Spatial pattern of trees influences species productivity in a mature oak-pine mixed forest

Spatial pattern has a key role in the interactions between species in plant communities. These interactions influence ecological processes involved in the species dynamics: growth, regeneration and mortality. In this study, we investigated the effect of spatial pattern on productivity in mature mixed forests of sessile oak and Scots pine. We simulated tree locations with point process models and tree growth with spatially explicit individual growth models. The point process models and growth models were fitted with field data from the same stands. We compared species productivity obtained in two types of mixture: a patchy mixture and an intimate mixture. Our results show that the productivity of both species is higher in an intimate mixture than in a patchy mixture. Productivity difference between the two types of mixture was 11.3% for pine and 14.7% for oak. Both species were favored in the intimate mixture because, for both, intraspecific competition was more severe than interspecific competition. Our results clearly support favoring intimate mixtures in mature oak-pine stands to optimize tree species productivity; oak is the species that benefits the most from this type of management. Our work also shows that models and simulations can provide interesting results for complex forests with mixtures, results that would be difficult to obtain through experimentation

NRLMSIS 2.1: An Empirical Model of Nitric Oxide Incorporated Into MSIS

We have developed an empirical model of nitric oxide (NO) number density at altitudes from similar to 73 km to the exobase, as a function of altitude, latitude, day of year, solar zenith angle, solar activity, and geomagnetic activity. The model is part of the NRLMSIS (R) 2.1 empirical model of atmospheric temperature and species densities; this upgrade to NRLMSIS 2.0 consists solely of the addition of NO. MSIS 2.1 assimilates observations from six space-based instruments: UARS/HALOE, SNOE, Envisat/MIPAS, ACE/FTS, Odin/SMR, and AIM/SOFIE. We additionally evaluated the new model against independent extant NO data sets. In this paper, we describe the formulation and fitting of the model, examine biases between the data sets and model and among the data sets, compare with another empirical NO model (NOEM), and discuss scientific aspects of our analysis

Efficient Algorithm on a Non-staggered Mesh for Simulating Rayleigh-Benard Convection in a Box

An efficient semi-implicit second-order-accurate finite-difference method is described for studying incompressible Rayleigh-Benard convection in a box, with sidewalls that are periodic, thermally insulated, or thermally conducting. Operator-splitting and a projection method reduce the algorithm at each time step to the solution of four Helmholtz equations and one Poisson equation, and these are are solved by fast direct methods. The method is numerically stable even though all field values are placed on a single non-staggered mesh commensurate with the boundaries. The efficiency and accuracy of the method are characterized for several representative convection problems.Comment: REVTeX, 30 pages, 5 figure

3D visualization processes for recreating and studying organismal form

The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT-scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two data sets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus

In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers

The search for druggable pockets on the surface of a protein is often performed on a single conformer, treated as a rigid body. Transient druggable pockets may be missed in this approach. Here, we describe a methodology for systematic in silico analysis of surface clefts across multiple conformers of the metastable protein α1-antitrypsin (A1AT). Pathological mutations disturb the conformational landscape of A1AT, triggering polymerisation that leads to emphysema and hepatic cirrhosis. Computational screens for small molecule inhibitors of polymerisation have generally focused on one major druggable site visible in all crystal structures of native A1AT. In an alternative approach, we scan all surface clefts observed in crystal structures of A1AT and in 100 computationally produced conformers, mimicking the native solution ensemble. We assess the persistence, variability and druggability of these pockets. Finally, we employ molecular docking using publicly available libraries of small molecules to explore scaffold preferences for each site. Our approach identifies a number of novel target sites for drug design. In particular one transient site shows favourable characteristics for druggability due to high enclosure and hydrophobicity. Hits against this and other druggable sites achieve docking scores corresponding to a Kd in the µM–nM range, comparing favourably with a recently identified promising lead. Preliminary ThermoFluor studies support the docking predictions. In conclusion, our strategy shows considerable promise compared with the conventional single pocket/single conformer approach to in silico screening. Our best-scoring ligands warrant further experimental investigation

Lattice Boltzmann simulations in microfluidics: probing the no-slip boundary condition in hydrophobic, rough, and surface nanobubble laden microchannels

In this contribution we review recent efforts on investigations of the effect of (apparent) boundary slip by utilizing lattice Boltzmann simulations. We demonstrate the applicability of the method to treat fundamental questions in microfluidics by investigating fluid flow in hydrophobic and rough microchannels as well as over surfaces covered by nano- or microscale gas bubbles.Comment: 11 pages, 6 figure

T(6;9)(p22;q34)/DEK-NUP214-rearranged pediatric myeloid leukemia: An international study of 62 patients

Acute myeloid leukemia with t(6;9)(p22;q34) is listed as a distinct entity in the 2008 World Health Organization classification, but little is known about the clinical implications of t(6;9)-positive myeloid leukemia in children. This international multicenter study presents the clinical and genetic characteristics of 62 pediatric patients with t(6;9)/DEK-NUP214-rearranged myeloid leukemia; 54 diagnosed as having acute myeloid leukemia, representing <1% of all childhood acute myeloid leukemia, and eight as having myelodysplastic syndrome. The t(6;9)/DEK-NUP214 was associated with relatively late onset (median age 10.4 years), male predominance (sex ratio 1.7), French-American-British M2 classification (54%), myelodysplasia (100%), and FLT3-ITD (42%). Outcome was substantially better than previously reported with a 5-year event-free survival of 32%, 5-year overall survival of 53%, and a 5-year cumulative incidence of relapse of 57%. Hematopoietic stem cell transplantation in first complete remission improved the 5-year event-free survival compared with chemotherapy alone (68% versus 18%; P<0.01) but not the overall survival (68% versus 54%; P=0.48). The presence of FLT3-ITD had a non-significant negative effect on 5-year overall survival compared with non-mutated cases (22% versus 62%; P=0.13). Gene expression profiling showed a unique signature characterized by significantly higher expression of EYA3, SESN1, PRDM2/RIZ, and HIST2H4 genes. In conclusion, t(6;9)/DEK-NUP214 represents a unique subtype of acute myeloid leukemia with a high risk of relapse, high frequency of FLT3-ITD, and a specific gene expression signature

The identification and treatment of mental health and substance misuse problems in sexual assault services: A systematic review

BackgroundSpecialist sexual assault services, which collect forensic evidence and offer holistic healthcare to people following sexual assault, have been established internationally. In England, these services are called sexual assault referral centres (SARCs). Mental health and substance misuse problems are common among SARC attendees, but little is known about how SARCs should address these needs. This review aims to seek and synthesise evidence regarding approaches to identification and support for mental health and substance misuse problems in SARCs and corresponding services internationally; empirical evidence regarding effective service models; and stakeholders’ views and policy recommendations about optimal SARC practice.MethodsA systematic review was undertaken. PsycINFO, MEDLINE, IBSS and CINAHL were searched from 1975 to August 2018. A web-based search up to December 2018 was also conducted to identify government and expert guidelines on SARCs. Quality assessment and narrative synthesis were conducted.ResultsWe included 107 papers. We found that identification based on clinical judgement, supportive counselling and referral to other services without active follow-up were the most common approaches. Evaluations of interventions for post-rape psychopathology in attendees of sexual assault services provided mixed evidence of moderate quality. Very little evidence was found regarding interventions or support for substance misuse. Stakeholders emphasised the importance of accessibility, flexibility, continuity of care, in-house psychological support, staff trained in mental health as well as specialist support for LGBT groups and people with learning difficulties. Guidelines suggested that SARCs should assess for mental health and substance misuse and provide in-house emotional support, but the extent and nature of support were not clarified. Both stakeholders and guidelines recommended close partnership between sexual assault services and local counselling services.ConclusionsThis review suggests that there is big variation in the mental health and substance misuse provision both across and within different sexual assault service models. We found no robust evidence about how sexual assault services can achieve good mental health and substance misuse outcomes for service users. Clearer guidance for service planners and commissioners, informed by robust evidence about optimal service organisations and pathways, is required.PROSPERO registration number: CRD4201811970

Where are we now with European forest multi-taxon biodiversity and where can we head to?

The European biodiversity and forest strategies rely on forest sustainable management (SFM) to conserve forest biodiversity. However, current sustainability assessments hardly account for direct biodiversity indicators. We focused on forest multi-taxon biodiversity to: i) gather and map the existing information; ii) identify knowledge and research gaps; iii) discuss its research potential. We established a research network to fit data on species, standing trees, lying deadwood and sampling unit description from 34 local datasets across 3591 sampling units. A total of 8724 species were represented, with the share of common and rare species varying across taxonomic classes: some included many species with several rare ones (e.g., Insecta); others (e.g., Bryopsida) were represented by few common species. Tree-related structural attributes were sampled in a subset of sampling units (2889; 2356; 2309 and 1388 respectively for diameter, height, deadwood and microhabitats). Overall, multi-taxon studies are biased towards mature forests and may underrepresent the species related to other developmental phases. European forest compositional categories were all represented, but beech forests were over-represented as compared to thermophilous and boreal forests. Most sampling units (94%) were referred to a habitat type of conservation concern. Existing information may support European conservation and SFM strategies in: (i) methodological harmonization and coordinated monitoring; (ii) definition and testing of SFM indicators and thresholds; (iii) data-driven assessment of the effects of environmental and management drivers on multi-taxon forest biological and functional diversity, (iv) multi-scale forest monitoring integrating in-situ and remotely sensed information