Mechanistic study of the atomic layer deposition of cobalt: a combined mass spectrometric and computational approach.

Cobaltcarbonyl-tert-butylacetylene (CCTBA) is a conventional precursor for the selective atomic layer deposition of Co onto silicon surfaces. However, a limited understanding of the deposition mechanism of such cobalt precursors curbs rational improvements on their design for increased efficiency and tuneable selectivity. The impact of using a less reactive internal alkyne instead of a terminal alkyne was investigated using experimental and computational methods. Using electrospray-ionization mass spectrometry, the formation of CCTBA analogs and their gas phase decomposition pathways were studied. Decomposition experiments show very similar decomposition pathways between the two complexes. The internal alkyne dissociates from the Co complex at slightly lower energies than the terminal alkyne, suggesting that an internal alkynyl ligand may be more suited to low temperature ALD. In addition, transition state calculations using the nudged elastic band method confirm an increased reaction barrier between the internal alkyne and the Si-H surface bonds on Si(111). These results suggests that using a less reactive internal alkyne will result in fewer embedded carbon impurities during deposition onto Si wafers. DFT calculations using the PBE functional and periodic boundary conditions also predict increased surface binding with the metal centers of the internal alkynyl complex.

A century of statistical Ecology.

As data and computing power have surged in recent decades, statistical modeling has become an important tool for understanding ecological patterns and processes. Statistical modeling in ecology faces two major challenges. First, ecological data may not conform to traditional methods, and second, professional ecologists often do not receive extensive statistical training. In response to these challenges, the journal Ecology has published many innovative statistical ecology papers that introduced novel modeling methods and provided accessible guides to statistical best practices. In this paper, we reflect on Ecology's history and its role in the emergence of the subdiscipline of statistical ecology, which we define as the study of ecological systems using mathematical equations, probability, and empirical data. We showcase 36 influential statistical ecology papers that have been published in Ecology over the last century and, in so doing, comment on the evolution of the field. As data and computing power continue to increase, we anticipate continued growth in statistical ecology to tackle complex analyses and an expanding role for Ecology to publish innovative and influential papers, advancing the discipline and guiding practicing ecologists.

Deep biogeographic barriers explain divergent global vertebrate communities.

Biogeographic history can lead to variation in biodiversity across regions, but it remains unclear how the degree of biogeographic isolation among communities may lead to differences in biodiversity. Biogeographic analyses generally treat regions as discrete units, but species assemblages differ in how much biogeographic history they share, just as species differ in how much evolutionary history they share. Here, we use a continuous measure of biogeographic distance, phylobetadiversity, to analyze the influence of biogeographic isolation on the taxonomic and functional diversity of global mammal and bird assemblages. On average, biodiversity is better predicted by environment than by isolation, especially for birds. However, mammals in deeply isolated regions are strongly influenced by isolation; mammal assemblages in Australia and Madagascar, for example, are much less diverse than predicted by environment alone and contain unique combinations of functional traits compared to other regions. Neotropical bat assemblages are far more functionally diverse than Paleotropical assemblages, reflecting the different trajectories of bat communities that have developed in isolation over tens of millions of years. Our results elucidate how long-lasting biogeographic barriers can lead to divergent diversity patterns, against the backdrop of environmental determinism that predominantly structures diversity across most of the world.

Enhanced Mechanistic Understanding Through the Detection of Radical Intermediates in Organic Reactions.

Two applications of a radical trap based on a homolytic substitution reaction (SH2') are presented for the trapping of short-lived radical intermediates in organic reactions. The first example is a photochemical cyanomethylation catalyzed by a Ru complex. Two intermediate radicals in the radical chain propagation have been trapped and detected using mass spectrometry (MS), along with the starting materials, products and catalyst degradation fragments. Although qualitative, these results helped to elucidate the reaction mechanism. In the second example, the trapping method was applied to study the radical initiation catalyzed by a triethylboronoxygen mixture. In this case, the concentration of trapped radicals was sufficiently high to enable their detection by nuclear magnetic resonance (NMR). Quantitative measurements made it possible to characterize the radical flux in the system under different reaction conditions (including variations of solvent, temperature and concentration) where modelling was complicated by chain reactions and heterogeneous mass transfer.

OptiMS: An Accessible Program for Automating Mass Spectrometry Parameter Optimization and Configuration.

Mass spectrometers have an enormous number of user-changeable parameters that drastically affect the observed mass spectrum. Using optimal parameters can significantly improve mass spectrometric data by increasing signal stability and signal-to-noise ratio, which decreases the limit of detection, thus revealing previously unobservable species. However, ascertaining optimal parameters is time-consuming, tedious, and made further challenging by the fact that parameters can act dependently on each other. Consequently, suboptimal parameters are frequently used during characterization, reducing the quality of results. OptiMS, an open-source, cross-platform program, was developed to simplify, accelerate, and more accurately determine optimal mass spectrometer parameters for a given system. It addresses common difficulties associated with existing software such as slow performance, high costs, and limited functionality. OptiMS efficacy was demonstrated through its application to multiple systems, quickly and successfully optimizing instrument parameters unassisted to maximize a user-defined metric, such as the intensity of a particular analyte. Additionally, among other features, OptiMS allows running of a sequence of predefined parameter configurations, reducing the workload of users wishing to obtain mass spectra under multiple sets of conditions.

Microstructural Analysis of Benzoxazine Cationic Ring-Opening Polymerization Pathways.

Herein, an evaluation of the initial step of benzoxazine polymerization is presented by mass spectrometry, with a focus on differentiating the phenoxy and phenolic products formed by distinct pathways of the cationic ring opening polymerization (ROP) mechanism of polybenzoxazine formation. The use of infrared multiple photon dissociation (IRMPD) and ion mobility spectrometry (IMS) techniques allows for differentiation of the two pathways and provides valuable insights into the ROP mechanism. The results suggest that type I pathway is favored in the initial stages of the reaction yielding the phenoxy product, while type II product should be observed at later stages when the phenoxy product would interconvert to the most stable type II phenolic product. Overall, the findings presented here provide important information on the initial step of the benzoxazine polymerization, allowing the development of optimal polymerization conditions and represents a way to evaluate other multifunctional polymerization processes.

Continuous addition kinetic elucidation: catalyst and reactant order, rate constant, and poisoning from a single experiment.

Kinetic analysis of catalytic reactions is a powerful tool for mechanistic elucidation but is often challenging to perform, limiting understanding and therefore development of these reactions. Establishing order in a catalyst is usually achieved by running several reactions at different loadings, which is both time-consuming and complicated by the challenge of maintaining consistent run-to-run experimental conditions. Continuous addition kinetic elucidation (CAKE) was developed to circumvent these issues by continuously injecting a catalyst into a reaction, while monitoring reaction progress over time. For reactions that are mth order in a single yield-limiting reactant and nth order in catalyst, a plot of reactant concentration against time has a shape dependent only on the orders m and n. Therefore, fitting experimental CAKE data (using open access code or a convenient web tool) allows the reactant and catalyst orders, rate constant, and the amount of complete catalyst inhibition to be determined from a single experiment. Kinetic information obtained from CAKE experiments showed good agreement with the literature.

Landscape-scale benefits of protected areas for tropical biodiversity.

The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines1. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear2-5. Unregulated hunting can empty PAs of large animals6, illegal tree felling can degrade habitat quality7, and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape8 (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites9 (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.

New Approach to the Detection of Short-Lived Radical Intermediates.

We report a new general method for trapping short-lived radicals, based on a homolytic substitution reaction SH2'. This departure from conventional radical trapping by addition or radical-radical cross-coupling results in high sensitivity, detailed structural information, and general applicability of the new approach. The radical traps in this method are terminal alkenes possessing a nitroxide leaving group (e.g., allyl-TEMPO derivatives). The trapping process thus yields stable products which can be stored and subsequently analyzed by mass spectrometry (MS) supported by well-established techniques such as isotope exchange, tandem MS, and high-performance liquid chromatography-MS. The new method was applied to a range of model radical reactions in both liquid and gas phases including a photoredox-catalyzed thiol-ene reaction and alkene ozonolysis. An unprecedented range of radical intermediates was observed in complex reaction mixtures, offering new mechanistic insights. Gas-phase radicals can be detected at concentrations relevant to atmospheric chemistry.

δ18O as a tracer of PO43- losses from agricultural landscapes.

Accurately tracing the sources and fate of excess PO43- in waterways is necessary for sustainable catchment management. The natural abundance isotopic composition of O in PO43- (δ18OP) is a promising tracer of point source pollution, but its ability to track diffuse agricultural pollution is unclear. We tested the hypothesis that δ18OP could distinguish between agricultural PO43- sources by measuring the integrated δ18OP composition and P speciation of contrasting inorganic fertilisers (compound vs rock) and soil textures (sand, loam, clay) in southwestern Australia. δ18OP composition differed between the three soil textures sampled across six livestock farms: sandy soils had lower overall δ18OP values (21 ± 1‰) than the loams (23 ± 1‰), which corresponded with a smaller, but more readily leachable, PO43- pool. Fertilisers had greater δ18OP variability (∼8‰), with fluctuations due to type and manufacturing year. Consequently, catchment 'agricultural soil leaching' δ18OP signatures could span from 18 to 25‰ depending on both fertiliser type and timing (lag between application and leaching). These findings emphasise the potential of δ18OP to untangle soil-fertiliser P dynamics under controlled conditions, but that its use to trace catchment-scale agricultural PO43- losses is limited by uncertainties in soil biological P cycling and its associated isotopic fractionation.

Grain size and organic carbon controls polyaromatic hydrocarbons (PAH), mercury (Hg) and toxicity of surface sediments in the River Conwy Estuary, Wales, UK.

The Conwy estuary was evaluated for sediment quality. Microtox bioassay revealed 38 of 39 sites were non-toxic. Hg ranged from 0.001 to 0.153 µg kg-1, mean 0.026 mg kg-1, Σ16 PAH from 18 to 1578 µg kg-1, mean 269 µg kg-1, Σ22 PAH, 18 to 1871 µg kg-1 mean to 312 µg kg-1, two sites had high perylene relative to ΣPAH. Σ22PAH correlated positively with TOC, clay and silt (R2 0.89, 0.92, 0.90) and negatively with sand. Multivariate statistics, delineated four spatial (site) and five variable (measurements) clusters. Spatial clustering relates to sediment grain size, in response to hydrodynamic processes in estuary; fine (clay to silt) sized sediments exhibit the highest Hg and PAH content, because these components partitioned into the fine fraction. Comparison to national and international environmental standards suggests Hg and PAH content of Conwy sediments are unlikely to harm ecology or transfer up into the human food chain.

Hexavalent chromium bioreduction and chemical precipitation of sulphate as a treatment of site-specific fly ash leachates.

Most of the power generation globally is by coal-fired power plants resulting in large stockpiles of fly ash. The trace elements associated with the ash particles are subjected to the leaching effects of precipitation which may lead to the subsequent contamination of surface and groundwater systems. In this study, we successfully demonstrate an efficient and sustainable dual treatment remediation strategy for the removal of high levels of Cr6+ and SO42- introduced by fly ash leachate generated by a power station situation in Mpumalanga, South Africa. The treatment consisted of a primary fixed-bed bioreactor kept at a reduction potential for Cr6+ reduction. Metagenome sequencing clearly indicated a diverse bacterial community containing various bacteria, predominantly of the phylum Proteobacteria which includes numerous species known for their ability to detoxify metals such as Cr6+. This was followed by a secondary BaCO3/dispersed alkaline substrate column for SO42- removal. The combination of these two systems resulted in the removal of 99% Cr6+ and 90% SO42-. This is the first effective demonstration of an integrated system combining a biological and chemical strategy for the remediation of multi-contaminants present in fly ash leachate in South Africa.

A multi-stable isotope framework to understand eutrophication in aquatic ecosystems.

Eutrophication is a globally significant challenge facing aquatic ecosystems, associated with human induced enrichment of these ecosystems with nitrogen (N) and phosphorus (P). However, the limited availability of inherent labels for P and N has constrained understanding of the triggers for eutrophication in natural ecosystems and appropriate targeting of management responses. This paper proposes and evaluates a new multi-stable isotope framework that offers inherent labels to track biogeochemical reactions governing both P and N in natural ecosystems. The framework couples highly novel analysis of the oxygen isotope composition of phosphate (δ(18)OPO4) with dual isotope analysis of oxygen and N within nitrate (δ(15)NNO3, δ(18)ONO3) and with stable N isotope analysis in ammonium (δ(15)NNH4). The River Beult in England is used as an exemplar system for initial evaluation of this framework. Our data demonstrate the potential to use stable isotope labels to track the input and downstream fate of nutrients from point sources, on the basis of isotopic differentiation for both P and N between river water and waste water treatment work effluent (mean difference = +1.7‰ for δ(18)OPO4; +15.5‰ for δ(15)NNH4 (under high flow); +7.3‰ for δ(18)ONO3 and +4.4‰ for δ(15)NNO3). Stable isotope data reveal nutrient inputs to the river upstream of the waste water treatment works that are consistent with partially denitrified sewage or livestock sources of nitrate (δ(15)NNO3 range = +11.5 to +13.1‰) and with agricultural sources of phosphate (δ(18)OPO4 range = +16.6 to +19.0‰). The importance of abiotic and metabolic processes for the in-river fate of N and P are also explored through the stable isotope framework. Microbial uptake of ammonium to meet metabolic demand for N is suggested by substantial enrichment of δ(15)NNH4 (by 10.2‰ over a 100 m reach) under summer low flow conditions. Whilst the concentration of both nitrate and phosphate decreased substantially along the same reach, the stable isotope composition of these ions did not vary significantly, indicating that concentration changes are likely driven by abiotic processes of dilution or sorption. The in-river stable isotope composition and the concentration of P and N were also largely constant downstream of the waste water treatment works, indicating that effluent-derived nutrients were not strongly coupled to metabolism along this in-river transect. Combined with in-situ and laboratory hydrochemical data, we believe that a multi-stable isotope framework represents a powerful approach for understanding and managing eutrophication in natural aquatic ecosystems.

The value of survival analyses for evidence-based rural medical workforce planning.

BACKGROUND: Globally, abundant opportunities exist for policymakers to improve the accessibility of rural and remote populations to primary health care through improving workforce retention. This paper aims to identify and quantify the most important factors associated with rural and remote Australian family physician turnover, and to demonstrate how evidence generated by survival analysis of health workforce data can inform rural workforce policy making. METHODS: A secondary analysis of longitudinal data collected by the New South Wales (NSW) Rural Doctors Network for all family physicians working in rural or remote NSW between January 1(st) 2003 and December 31(st) 2012 was performed. The Prentice, Williams and Peterson statistical model for survival analysis was used to identify and quantify risk factors for rural NSW family physician turnover. RESULTS: Multivariate modelling revealed a higher (2.65-fold) risk of family physician turnover in small, remote locations compared to that in small closely settled locations. Family physicians who graduated from countries other than Australia, United Kingdom, United States of America, New Zealand, Ireland, and Canada also had a higher (1.45-fold) risk of turnover compared to Australian trained family physicians. This was after adjusting for the effects of conditional registration. Procedural skills and public hospital admitting rights were associated with a lower risk of turnover. These risks translate to a predicted median survival of 11 years for Australian-trained family physician non-proceduralists with hospital admitting rights working in small coastal closely settled locations compared to 3 years for family physicians in remote locations. CONCLUSIONS: This study provides rigorous empirical evidence of the strong association between population size and geographical location and the retention of family physicians in rural and remote NSW. This has important policy ramifications since retention grants for rural and remote family physicians in Australia are currently based on a geographical 'remoteness' classification rather than population size. In addition, this study demonstrates how survival analysis assists health workforce planning, such as through generating evidence to assist in benchmarking 'reasonable' lengths of practice in different geographic settings that might guide service obligation requirements.

Using boreholes as windows into groundwater ecosystems.

Groundwater ecosystems remain poorly understood yet may provide ecosystem services, make a unique contribution to biodiversity and contain useful bio-indicators of water quality. Little is known about ecosystem variability, the distribution of invertebrates within aquifers, or how representative boreholes are of aquifers. We addressed these issues using borehole imaging and single borehole dilution tests to identify three potential aquifer habitats (fractures, fissures or conduits) intercepted by two Chalk boreholes at different depths beneath the surface (34 to 98 m). These habitats were characterised by sampling the invertebrates, microbiology and hydrochemistry using a packer system to isolate them. Samples were taken with progressively increasing pumped volume to assess differences between borehole and aquifer communities. The study provides a new conceptual framework to infer the origin of water, invertebrates and microbes sampled from boreholes. It demonstrates that pumping 5 m(3) at 0.4-1.8 l/sec was sufficient to entrain invertebrates from five to tens of metres into the aquifer during these packer tests. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. There was some variability in invertebrate abundance and bacterial community structure between habitats, indicating ecological heterogeneity within the aquifer. However, invertebrates were captured in all aquifer samples, and bacterial abundance, major ion chemistry and dissolved oxygen remained similar. Therefore the study demonstrates that in the Chalk, ecosystems comprising bacteria and invertebrates extend from around the water table to 70 m below it. Hydrogeological techniques provide excellent scope for tackling outstanding questions in groundwater ecology, provided an appropriate conceptual hydrogeological understanding is applied.

Characterization of suboxic groundwater colloids using a multi-method approach.

Anoxic groundwater colloid properties were measured using a minimally perturbing procedure for sampling, processing, and analysis. Analytical methods included atomic force microscopy (AFM), flow field flow fractionation (FlFFF), and transmission and scanning electron microscopy (TEM and SEM). Shallow groundwater samples showed abundant iron rich nanoparticles (NP) with diameters of 10-30 nm as well as a smaller heterogeneous polydisperse dissolved organic matter (DOM) fraction. AFM results showed NP with average heights of 10 ± 2 nm, which was corroborated by high-resolution TEM and SEM. FlFFF with UV254 nm detection found particles with number average diffusion coefficients of 2-3 × 10(-10) m(2) s(-1) and hydrodynamic diameters between 1.5 and 2 nm probably representing smaller organic macromolecules. Aeration of the samples resulted in extensive agglomeration of NP to form larger (>50 nm) colloids, and a reduction of UV-absorbing material in the 0.5-4 nm range. The complementary methods described have potential applications for investigating the fate and transport of NP in suboxic hotspots such as leachate plumes, wastewater treatment plants, and within the hyporheic mixing zone.

The oligotrophic ocean is autotrophic.

In vitro observations of net community production (NCP) imply that the oligotrophic subtropical gyres of the open ocean are net heterotrophic; in situ observations, in contrast, consistently imply that they are net autotrophic. At least one approach must be returning an incorrect answer. We find that (a) no bias in in situ oxygen-based production estimates would give false-positive (net autotrophy) rates, (b) observed (13)C enrichment of surface water dissolved inorganic carbon (DIC) can be explained only by positive NCP (net autotrophy), (c) lateral and vertical inputs of organic carbon are insufficient to sustain net heterotrophy, and (d) atmospheric input of organic material is too small to support in vitro rates of net heterotrophy and would yield δ(13)C depletion of surface DIC, quite the opposite of what is observed in the subtropical gyres. We conclude that the in vitro observations, implying net heterotrophy, must contain a bias that is due to an underestimate of photosynthetic rate and/or an overestimate of respiration rate.

Sidelobes in the response of arrayed waveguide gratings caused by polarization rotation.

Earlier it was observed that polarization rotation in an AWG built from birefringent waveguides can result in sidelobes in its response. This effect was measured in a polarization sensitive AWG with an orthogonal layout. Now we investigate through detailed simulation whether this effect also exists in polarization desensitised AWGs. It is shown that a dispersion compensated AWG does not suffer from a polarization sidelobe. Alternatively, the AWG can be designed to minimize polarization rotation to suppress the sidelobe.