RMG Database for Chemical Property Prediction.

The Reaction Mechanism Generator (RMG) database for chemical property prediction is presented. The RMG database consists of curated datasets and estimators for accurately predicting the parameters necessary for constructing a wide variety of chemical kinetic mechanisms. These datasets and estimators are mostly published and enable prediction of thermodynamics, kinetics, solvation effects, and transport properties. For thermochemistry prediction, the RMG database contains 45 libraries of thermochemical parameters with a combination of 4564 entries and a group additivity scheme with 9 types of corrections including radical, polycyclic, and surface absorption corrections with 1580 total curated groups and parameters for a graph convolutional neural network trained using transfer learning from a set of >130 000 DFT calculations to 10 000 high-quality values. Correction schemes for solvent-solute effects, important for thermochemistry in the liquid phase, are available. They include tabulated values for 195 pure solvents and 152 common solutes and a group additivity scheme for predicting the properties of arbitrary solutes. For kinetics estimation, the database contains 92 libraries of kinetic parameters containing a combined 21 000 reactions and contains rate rule schemes for 87 reaction classes trained on 8655 curated training reactions. Additional libraries and estimators are available for transport properties. All of this information is easily accessible through the graphical user interface at https://rmg.mit.edu. Bulk or on-the-fly use can be facilitated by interfacing directly with the RMG Python package which can be installed from Anaconda. The RMG database provides kineticists with easy access to estimates of the many parameters they need to model and analyze kinetic systems. This helps to speed up and facilitate kinetic analysis by enabling easy hypothesis testing on pathways, by providing parameters for model construction, and by providing checks on kinetic parameters from other sources.

Increases in Future AR Count and Size: Overview of the ARTMIP Tier 2 CMIP5/6 Experiment.

The Atmospheric River (AR) Tracking Method Intercomparison Project (ARTMIP) is a community effort to systematically assess how the uncertainties from AR detectors (ARDTs) impact our scientific understanding of ARs. This study describes the ARTMIP Tier 2 experimental design and initial results using the Coupled Model Intercomparison Project (CMIP) Phases 5 and 6 multi-model ensembles. We show that AR statistics from a given ARDT in CMIP5/6 historical simulations compare remarkably well with the MERRA-2 reanalysis. In CMIP5/6 future simulations, most ARDTs project a global increase in AR frequency, counts, and sizes, especially along the western coastlines of the Pacific and Atlantic oceans. We find that the choice of ARDT is the dominant contributor to the uncertainty in projected AR frequency when compared with model choice. These results imply that new projects investigating future changes in ARs should explicitly consider ARDT uncertainty as a core part of the experimental design.

A High-End Estimate of Sea Level Rise for Practitioners.

Sea level rise (SLR) is a long-lasting consequence of climate change because global anthropogenic warming takes centuries to millennia to equilibrate for the deep ocean and ice sheets. SLR projections based on climate models support policy analysis, risk assessment and adaptation planning today, despite their large uncertainties. The central range of the SLR distribution is estimated by process-based models. However, risk-averse practitioners often require information about plausible future conditions that lie in the tails of the SLR distribution, which are poorly defined by existing models. Here, a community effort combining scientists and practitioners builds on a framework of discussing physical evidence to quantify high-end global SLR for practitioners. The approach is complementary to the IPCC AR6 report and provides further physically plausible high-end scenarios. High-end estimates for the different SLR components are developed for two climate scenarios at two timescales. For global warming of +2°C in 2100 (RCP2.6/SSP1-2.6) relative to pre-industrial values our high-end global SLR estimates are up to 0.9 m in 2100 and 2.5 m in 2300. Similarly, for a (RCP8.5/SSP5-8.5), we estimate up to 1.6 m in 2100 and up to 10.4 m in 2300. The large and growing differences between the scenarios beyond 2100 emphasize the long-term benefits of mitigation. However, even a modest 2°C warming may cause multi-meter SLR on centennial time scales with profound consequences for coastal areas. Earlier high-end assessments focused on instability mechanisms in Antarctica, while here we emphasize the importance of the timing of ice shelf collapse around Antarctica. This is highly uncertain due to low understanding of the driving processes. Hence both process understanding and emission scenario control high-end SLR.

Improving image quality in transcranial magnetic resonance guided focused ultrasound using a conductive screen.

Transcranial Magnetic Resonance guided Focused Ultrasound (TcMRgFUS) has been proven to be an effective treatment for some neurological disorders such as essential and Parkinson's tremor. However, magnetic resonance guidance at 3 Tesla (3T) frequencies and using the large hemispherical transducers required for TcMRgFUS results in artifactual low-signal bands that pass through key regions of the brain. The purpose of this work was to investigate the use of a circular conductive Radio Frequency (RF) screen, that is bent to have a 12 cm radius in one direction and positioned near the top or back of the head, to reduce or remove these artifactual low-signal bands in TcMRgFUS. The impact of using an RF screen to remove these low signal bands was studied in both imaging experiments and electromagnetic simulations. Hydrophone measurements of the acoustic transparency of the bronze 2 mm diameter square mesh screen used in the imaging studies were compared with temperature measurements with and without the screen in heating studies in the TcMRgFUS system. The imaging and simulation studies both show that for the different screen configurations studied in this work, RF screen removes the low-signal bands and increases both homogeneity and signal-to-noise ratio (SNR) throughout the region of the brain. Hydrophone and heating studies indicate that even a 2 mm wire mesh provides minimal attenuation to the ultrasound beam. Simulation results also suggest that a 1 cm mesh will provide adequate artifact suppression with even less ultrasound attenuation. An RF screen that disrupts the natural waveguide nature of the transducer in the 3T MR environment can change the electromagnetic field profile to reduce unwanted artifacts and provide an imaging region which has more homogeneity and higher SNR throughout the brain.

Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation.

In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. Most notably, RMG can now generate heterogeneous catalysis models in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release includes parallelization for faster model generation and a new molecule isomorphism approach to improve computational performance. RMG has also been updated to use Python 3, ensuring compatibility with the latest cheminformatics and machine learning packages. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.

Effects of a large-scale, natural sediment deposition event on plant cover in a Massachusetts salt marsh.

In mid-winter 2018, an unprecedented sediment deposition event occurred throughout portions of the Great Marsh in Massachusetts. Evaluation of this event in distinct marsh areas spanning three towns (Essex, Ipswich, and Newbury) revealed deposition covering 29.2 hectares with an average thickness of 30.1±2.1 mm measured shortly after deposition. While sediment deposition helps marshes survive sea level rise by building elevation, effects of such a large-scale deposition on New England marshes are unknown. This natural event provided an opportunity to study effects of large-scale sediment addition on plant cover and soil chemistry, with implications for marsh resilience. Sediment thickness did not differ significantly between winter and summer, indicating sediment is not eroding or compacting. The deposited sediment at each site had similar characteristics to that of the adjacent mudflat (e.g., texture, bivalve shells), suggesting that deposited materials resulted from ice rafting from adjacent flats, a natural phenomenon noted by other authors. Vegetative cover was significantly lower in plots with rafted sediment (75.6±2.3%) than sediment-free controls (93.1±1.6%) after one growing season. When sorted by sediment thickness categories, the low thickness level (1-19 mm) had significantly greater percent cover than medium (20-39 mm) and high (40-90 mm) categories. Given that sediment accretion in the Great Marsh was found to average 2.7 mm per year, the sediment thickness documented herein represents ~11 years of sediment accretion with only a 25% reduction in plant cover, suggesting this natural sediment event will likely increase long-term marsh resilience to sea level rise.

Safety of immediate skin-to-skin contact after vaginal birth in vigorous late preterm neonates - A pilot study.

BACKGROUND: To evaluate the safety of immediate skin-to-skin contact (SSC) in vigorous late preterm neonates, where observation under radiant warmer is standard of care, in a prospective, randomized, controlled, and equivalence pilot study. METHODS: Singletons born vaginally at 35-36 6/7 weeks gestation were randomized to initiate immediate SSC or standard of care with continuous pulse oximeter monitoring for the first hour of life. RESULTS: Forty-seven dyads were randomized to SSC (n = 21) or radiant warmer (n = 26). Vitals were recorded at designated time intervals to assess tolerance of postnatal transitioning. We found no significant difference in the number of SSC interruptions, pulse oximeter readings, initial glucose level, and rates of hypoglycemia, hypothermia, or NICU admission between the two groups. CONCLUSIONS: Vigorous late preterm neonates transitioned to immediate SSC without additional risks compared to control counterparts. Large, multicenter, and randomized-control studies need to be conducted to establish standardized guidelines for this practice.

Improved detection of sinusoidal obstructive syndrome using pediatric-AYA diagnostic criteria and severity grading.

New diagnostic criteria and severity grading for sinusoidal obstructive syndrome (SOS) among pediatric and adolescent young adult (AYA) patients have been recently endorsed by international consensus. The extent to which these have been adopted in the US remains unclear. We sought to assess the potential impact via retrospective application of these criteria among patients treated at a large academic center in the United States. This is a single center retrospective study of pediatric-AYA patients who underwent hematopoietic cell transplantation (HCT) between July 2009 and 2019. The incidence of SOS was assessed using historic Baltimore and Seattle diagnostic criteria and compared with more recent guidelines (pEBMT) as proposed by the Paediatric Diseases Working Party of the European Society for Blood and Marrow Transplantation. Among 226 patients, application of the pEBMT diagnostic criteria was associated with a higher incidence (15.9%) and earlier time to diagnosis of SOS (by 2.5-3 days) compared with the modified Seattle (12.3%), and Baltimore (6.6%) criteria, respectively. The pEBMT criteria were sensitive and highly specific. Refractory thrombocytopenia was present in 75% of patients at diagnosis. Approximately 61% of patients with SOS were anicteric at diagnosis, though the majority (94.4%) developed hyperbilirubinemia as SOS progressed over a median time of 4 (1-57) days. Application of pEBMT criteria may have resulted in earlier indication for definitive treatment by 3 days. Timely diagnosis and administration of definitive treatment of SOS has been associated with improved outcomes. Prospective studies may better characterize the risk factors and natural course of SOS using pEBMT criteria.

The COVID-19 Pandemic: The effect on open lower limb fractures in a London major trauma centre - a plastic surgery perspective.

BACKGROUND: COVID-19 has created huge pressures on healthcare systems. The ongoing provision of major trauma services during this time has proved challenging. We report our experience of managing open lower limb fractures (oLLFs) during the pandemic in a London major trauma centre (MTC). METHODS: This was a prospective study of all open lower limb fractures presenting to our unit over the initial 48 days of UK government lockdown - 24th March till 10th May 2020. Results were compared to the same time period in 2019 retrospectively. Epidemiological data, mechanism, Gustilo-Anderson (G-A) severity grading, time to initial debridement and definitive coverage were analysed. RESULTS: There was a 64% reduction in emergency department (ED) attendances (25,264 vs 9042). There was an 18% reduction in oLLFs (22 vs 18). Approximately three-quarters of injuries were in males across both cohorts (77% vs 78%) and tended to occur in younger patients (median age, 37 vs 35). Road-traffic-accidents (RTAs) were the most common injury mechanism in both 2019 and lockdown, but a rise in jumpers from height was seen in the latter. A similar pattern of G-A severities were seen, however only 3 injuries during lockdown required major soft tissue reconstruction. There was no significant difference in times taken for initial debridement (p = 0.72786) or definitive wound coverage (p = 0.16152). A greater proportion of independent operating was seen during lockdown between orthopaedics and plastic surgery. CONCLUSIONS: Despite government lockdown measures, oLLFs still placed significant burden on our MTC. Notwithstanding significant staffing alterations and theatre pressures, we have been able to ensure these lower limb emergencies remain a surgical priority and have managed to utilise resources appropriately.

Inducing remission in paediatric Crohn's disease using nutritional therapies - A systematic review.

BACKGROUND: Exclusive enteral nutrition (EEN) is known to be a safe and effective treatment option for managing active Crohn's disease (CD) in children, although no uniform protocol exists. The aim of this systematic review was to evaluate and compare the clinical effectiveness of aspects of EEN protocols to ascertain whether an optimum regimen can be identified. METHODS: A systematic search of the Cochrane Library, PubMed, MEDLINE, EMBASE, CINAHL and AMED was conducted for studies published between 1998 and 2018 that examined paediatric patients being treated with an enteral nutrition protocol to induce remission. Studies that included patients receiving concurrent medication for active disease were excluded. Quality assessment was performed using separate tools for randomised controlled trials, cohort studies and for studies without a control group. RESULTS: Sixteen studies met the inclusion criteria. Of these, six found insufficient evidence to support use of a specific formula. One study examined the route of EEN, finding no difference between oral or nasogastric tube administration with respect to inducing remission. Three examined the use of partial enteral nutrition to induce remission, although conflicting results were seen. No studies explored the effect of length of treatment or energy prescription on remission rates CONCLUSIONS: An optimum enteral nutrition protocol for inducing remission cannot be identified. Further focused research is required by well designed, adequately powered prospective clinical trials to examine aspects of enteral feeding protocols that remain uncertain, including the use of partial enteral nutrition as a potential alternative to EEN.

The human imperative of stabilizing global climate change at 1.5°C.

Increased concentrations of atmospheric greenhouse gases have led to a global mean surface temperature 1.0°C higher than during the pre-industrial period. We expand on the recent IPCC Special Report on global warming of 1.5°C and review the additional risks associated with higher levels of warming, each having major implications for multiple geographies, climates, and ecosystems. Limiting warming to 1.5°C rather than 2.0°C would be required to maintain substantial proportions of ecosystems and would have clear benefits for human health and economies. These conclusions are relevant for people everywhere, particularly in low- and middle-income countries, where the escalation of climate-related risks may prevent the achievement of the United Nations Sustainable Development Goals.

Development and validation of the African Women Awareness of CANcer (AWACAN) tool for breast and cervical cancer.

BACKGROUND: Measuring factors influencing time to presentation is important in developing and evaluating interventions to promote timely cancer diagnosis, yet there is a lack of validated, culturally relevant measurement tools. This study aimed to develop and validate the African Women Awareness of CANcer (AWACAN) tool to measure awareness of breast and cervical cancer in Sub-Saharan Africa (SSA). METHODS: Development of the AWACAN tool followed 4 steps: 1) Item generation based on existing measures and relevant literature. 2) Refinement of items via assessment of content and face validity using cancer experts' ratings and think aloud interviews with community participants in Uganda and South Africa. 3) Administration of the tool to community participants, university staff and cancer experts for assessment of validity using test-retest reliability (using Intra-Class Correlation (ICC) and adjusted Kappa coefficients), construct validity (comparing expert and community participant responses using t-tests) and internal reliability (using the Kuder-Richarson (KR-20) coefficient). 4) Translation of the final AWACAN tool into isiXhosa and Acholi. RESULTS: ICC scores indicated good test-retest reliability (≥ 0.7) for all breast cancer knowledge domains and cervical cancer risk factor and lay belief domains. Experts had higher knowledge of breast cancer risk factors (p < 0.001), and cervical cancer risk factors (p = 0.003) and symptoms (p = 0.001) than community participants, but similar knowledge of breast cancer symptoms (p = 0.066). Internal reliability for breast cancer risk factors, lay beliefs and symptom and cervical cancer symptom subscales was good with KR-20 values > 0.7, and lower (0.6) for the cervical cancer risk subscale. CONCLUSION: The final AWACAN tool includes items on socio-demographic details; breast and cervical cancer symptom awareness, risk factor awareness, lay beliefs, anticipated help-seeking behaviour; and barriers to seeking care. The tools showed evidence of content, face, construct and internal validity and test-retrest reliability and are available for use in SSA in three languages.

Development and validation of a weather-based warning system to advise fungicide applications to control dollar spot on turfgrass.

Dollar spot is one of the most common diseases of golf course turfgrass and numerous fungicide applications are often required to provide adequate control. Weather-based disease warning systems have been developed to more accurately time fungicide applications; however, they tend to be ineffective and are not currently in widespread use. The primary objective of this research was to develop a new weather-based disease warning system to more accurately advise fungicide applications to control dollar spot activity across a broad geographic and climactic range. The new dollar spot warning system was developed from data collected at field sites in Madison, WI and Stillwater, OK in 2008 and warning system validation sites were established in Madison, WI, Stillwater, OK, Knoxville, TN, State College, PA, Starkville, MS, and Storrs, CT between 2011 and 2016. A meta-analysis of all site-years was conducted and the most effective warning system for dollar spot development consisted of a five-day moving average of relative humidity and average daily temperature. Using this model the highest effective probability that provided dollar spot control similar to that of a calendar-based program across the numerous sites and years was 20%. Additional analysis found that the 20% spray threshold provided comparable control to the calendar-based program while reducing fungicide usage by up to 30%, though further refinement may be needed as practitioners implement this warning system in a range of environments not tested here. The weather-based dollar spot warning system presented here will likely become an important tool for implementing precision disease management strategies for future turfgrass managers, especially as financial and regulatory pressures increase the need to reduce pesticide usage on golf course turfgrass.