TLS2trees: A scalable tree segmentation pipeline for TLS data

1. Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. / 2. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data captured across 10 plots of seven forest types; from open savanna to dense tropical rainforest. / 3. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3 and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of semantic segmentation step. / 4. The volume and scale of TLS data captured in forest plots is increasing. It is suggested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software

Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke

Genetic factors have been implicated in stroke risk but few replicated associations have been reported. We conducted a genome-wide association study (GWAS) in ischemic stroke and its subtypes in 3,548 cases and 5,972 controls, all of European ancestry. Replication of potential signals was performed in 5,859 cases and 6,281 controls. We replicated reported associations between variants close to PITX2 and ZFHX3 with cardioembolic stroke, and a 9p21 locus with large vessel stroke. We identified a novel association for a SNP within the histone deacetylase 9(HDAC9) gene on chromosome 7p21.1 which was associated with large vessel stroke including additional replication in a further 735 cases and 28583 controls (rs11984041, combined P = 1.87×10−11, OR=1.42 (95% CI) 1.28-1.57). All four loci exhibit evidence for heterogeneity of effect across the stroke subtypes, with some, and possibly all, affecting risk for only one subtype. This suggests differing genetic architectures for different stroke subtypes

Resonance-Enhanced Multiphoton Ionization in the X-Ray Regime

Here, we report on the nonlinear ionization of argon atoms in the short wavelength regime using ultraintense x rays from the European XFEL. After sequential multiphoton ionization, high charge states are obtained. For photon energies that are insufficient to directly ionize a 1s electron, a different mechanism is required to obtain ionization to Ar17+. We propose this occurs through a two-color process where the second harmonic of the FEL pulse resonantly excites the system via a 1s -> 2p transition followed by ionization by the fundamental FEL pulse, which is a type of x-ray resonance-enhanced multiphoton ionization (REMPI). This resonant phenomenon occurs not only for Ar16+, but also through lower charge states, where multiple ionization competes with decay lifetimes, making x-ray REMPI distinctive from conventional REMPI. With the aid of state-of-the-art theoretical calculations, we explain the effects of x-ray REMPI on the relevant ion yields and spectral profile

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins

Statins effectively lower LDL cholesterol levels in large studies and the observed interindividual response variability may be partially explained by genetic variation. Here we perform a pharmacogenetic meta-analysis of genome-wide association studies (GWAS) in studies addressing the LDL cholesterol response to statins, including up to 18,596 statin-treated subjects. We validate the most promising signals in a further 22,318 statin recipients and identify two loci, SORT1/CELSR2/PSRC1 and SLCO1B1, not previously identified in GWAS. Moreover, we confirm the previously described associations with APOE and LPA. Our findings advance the understanding of the pharmacogenetic architecture of statin response

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

publisher: Elsevier articletitle: Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes journaltitle: Cell articlelink: https://doi.org/10.1016/j.cell.2018.05.046 content_type: article copyright: © 2018 Elsevier Inc

Shaping Amine-Based Solid CO₂ Adsorbents: Effects of Pelletization Pressure on the Physical and Chemical Properties

Amine-based solid adsorbents are promising candidates for the separation of CO₂ from dilute gas streams. Here we report the effect of pelletization pressure on the physical and chemical properties of an array of supported amine adsorbents, based on mesoporous silica and γ-alumina supports. The virgin powders based on poly(ethyleneimine) (PEI) and 3-aminopropyltrimethoxysilane (APS) functionalized oxides are pressed at 1000 and 5000 psig pressure to form self-supporting pellets and their physical and chemical properties are compared. No change in chemical structure of the adsorbents is observed after pelletization, though the porosity of each material changes to some degree. Of the three mesoporous supports examined in this study, the commercial porous silica is the most stable support for both class 1 and class 2 adsorbents, whereas lab synthesized mesoporous SBA-15 silica and lab synthesized mesoporous γ-alumina are found to be the least stable supports for class 1 and class 2 adsorbents, respectively. The CO₂ uptake results show a significant drop in equilibrium capacity for the pellets pressed at 5000 psig, regardless of the support used, while the 1000 psig pellets retain their capacity and show comparable performance to their powder counterparts. CO₂ breakthrough experiments suggest an increase in mass transfer resistance for the pellet samples as compared with virgin powders, resulting in the dispersion of the concentration fronts during CO₂ breakthrough using a fixed bed. These findings suggest that shaping solid supported amine adsorbents into binderless pellets requires pressing the powders at low to moderate pressures to ensure that these materials retain their performance in processes that require pelletized samples

Disinfection of Contaminated Water by Using Solar Irradiation

Contaminated water causes an estimated 6 to 60 billion cases of gastrointestinal illness annually. The majority of these cases occur in rural areas of developing nations where the water supply remains polluted and adequate sanitation is unavailable. A portable, low-cost, and low-maintenance solar unit to disinfect unpotable water has been designed and tested. The solar disinfection unit was tested with both river water and partially processed water from two wastewater treatment plants. In less than 30 min in midday sunlight, the unit eradicated more than 4 log(10) U (99.99%) of bacteria contained in highly contaminated water samples. The solar disinfection unit has been field tested by Centro Panamericano de Ingenieria Sanitaria y Ciencias del Ambiente in Lima, Peru. At moderate light intensity, the solar disinfection unit was capable of reducing the bacterial load in a controlled contaminated water sample by 4 log(10) U and disinfected approximately 1 liter of water in 30 min