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Background Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results. Methods and results Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception ( n  = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5). Conclusions Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes . Microbiome optimization may provide a novel strategy for preventing NEC.

Elemental compositions of organic aerosol (OA) particles provide useful constraints on OA sources, chemical evolution, and effects. The Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA elemental composition. This study evaluates AMS measurements of atomic oxygen-to-carbon (O : C), hydrogen-to-carbon (H : C), and organic mass-to-organic carbon (OM : OC) ratios, and of carbon oxidation state (OS C) for a vastly expanded laboratory data set of multifunctional oxidized OA standards. For the expanded standard data set, the method introduced by Aiken et al. (2008), which uses experimentally measured ion intensities at all ions to determine elemental ratios (referred to here as \"Aiken-Explicit\"), reproduces known O : C and H : C ratio values within 20% (average absolute value of relative errors) and 12%, respectively. The more commonly used method, which uses empirically estimated H2O+ and CO+ ion intensities to avoid gas phase air interferences at these ions (referred to here as \"Aiken-Ambient\"), reproduces O : C and H : C of multifunctional oxidized species within 28 and 14% of known values. The values from the latter method are systematically biased low, however, with larger biases observed for alcohols and simple diacids. A detailed examination of the H2O+, CO+, and CO2+ fragments in the high-resolution mass spectra of the standard compounds indicates that the Aiken-Ambient method underestimates the CO+ and especially H2O+ produced from many oxidized species. Combined AMS–vacuum ultraviolet (VUV) ionization measurements indicate that these ions are produced by dehydration and decarboxylation on the AMS vaporizer (usually operated at 600 °C). Thermal decomposition is observed to be efficient at vaporizer temperatures down to 200 °C. These results are used together to develop an \"Improved-Ambient\" elemental analysis method for AMS spectra measured in air. The Improved-Ambient method uses specific ion fragments as markers to correct for molecular functionality-dependent systematic biases and reproduces known O : C (H : C) ratios of individual oxidized standards within 28% (13%) of the known molecular values. The error in Improved-Ambient O : C (H : C) values is smaller for theoretical standard mixtures of the oxidized organic standards, which are more representative of the complex mix of species present in ambient OA. For ambient OA, the Improved-Ambient method produces O : C (H : C) values that are 27% (11%) larger than previously published Aiken-Ambient values; a corresponding increase of 9% is observed for OM : OC values. These results imply that ambient OA has a higher relative oxygen content than previously estimated. The OS C values calculated for ambient OA by the two methods agree well, however (average relative difference of 0.06 OS C units). This indicates that OS C is a more robust metric of oxidation than O : C, likely since OS C is not affected by hydration or dehydration, either in the atmosphere or during analysis.

We discuss the use of a two-dimensional volatility-oxidation space (2-D-VBS) to describe organic-aerosol chemical evolution. The space is built around two coordinates, volatility and the degree of oxidation, both of which can be constrained observationally or specified for known molecules. Earlier work presented the thermodynamics of organics forming the foundation of this 2-D-VBS, allowing us to define the average composition (C, H, and O) of organics, including organic aerosol (OA) based on volatility and oxidation state. Here we discuss how we can analyze experimental data, using the 2-D-VBS to gain fundamental insight into organic-aerosol chemistry. We first present a well-understood \"traditional\" secondary organic aerosol (SOA) system – SOA from α-pinene + ozone, and then turn to two examples of \"non-traditional\" SOA formation – SOA from wood smoke and dilute diesel-engine emissions. Finally, we discuss the broader implications of this analysis.

We performed a systematic intercomparison study of the chemistry and yields of secondary organic aerosol (SOA) generated from OH oxidation of a common set of gas-phase precursors in a Potential Aerosol Mass (PAM) continuous flow reactor and several environmental chambers. In the flow reactor, SOA precursors were oxidized using OH concentrations ranging from 2.0 × 108 to 2.2 × 1010 molec cm−3 over exposure times of 100 s. In the environmental chambers, precursors were oxidized using OH concentrations ranging from 2 × 106 to 2 × 107 molec cm−3 over exposure times of several hours. The OH concentration in the chamber experiments is close to that found in the atmosphere, but the integrated OH exposure in the flow reactor can simulate atmospheric exposure times of multiple days compared to chamber exposure times of only a day or so. In most cases, for a specific SOA type the most-oxidized chamber SOA and the least-oxidized flow reactor SOA have similar mass spectra, oxygen-to-carbon and hydrogen-to-carbon ratios, and carbon oxidation states at integrated OH exposures between approximately 1 × 1011 and 2 × 1011 molec cm−3 s, or about 1–2 days of equivalent atmospheric oxidation. This observation suggests that in the range of available OH exposure overlap for the flow reactor and chambers, SOA elemental composition as measured by an aerosol mass spectrometer is similar whether the precursor is exposed to low OH concentrations over long exposure times or high OH concentrations over short exposure times. This similarity in turn suggests that both in the flow reactor and in chambers, SOA chemical composition at low OH exposure is governed primarily by gas-phase OH oxidation of the precursors rather than heterogeneous oxidation of the condensed particles. In general, SOA yields measured in the flow reactor are lower than measured in chambers for the range of equivalent OH exposures that can be measured in both the flow reactor and chambers. The influence of sulfate seed particles on isoprene SOA yield measurements was examined in the flow reactor. The studies show that seed particles increase the yield of SOA produced in flow reactors by a factor of 3 to 5 and may also account in part for higher SOA yields obtained in the chambers, where seed particles are routinely used.

Background. Necrotizing enterocolitis (NEC) is a devastating inflammatory bowel disease of premature infants speculatively associated with infection. Suspected NEC can be indistinguishable from sepsis, and in established cases an infant may die within hours of diagnosis. Present treatment is supportive. A means of presymptomatic diagnosis is urgently needed. We aimed to identify microbial signatures in the gastrointestinal microbiota preceding NEC diagnosis in premature infants. Methods. Fecal samples and clinical data were collected from a 2-year cohort of 369 premature neonates. Next-generation sequencing of 16S ribosomal RNA gene regions was used to characterize the microbiota of prediagnosis fecal samples from 12 neonates with NEC, 8 with suspected NEC, and 44 controls. Logistic regression was used to determine clinical characteristics and operational taxonomic units (OTUs) discriminating cases from controls. Samples were cultured and isolates identified using matrix-assisted laser desorption/ionization–time of flight. Clostridial isolates were typed and toxin genes detected. Results. A clostridial OTU was overabundant in prediagnosis samples from infants with established NEC (P = .006). Culture confirmed the presence of Clostridium perfringens type A. Fluorescent amplified fragment-length polymorphism typing established that no isolates were identical. Prediagnosis samples from NEC infants not carrying profuse C. perfringens revealed an overabundance of a Klebsiella OTU (P = .049). Prolonged continuous positive airway pressure (CPAP) therapy with supplemental oxygen was also associated with increased NEC risk. Conclusions. Two fecal microbiota signatures (Clostridium and Klebsiella OTUs) and need for prolonged CPAP oxygen signal increased risk of NEC in presymptomatic infants. These biomarkers will assist development of a screening tool to allow very early diagnosis of NEC.

The direct radiative effect (DRE) of aerosols, which is the instantaneous radiative impact of all atmospheric particles on the Earth's energy balance, is sometimes confused with the direct radiative forcing (DRF), which is the change in DRE from pre-industrial to present-day (not including climate feedbacks). In this study we couple a global chemical transport model (GEOS-Chem) with a radiative transfer model (RRTMG) to contrast these concepts. We estimate a global mean all-sky aerosol DRF of −0.36 Wm−2 and a DRE of −1.83 Wm−2 for 2010. Therefore, natural sources of aerosol (here including fire) affect the global energy balance over four times more than do present-day anthropogenic aerosols. If global anthropogenic emissions of aerosols and their precursors continue to decline as projected in recent scenarios due to effective pollution emission controls, the DRF will shrink (−0.22 Wm−2 for 2100). Secondary metrics, like DRE, that quantify temporal changes in both natural and anthropogenic aerosol burdens are therefore needed to quantify the total effect of aerosols on climate.

Organic aerosol (OA) in the atmosphere consists of a multitude of organic species which are either directly emitted or the products of a variety of chemical reactions. This complexity challenges our ability to explicitly characterize the chemical composition of these particles. We find that the bulk composition of OA from a variety of environments (laboratory and field) occupies a narrow range in the space of a Van Krevelen diagram (H:C versus O:C), characterized by a slope of ∼−1. The data show that atmospheric aging, involving processes such as volatilization, oxidation, mixing of air masses or condensation of further products, is consistent with movement along this line, producing a more oxidized aerosol. This finding has implications for our understanding of the evolution of atmospheric OA and representation of these processes in models.

Circuit quantum electrodynamics has proven to be a powerful tool to probe mesoscopic effects in hybrid systems and is used in several quantum computing (QC) proposals that require a transmon qubit able to operate in strong magnetic fields. To address this we integrate monolayer graphene Josephson junctions into microwave frequency superconducting circuits to create graphene based transmons. Using dispersive microwave spectroscopy we resolve graphene’s characteristic band dispersion and observe coherent electronic interference effects confirming the ballistic nature of our graphene Josephson junctions. We show that the monoatomic thickness of graphene renders the device insensitive to an applied magnetic field, allowing us to perform energy level spectroscopy of the circuit in a parallel magnetic field of 1 T, an order of magnitude higher than previous studies. These results establish graphene based superconducting circuits as a promising platform for QC and the study of mesoscopic quantum effects that appear in strong magnetic fields. A transmon qubit insensitive to magnetic fields is a crucial element in topological quantum computing. Here, Kroll et al. create graphene transmons by integrating monolayer graphene Josephson junctions into microwave frequency superconducting circuits, allowing them to operate in a parallel magnetic field of 1 T.

Suboptimal childhood vaccination uptake results in disease outbreaks, and in developed countries is largely attributable to parental choice. To inform evidence-based interventions, we conducted a systematic review of factors underlying parental vaccination decisions. Thirty-one studies were reviewed. Outcomes and methods are disparate, which limits synthesis; however parents are consistently shown to act in line with their attitudes to combination childhood vaccinations. Vaccine-declining parents believe that vaccines are unsafe and ineffective and that the diseases they are given to prevent are mild and uncommon; they mistrust their health professionals, Government and officially-endorsed vaccine research but trust media and non-official information sources and resent perceived pressure to risk their own child's safety for public health benefit. Interventions should focus on detailed decision mechanisms including disease-related anticipated regret and perception of anecdotal information as statistically representative. Self-reported vaccine uptake, retrospective attitude assessment and unrepresentative samples limit the reliability of reviewed data – methodological improvements are required in this area.

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological \"species\" in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations.