Search

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.ACM Reference FormatAbigail Dommer1†, Lorenzo Casalino1†, Fiona Kearns1†, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael O’Connor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. InSupercomputing ‘21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages.https://doi.org/finalDOI

Full documentation for the GROMACS 2023.1 release version.

Invasive non-native species are recognized as a major threat to island biodiversity, ecosystems, and economies globally. Preventing high-risk invasive non-native species from being introduced is the most cost-effective way to avoid their adverse impacts. We applied a horizon scanning approach to identify potentially invasive non-native species in the United Kingdom Overseas Territories (OTs), ranging from Antarctica to the Caribbean, and from the Pacific to the Atlantic. High-risk species were identified according to their potential for arrival, establishment and likely impacts to biodiversity and ecosystem function, economies and human health. Across OTs, 231 taxa were included on high-risk lists. The highest-ranking species were the Asian green mussel (Perna viridis), little fire ant (Wasmannia auropunctata), brown rat (Rattus norvegicus) and mesquite tree (Prosopis juliflora). Shipping containers were identified as the introduction pathway associated with the most species. The shared high-risk species and pathways identified provide a guide for other remote islands and archipelagos to focus ongoing biosecurity and surveillance aimed at preventing future incursions.

[Motivation] Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes., [Main types of variable contained] We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves., [Spatial location and grain] We surveyed between 18 and 22 populations per species, 141 in total, across Europe., [Time period] Leaf sampling took place between 2016 and 2017., [Major taxa and level of measurement] We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea., [Software format] The data files are in ASCII text, tab delimited, not compressed., All authors acknowledge support from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 676876 (Project GenTree). Laboratory work was also supported by other projects: COMEDIAS (CGL2017- 83170-R, Spanish Ministry of Science, Innovation and Universities), REMEDINAL IV (TE-CM S2018/EMT-4338, Project of the Autonomous Community of Madrid, Spain), SPONFOREST (BIODIVERSA-3, PCIN-2016-055), and International Laboratory of Global Change (LINCGlobal 4540-143AP). The Swiss contribution was supported by the Swiss Secretariat for Education, Research and Innovation (SERI) under contract no. 6.0032. BC was funded by a Scholarship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil).

Background Red blood cells (RBC) change upon hypothermic conservation, and storage for 6 weeks is associated with the short-term clearance of 15% to 20% of transfused RBCs. Metabolic rejuvenation applied to RBCs before transfusion replenishes energetic sources and reverses most storage-related alterations, but how it impacts RBC circulatory functions has not been fully elucidated. Study design and methods Six RBC units stored under blood bank conditions were analyzed weekly for 6 weeks and rejuvenated on Day 42 with an adenine-inosine-rich solution. Impact of storage and rejuvenation on adenosine triphosphate (ATP) levels, morphology, accumulation of storage-induced microerythrocytes (SMEs), elongation under an osmotic gradient (by LORRCA), hemolysis, and phosphatidylserine (PS) exposure was evaluated. The impact of rejuvenation on filterability and adhesive properties of stored RBCs was also assessed. Results Rejuvenation of RBCs restored intracellular ATP to almost normal levels and decreased the PS exposure from 2.78% to 0.41%. Upon rejuvenation, the proportion of SME dropped from 28.2% to 9.5%, while the proportion of normal-shaped RBCs (discocytes and echinocytes 1) increased from 47.7% to 67.1%. In LORCCA experiments, rejuvenation did not modify the capacity of RBCs to elongate and induced a reduction in cell volume. In functional tests, rejuvenation increased RBC filterability in a biomimetic splenic filter (+16%) and prevented their adhesion to endothelial cells (-87%). Conclusion Rejuvenation reduces the proportion of morphologically altered and adhesive RBCs that accumulate during storage. Along with the improvement in their filterability, these data show that rejuvenation improves RBC properties related to their capacity to persist in circulation after transfusion.

The future status of peatlands as carbon stores/sinks is uncertain given current and predicted environmental change. Several factors can affect the magnitude of the peatland carbon sink including disturbances such as wildfire. There is at present little evidence of how wildfire affects the emission of carbon dioxide (CO2) and methane (CH4) via perturbation to aerobic and anaerobic respiration. The greatest effects, which are likely to vary according to wildfire severity, would be expected in the immediate post-fire stages when little recovery has taken place. Here, we investigate five UK peatland wildfires (2011–2012) in the immediate post-wildfire period measuring CO2 and CH4 fluxes using static chambers. Fire severity was described using a modified form of the composite burn index. A hierarchical partitioning approach indicated time since fire was the most strongly associated variable that fluxes of both CO2, and CH4 followed by soil temperature for CO2 and fire severity for CH4. Using a liner mixed modelling approach to account for repeated measures; fire severity was a significant term for CH4 and borderline significant for CO2. Mean fluxes of CH4 were consistently lower on burnt sites. In contrast, data from a fire in the north of Scotland appeared to show the opposite relationship for CH4 with higher fluxes on the burnt sites. These results suggest that wildfire can affect gaseous carbon fluxes, but the responses can be variable in both space and time and that disruption to anaerobic processes may be site and/or fire dependent.

Objectives/hypothesis The role of elective neck dissection (END) in patients with clinically N0 (cN0), high-grade parotid carcinoma is unclear. The objective of this study was to assess the association between END and survival in patients with cN0, high-grade parotid carcinoma. Study design Retrospective, multicenter cohort study. Methods A review of hospital-based cases from the National Cancer Data Base was performed. Participants included patients diagnosed with cN0, high-grade parotid cancer between January 1, 2004 and December 31, 2013. The primary exposure was receipt of neck dissection. Secondary exposures included receipt of adjuvant radiation and/or chemotherapy. Univariate and multivariate survival analyses were performed. Unadjusted and adjusted survival estimates were determined. Results Overall, 1,547 patients were included, with a median follow-up time of 48 months. END did not have a statistically significant effect on 3-year survival (3-year: 69.9%, 95% confidence interval [CI]: 67.2 to 72.6). Survival at 3-years among those not receiving END was 66.1% (95% CI: 62.7 to 69.5). Parotidectomy and adjuvant radiotherapy had the strongest effect on mortality. There was no difference in 3-year survival among patients who underwent parotidectomy and adjuvant radiation stratified by receipt of END nor did END have a statistically significant effect on survival in mucoepidermoid carcinoma, adenocarcinoma, high-risk histology, high T stage, or academic center treatment subgroups. Conclusions END did not have a statistically significant effect on survival among cN0 patients with high-grade parotid cancer when taking into account receipt of adjuvant therapy and confounding. The role of END on survival and locoregional control remains to be further elucidated in prospective studies. Level of evidence 4 Laryngoscope, 130:1487-1495, 2020.

Background Red blood cell exchange (RCE) transfusions are a mainstay in the treatment of sickle cell anemia (SCA), and allow a temporary restoration of physiological parameters with respect to erythrocyte oxygen carrying capacity and systems metabolism. Recently, we noted that 1) RCE significantly impacts recipients' metabolism in SCA; 2) fresh and end-of-storage red blood cell (RBC) units differently impact systems of metabolism in healthy autologous recipients; and 3) phosphate/inosine/pyruvate/adenine (PIPA) solution reverses the metabolic age of stored RBCs. Therefore, we hypothesized that RCE with PIPA-treated RBC units could further increase the metabolic benefits of RCE in SCA patients. Study design and methods Circulating plasma and erythrocytes were collected from patients with SCA before and after RCE, with either conventional or PIPA-treated RBC units, prior to metabolomics analyses. Results Consistent with prior work, RCE significantly decreased circulating levels of markers of systemic hypoxemia (lactate, succinate) and decreased plasma levels of acyl-carnitines and amino acids. However, PIPA-treated exchanges were superior to untreated RCEs, with a higher energy state and an increased capacity to activate the pentose phosphate pathway and glutamine metabolism. In addition, RBCs and plasma from recipients of PIPA-treated RBC units resulted in significantly decreased levels of post-transfusion plasticizers, though at the expense of higher circulating levels of oxidized purines (hypoxanthine, xanthine, and the antioxidant urate). Conclusion Transfusion of PIPA-treated RBCs further increases the metabolic benefits of RCE to patients with SCA, significantly reducing the levels of post-transfusion plasticizers.

The Finite-Difference Time-Domain (FDTD) method is a popular numerical modelling technique in computational electromagnetics. The volumetric nature of the FDTD technique means simulations often require extensive computational resources (both processing time and memory). The simulation of Ground Penetrating Radar (GPR) is one such challenge, where the GPR transducer, subsurface/structure, and targets must all be included in the model, and must all be adequately discretised. Additionally, forward simulations of GPR can necessitate hundreds of models with different geometries (A-scans) to be executed. This is exacerbated by an order of magnitude when solving the inverse GPR problem or when using forward models to train machine learning algorithms. We have developed one of the first open source GPU-accelerated FDTD solvers specifically focused on modelling GPR. We designed optimal kernels for GPU execution using NVIDIA’s CUDA framework. Our GPU solver achieved performance throughputs of up to 1194 Mcells/s and 3405 Mcells/s on NVIDIA Kepler and Pascal architectures, respectively. This is up to 30 times faster than the parallelised (OpenMP) CPU solver can achieve on a commonly-used desktop CPU (Intel Core i7-4790K). We found the cost–performance benefit of the NVIDIA GeForce-series Pascal-based GPUs – targeted towards the gaming market – to be especially notable, potentially allowing many individuals to benefit from this work using commodity workstations. We also note that the equivalent Tesla-series P100 GPU – targeted towards data-centre usage – demonstrates significant overall performance advantages due to its use of high-bandwidth memory. The performance benefits of our GPU-accelerated solver were demonstrated in a GPR environment by running a large-scale, realistic (including dispersive media, rough surface topography, and detailed antenna model) simulation of a buried anti-personnel landmine scenario. New version program summary Program Title: gprMax Program Files doi: http://dx.doi.org/10.17632/kjjm4z87nj.1 Licensing provisions: GPLv3 Programming language: Python, Cython, CUDA Journal reference of previous version: Comput. Phys. Comm., 209 (2016), 163–170 Does the new version supersede the previous version?: Yes Reasons for the new version: Performance improvements due to implementation of CUDA-based GPU engine Summary of revisions: A FDTD solver has been written in CUDA for execution on NVIDIA GPUs. This is in addition to the existing FDTD solver which has been parallelised using Cython/OpenMP for running on CPUs. Nature of problem: Classical electrodynamics Solution method: Finite-Difference Time-Domain (FDTD)

Rationale Red blood cells (RBC) undergo morphologic and biochemical changes during storage which may lead to adverse health risks upon transfusion. In prior studies, the effect of RBC age on health outcomes has been conflicting. We designed the study to assess the effects of RBC units’ storage duration on health outcomes specifically for hospitalized patients undergoing hip fracture surgery or coronary artery bypass grafting (CABG) surgery. Methods Using International Classification of Diseases (ICD) 9 codes, hip fracture surgery and CABG surgery patients, who received RBC transfusions between 2008 and 2013, were retrospectively identified from the electronic medical records system. Hip fracture surgery and CABG cohorts were sub-divided into 3 blood age groups based upon RBC unit age at the time of transfusion: young blood (RBC units stored less than or equal to 14 days), old blood (RBC units were stored for greater than or equal to 28 days), or mixed blood for the remaining patients. Outcome variables were 30-day, 90-day, and inpatient mortality as well as hospital length of stay. Results A total of 3,182 patients were identified: 1,121 with hip fractures and 2,061 with CABG. Transfusion of old blood was associated with higher inpatient mortality in the hip fracture surgery cohort (OR 166.8, 95% CI 1.067-26064.7, p = 0.04) and a higher 30-day mortality in the CABG cohort (OR 4.55, 95% CI 1.01–20.49, p = 0.03). Conclusions Transfusing RBC units stored for greater than or equal to 28 days may be associated with a higher mortality for patients undergoing hip fracture or CABG.

Sound synthesis using physical modeling, emulating systems of a complexity approaching and even exceeding that of real-world acoustic musical instruments, is becoming possible, thanks to recent theoretical developments in musical acoustics and algorithm design. Severe practical difficulties remain, both at the level of the raw computational resources required, and at the level of user control. An approach to the first difficulty is through the use of large-scale parallelization, and results for a variety of physical modeling systems are presented here. Any progress with regard to the second difficulty requires, necessarily, the experience and advice of professional musicians. A basic interface to a parallelized large-scale physical modeling synthesis system is presented here, accompanied by first-hand descriptions of the working methods of five composers, each of whom generated complete multichannel pieces using the system.

International audience; Ecosystems face multiple, potentially interacting, anthropogenic pressures that can modify biodiversity and ecosystem functioning. Using a bryophyte–microarthropod microecosystem we tested the combined effects of habitat loss, episodic heat-shocks and an introduced non-native apex predator on ecosystem function (chlorophyll fluorescence as an indicatorof photosystem II function) and microarthropod communities (abundance and body size). The photosynthetic function was degraded by the sequence of heat-shock episodes, but unaffected by microecosystem patch size or top-down pressure from the introduced predator. In small microecosystem patches without the non-native predator, Acari abundance decreased with heat-shock frequency, while Collembola abundance increased. These trends disappeared in larger microecosystem patches or when predators were introduced, although Acari abundance was lower in large patchesthat underwent heat-shocks and were exposed to the predator. Mean assemblage body length (Collembola) was reduced independently in small microecosystem patches and with greater heat-shock frequency. Our experimental simulation of episodic heatwaves, habitat loss and nonnative predation pressure in microecosystems produced evidence of individual and potentially synergistic and antagonistic effects on ecosystem function and microarthropod communities. Such complex outcomes of interactions between multiple stressors need to be considered when assessing anthropogenic risks for biota and ecosystem functioning.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios., Measurement(s)growth ring • wood densityTechnology Type(s)measuring table • calculationFactor Type(s)tree speciesSample Characteristic - OrganismBetula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraeaSample Characteristic - LocationEurope Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11294993

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios. Measurement(s) growth ring • wood density Technology Type(s) measuring table • calculation Factor Type(s) tree species Sample Characteristic - Organism Betula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraea Sample Characteristic - Location Europe Published

Cyber crime is rising at an unprecedented rate. Organisations are spending more than ever combating the human element through training and other interventions, such as simulated phishing. Organisations employ “carrots” (rewards) and “sticks” (sanctions) to reduce risky behaviour. Sanctions (such as locking computers and informing one’s line manager) are problematic as they lead to unintended consequences towards employee trust and productivity. This study explored how organisations use rewards and sanctions both in their campaigns and specifically following simulated phishing. We also assessed what factors (such as control over rewards, tendency to blame users) influenced security awareness professionals’ use of rewards and sanctions. The findings revealed that organisations use a variety of rewards and sanctions within their campaigns, with sanctions being used across 90% of the organisations. We did not find any factors that influence security awareness professionals’ usage of rewards and sanctions. Our findings suggest the need for a greater consideration of the human element of cyber security. In particular, campaigns should take a more informed approach to use of behaviour change strategies that consider the organisational structure in which they are implemented and the role (and influence) of security awareness professionals within that structure.

We present an analysis of the invertebrates of St Helena using an invertebrate conservation evaluation framework, to review invertebrate data, highlight knowledge gaps and prioritise invertebrate conservation needs that perhaps could be applied to other regions of the world. St Helena’s invertebrate fauna has 891 genera and 1133 species. The fauna has a high level of endemism with 450 species (equal to 96% of all native species) but the total species richness now comprises many introduced species (664) with 93 species in 24 orders that are entirely novel to St Helena. The elevation ranges of native species appear to be narrow, most being confined to higher elevations above 500 m. St Helena has had a large number of probable extinction events; 30 insects, and 19 molluscs, and the threat of further extinctions remains high. The cumulative invertebrate extinctions on St Helena exceed the global background extinction rate on an island barely covering 122 km2. We present actions and timelines to focus invertebrate conservation on St Helena; taxonomy, ecology, long term monitoring and invasive species control are priority areas to reduce extinction risk.