distal environmental factors, then they cast doubt on the hypothesis that such factors have large effects on the epigenome.

Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N=53949).

General cognitive function is substantially heritable across the human life course from adolescence to old age. We investigated the genetic contribution to variation in this important, health- and well-being-related trait in middle-aged and older adults. We conducted a meta-analysis of genome-wide association studies of 31 cohorts (N=53,949) in which the participants had undertaken multiple, diverse cognitive tests. A general cognitive function phenotype was tested for, and created in each cohort by principal component analysis. We report 13 genome-wide significant single-nucleotide polymorphism (SNP) associations in three genomic regions, 6q16.1, 14q12 and 19q13.32 (best SNP and closest gene, respectively: rs10457441, P=3.93 × 10(-9), MIR2113; rs17522122, P=2.55 × 10(-8), AKAP6; rs10119, P=5.67 × 10(-9), APOE/TOMM40). We report one gene-based significant association with the HMGN1 gene located on chromosome 21 (P=1 × 10(-6)). These genes have previously been associated with neuropsychiatric phenotypes. Meta-analysis results are consistent with a polygenic model of inheritance. To estimate SNP-based heritability, the genome-wide complex trait analysis procedure was applied to two large cohorts, the Atherosclerosis Risk in Communities Study (N=6617) and the Health and Retirement Study (N=5976). The proportion of phenotypic variation accounted for by all genotyped common SNPs was 29% (s.e.=5%) and 28% (s.e.=7%), respectively. Using polygenic prediction analysis, ~1.2% of the variance in general cognitive function was predicted in the Generation Scotland cohort (N=5487; P=1.5 × 10(-17)). In hypothesis-driven tests, there was significant association between general cognitive function and four genes previously associated with Alzheimer's disease: TOMM40, APOE, ABCG1 and MEF2C.

CCR5-Δ32 genotype does not improve predictive value of IL28B polymorphisms for treatment response in chronic HCV infection.

IL28B polymorphisms strongly predict spontaneous and treatment-induced clearance of hepatitis C virus (HCV) infection. A recent study proposed a 32-base pair deletion in the CC-chemokine receptor 5 (CCR5) gene (CCR5-Δ32) interacting with the IL28B polymorphisms to influence spontaneous HCV clearance. The aim of this study was to clarify the role of CCR5-Δ32 in treatment-induced clearance of chronic hepatitis C (CHC). A cross-sectional cohort of 813 Caucasian patients with CHC genotype 1 (365 responders and 448 non-responders) who had received standard of care dual therapy with interferon (IFN)-α and ribavirin (RBV) was genotyped for the CCR5-Δ32 and IL28B polymorphisms to examine their interaction with respect to treatment response. CCR5-Δ32 did not influence treatment-induced recovery to IFN-α/RBV in CHC, and did not improve prediction of sustained virological response in the context of the IL28B polymorphisms in a multivariate model. CCR5-Δ32 homozygotes were significantly more frequent in those with CHC than healthy controls in the European cohorts (2.9% vs 0.4%, P<0.0001), but not in Australians of European ancestry. In conclusion, CCR5-Δ32 does not influence treatment response in the context of IL28B polymorphisms. Although CCR5-Δ32 may affect viral clearance within closely controlled geographical and genetic environments, we found no effect in larger cohorts treated with dual therapy.

Standard- or high-dose oxytocin for nulliparous women with confirmed delay in labour: quantitative and qualitative results from a pilot randomised controlled trial.

OBJECTIVE: Evidence suggests that a high dose of oxytocin for nulliparous women at 37-42 weeks of gestation with confirmed delay in labour increases spontaneous vaginal birth. We undertook a pilot study to test the feasibility of this treatment. DESIGN: Pilot double-blind randomised controlled trial. SETTING: Three teaching hospitals in the UK. POPULATION: A total of 94 consenting nulliparous women at term with confirmed delay in labour were recruited, and 18 were interviewed. METHODS: Women were assigned to either a standard (2 mU/min, increasing every 30 minutes to 32 mU/minute) or a high-dose regimen (4 mU/minute, increasing every 30 minutes to 64 mU/minutes) oxytocin by computer-generated randomisation. Simple descriptive statistics were used, as the sample size was insufficient to evaluate clinical outcomes. The constant comparative method was used to analyse the interviews. MAIN OUTCOMES MEASURES: The main outcome measures: number of women eligible; maternal and neonatal birth; safety; maternal psychological outcomes and experiences; health-related quality of life outcomes using validated tools and data on health service resource use; incidence of suspected delay of labour (cervical dilatation of <2 cm after 4 hours, once labour is established); and incidence of confirmed delay of labour (progress of <1 cm on repeat vaginal examination after a period of 2 hours). RESULTS: We successfully developed systems to recruit eligible women in labour and to collect data. Rates of spontaneous vaginal birth (10/47 versus 12/47, RR 1.2, 95% CI 0.6-2.5) and caesarean section (15/47 versus 17/47, RR 1.1, 95% CI 0.6-2.0) were increased, and rates of instrumental birth were reduced (21/47 versus 17/47, RR 0.8, 95% CI 0.5-1.3). No evidence of increased harm for either mother or baby was found. The incidences of suspected delay (14%) and confirmed delay (11%) in labour were less than anticipated. Of those who did not go on to have delayed labour confirmed, all except one woman gave birth vaginally. CONCLUSIONS: A pilot trial assessing the efficacy of high-dose oxytocin was feasible, but uncertainty remains, highlighting the need for a large definitive trial. The implementation of national guidance of suspected and confirmed delay in labour is likely to reduce intervention.

Cell type-specific translational profiling in the Xenopus laevis retina.

BACKGROUND: Translating Ribosome Affinity Purification (TRAP), a method recently developed to generate cell type-specific translational profiles, relies on creating transgenic lines of animals in which a tagged ribosomal protein is placed under regulatory control of a cell type-specific promoter. An antibody is then used to affinity purify the tagged ribosomes so that cell type-specific mRNAs can be isolated from whole tissue lysates. RESULTS: Here, cell type-specific transgenic lines were generated to enable TRAP studies for retinal ganglion cells and rod photoreceptors in the Xenopus laevis retina. Using real time quantitative PCR for assessing expression levels of cell type-specific mRNAs, the TRAP method was shown to selectively isolate mRNAs expressed in the targeted cell and was efficient at purifying mRNAs expressed at both high and low levels. Statistical measures used to distinguish cell type-specific RNAs from low level background and non-specific RNAs showed TRAP to be highly effective in Xenopus. CONCLUSIONS: TRAP can be used to purify mRNAs expressed in rod photoreceptors and retinal ganglion cells in X. laevis. The generated transgenic lines will enable numerous studies into the development, disease, and injury of the X. laevis retina.

Patient Preparation and Radiation Protection Guidance for Adult Patients Undergoing Radioiodine Treatment for Thyroid Cancer in the UK.

Radioactive iodine is a highly effective treatment for thyroid cancer and has now been used in clinical practice for more than 80 years. In general, the treatment is well tolerated. However, it can be logistically quite complex for patients due to the need to reduce iodine intake and achieve high levels of thyroid-stimulating hormone prior to treatment. Radiation protection precautions must also be taken to protect others from unnecessary radiation exposure following treatment. It has been well documented by thyroid cancer patient support groups that there is significant variation in practice across the UK. It is clear that some patients are being asked to observe unnecessarily burdensome restrictions that make it more difficult for them to tolerate the treatment. At the instigation of these support groups, a multidisciplinary group was assembled to examine the evidence and generate guidance on best practice for the preparation of patients for this treatment and the management of subsequent radiation protection precautions, with a focus on personalising the advice given to individual patients. The guidance includes advice about managing particularly challenging situations, for example treating patients who require haemodialysis. We have also worked together to produce a patient information leaflet covering these issues. We hope that the guidance document and patient information leaflet will assist centres in improving our patients' experience of receiving radioactive iodine. The patient information sheet is available as Supplementary Material to this article.

Establishing maximal oxygen uptake in young people during a ramp cycle test to exhaustion.

OBJECTIVES: This study tested the hypotheses that (1) secondary criteria (respiratory exchange ratio (RER), heart rate, blood [lactate]) traditionally used to verify the determination of maximum oxygen uptake (VO2(max)) in children can result in the acceptance of a 'submaximal' VO2(max) or falsely reject a 'true' VO(2max) and (2) the VO2(peak) recorded during a ramp test in children is comparable to the VO2(peak) achieved during supramaximal testing. METHODS: Thirteen children (9-10 years) completed a ramp cycle test to exhaustion to determine their VO2(peak). After 15 min of recovery, the participants performed a supramaximal cycle test to exhaustion at 105% of their ramp test peak power. RESULTS: Compared with the VO2(peak) during the ramp test, a significantly lower VO2 was recorded at a RER of 1.00 (1.293 litre/min (SD 0.265) vs 1.681 litre/min (SD 0.295), p < 0.001, n = 12), at a heart rate of 195 beats/min (1.556 litre/min (SD 0.265) vs 1.721 litre/min (SD 0.318), p < 0.001, n = 10) and at 85% of age-predicted maximum (1.345 litre/min (SD 0.228) vs 1.690 litre/min (SD 0.284), p < 0.001, n = 13). Supramaximal testing yielded a VO2(peak) that was not significantly different from the ramp test (1.615 litre/min (SD 0.307) vs 1.690 litre/min (SD 0.284), p = 0.090, respectively). CONCLUSIONS: The use of secondary criteria to verify a maximal effort in young people during ramp cycling exercise may result in the acceptance of a submaximal VO2(max). As supramaximal testing elicits a VO2(peak) similar to the ramp protocol, thus satisfying the plateau criterion, the use of such tests is recommended as the appropriate method of confirming a 'true' VO2(max) with children.

Taxonogenomics description of Arcanobacterium urinimassiliense sp. nov., a new bacterial species isolated from urine sample.

Strain Marseille-P3248т is a new species from the order Actinomycetales that was isolated from the urine sample of a girl aged 20 months with rotavirus gastroenteritis. It is a facultative anaerobic Gram-positive rod-shaped bacterium. Strain Marseille-P3248т exhibits 94.73% sequence similarity with Arcanobacterium pluranimalium strain M430/94/2, a phylogenetically related species with standing in nomenclature. Its genome size is 1 667 964 bp with 49.1% G + C content. Strain Marseille-P3248т (= CSURP3248) is the type strain of the new species Arcanobacterium urinimassiliense sp. nov.

Luxibacter massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota.

An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551T was considered to be a new genus within the phylum Firmicutes, as it exhibits a 91.87% similarity level with Faecalicatena orotica (NR_117129.1), the phylogenetically closest related species. The draft genome size of strain Marseille-P5551T is 4 142 938 bp with 44.4% of G + C content. We hereby suggest the creation of Luxibacter massiliensis gen. nov., sp. nov., as a new bacterial genus.

Virgibacillus doumboii sp. nov., a halophilic bacterium isolated from the stool of a healthy child in Mali.

A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).

Microdeletion 15q13.3: a locus with incomplete penetrance for autism, mental retardation, and psychiatric disorders.

BACKGROUND: Microdeletions within chromosome 15q13.3 are associated both with a recently recognised syndrome of mental retardation, seizures, and dysmorphic features, and with schizophrenia. METHODS AND RESULTS: Based on routine diagnostic testing of approximately 8200 samples using array comparative genomic hybridisation, we identified 20 individuals (14 children and six parents in 12 families) with microdeletions of 15q13.3. Phenotypes in the children included developmental delay, mental retardation, or borderline IQ in most and autistic spectrum disorder (6/14), speech delay, aggressiveness, attention deficit hyperactivity disorder, and other behavioural problems. Both parents were available in seven families, and the deletion was de novo in one, inherited from an apparently normal parent in four, and inherited from a parent with learning disability and bipolar disorder in two families. Of the 14 children, six in five families were adopted, and DNA was available for only one of these 10 biological parents; the deletion was very likely inherited for one of these families with two affected children. Among the unavailable parents, two mothers were described as having mental retardation, another mother as having "mental illness", and one father as having schizophrenia. We hypothesise that some of the unavailable parents have the deletion. CONCLUSIONS: The occurrence of increased adoption, frequent autism, bipolar disorder, and lack of penetrance are noteworthy findings in individuals with deletion 15q13.3. A high rate of adoption may be related to the presence of the deletion in biological parents. Unconfirmed histories of antisocial behaviours in unavailable biological parents raise the concern that future research may show that deletion 15q13.3 is associated with such behaviours.

Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool.

Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.