2015 Forest Resources Assessment shows positive global trends but forest loss and degradation persist in poor tropical countries

The Global Forest Resources Assessment 2015 shows that deforestation has slowed and afforestation has increased globally during 1990–2015. Planted forests have increasingly provided goods and services hitherto derived from natural forests, and mosaic forests in agricultural landscapes are increasing. Forest gain is occurring at higher latitudes and in richer countries whilst forest loss continues in poor countries in the tropics. Some middle income tropical countries are now also transitioning to forest gain. These transition countries are characterised by reforms to forest management and improvements in agricultural practices but also by significant expansions of planted forest, which account for ∼25–100% of gains. Forest-area estimates of the FRA align with satellite-derived estimates, with deviations of ⩽±7% globally and ⩽±17% for the tropics. Mosaics comprised of trees outside forests, remnant forest patches, and young regenerating forests constitute a modest proportion of the tropical forest estate and are seemingly well inventoried by the FRA. Extensive areas of forest experienced partial canopy cover reduction since 2000, particularly in the tropics where their area is ∼6.5 times that deforested since 1990. The likelihood of the eventual loss of these forests and a decline in their capacity to provide goods and services is a matter of concern. Demand for industrial wood and fuelwood increased 35% in the tropics since 1990, principally in poorer countries, and growth in demand will accelerate into the future, particularly in the Asia-Pacific region. Notwithstanding significant increases in forests within protected areas since 1990 to 517 Mha (16.3%) globally and 379 Mha (26.6%) in the tropics, increasing demands for ecological services, forest products, and climate change mitigation is likely to be met from an expanding area of planted forests more than from the declining area of natural forests, particularly in Africa. The global rate of planted-forest expansion since 1990 is close to a target rate of 2.4% per annum necessary to replace wood supplied from natural forests in the medium term, though the expansion rate has declined to 1.5% since 2005. Multiple-use forests permitting both production and conservation account for 26% of the global forest area and 17% of the tropical forest area, and have increased by 81.8 Mha or 8.5% globally since 1990, with most gains in the tropics. Sustainable forest management in low-income and tropical countries remains modest, with only 37% low-income country forests covered by forest inventories. International support has proven effective at increasing this coverage since 2010

Learning from local perceptions for strategic road development in Cambodia's protected forests

Road development in tropical forest landscapes is contentious. Local preferences are often subordinated to global economic and environmental concerns. Opportunities to seek solutions based on local context are rare. We examined local perspectives on road development within Cambodia's Keo Seima Wildlife Sanctuary to explore opportunities for optimizing conservation and development outcomes. We conducted household surveys to document the perceived benefits and risks of road development. We found that in the sanctuary, road rehabilitation may accelerate transitions to intensified agriculture and diversified, off-farm incomes. All households prefer good roads and poorer households prioritize road development over other village infrastructure. Households perceive the most prominent benefit of roads to be access to hospital. Local government authorities are responsible for controlling land use and conversion within village boundaries and are therefore highly influential in determining the social and environmental outcomes of roads. Strategies to mitigate environmental risks of roads without constraining development benefits must focus on improving local capacity for decision-making and transparency. Local institutions in tropical forest landscapes must have greater control over development benefits if they are to reinvest assets to achieve conservation success

Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas.

Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations

Individualized decision aid for diverse women with lupus nephritis (IDEA-WON): A randomized controlled trial.

BackgroundTreatment decision-making regarding immunosuppressive therapy is challenging for individuals with lupus. We assessed the effectiveness of a decision aid for immunosuppressive therapy in lupus nephritis.Methods and findingsIn a United States multicenter, open-label, randomized controlled trial (RCT), adult women with lupus nephritis, mostly from racial/ethnic minority backgrounds with low socioeconomic status (SES), seen in in- or outpatient settings, were randomized to an individualized, culturally tailored, computerized decision aid versus American College of Rheumatology (ACR) lupus pamphlet (1:1 ratio), using computer-generated randomization. We hypothesized that the co-primary outcomes of decisional conflict and informed choice regarding immunosuppressive medications would improve more in the decision aid group. Of 301 randomized women, 298 were analyzed; 47% were African-American, 26% Hispanic, and 15% white. Mean age (standard deviation [SD]) was 37 (12) years, 57% had annual income of <$40,000, and 36% had a high school education or less. Compared with the provision of the ACR lupus pamphlet (n = 147), participants randomized to the decision aid (n = 151) had (1) a clinically meaningful and statistically significant reduction in decisional conflict, 21.8 (standard error [SE], 2.5) versus 12.7 (SE, 2.0; p = 0.005) and (2) no difference in informed choice in the main analysis, 41% versus 31% (p = 0.08), but clinically meaningful and statistically significant difference in sensitivity analysis (net values for immunosuppressives positive [in favor] versus negative [against]), 50% versus 35% (p = 0.006). Unresolved decisional conflict was lower in the decision aid versus pamphlet groups, 22% versus 44% (p < 0.001). Significantly more patients in the decision aid versus pamphlet group rated information to be excellent for understanding lupus nephritis (49% versus 33%), risk factors (43% versus 27%), medication options (50% versus 33%; p ≤ 0.003 for all); and the ease of use of materials was higher in the decision aid versus pamphlet groups (51% versus 38%; p = 0.006). Key study limitations were the exclusion of men, short follow-up, and the lack of clinical outcomes, including medication adherence.ConclusionsAn individualized decision aid was more effective than usual care in reducing decisional conflict for choice of immunosuppressive medications in women with lupus nephritis.Trial registrationClinicaltrials.gov, NCT02319525

The Efficiency of CD4 Recruitment to Ligand-engaged TCR Controls the Agonist/Partial Agonist Properties of Peptide–MHC Molecule Ligands

One hypothesis seeking to explain the signaling and biological properties of T cell receptor for antigen (TCR) partial agonists and antagonists is the coreceptor density/kinetic model, which proposes that the pharmacologic behavior of a TCR ligand is largely determined by the relative rates of (a) dissociation of ligand from an engaged TCR and (b) recruitment of lck-linked coreceptors to this ligand-engaged receptor. Using several approaches to prevent or reduce the association of CD4 with occupied TCR, we demonstrate that consistent with this hypothesis, the biological and biochemical consequence of limiting this interaction is to convert typical agonists into partial agonist stimuli. Thus, adding anti-CD4 antibody to T cells recognizing a wild-type peptide–MHC class II ligand leads to disproportionate inhibition of interleukin-2 (IL-2) relative to IL-3 production, the same pattern seen using a TCR partial agonist/antagonist. In addition, T cells exposed to wild-type ligand in the presence of anti-CD4 antibodies show a pattern of TCR signaling resembling that seen using partial agonists, with predominant accumulation of the p21 tyrosine-phosphorylated form of TCR-ζ, reduced tyrosine phosphorylation of CD3ε, and no detectable phosphorylation of ZAP-70. Similar results are obtained when the wild-type ligand is presented by mutant class II MHC molecules unable to bind CD4. Likewise, antibody coligation of CD3 and CD4 results in an agonist-like phosphorylation pattern, whereas bivalent engagement of CD3 alone gives a partial agonist-like pattern. Finally, in accord with data showing that partial agonists often induce T cell anergy, CD4 blockade during antigen exposure renders cloned T cells unable to produce IL-2 upon restimulation. These results demonstrate that the biochemical and functional responses to variant TCR ligands with partial agonist properties can be largely reproduced by inhibiting recruitment of CD4 to a TCR binding a wild-type ligand, consistent with the idea that the relative rates of TCR–ligand disengagement and of association of engaged TCR with CD4 may play a key role in determining the pharmacologic properties of peptide–MHC molecule ligands. Beyond this insight into signaling through the TCR, these results have implications for models of thymocyte selection and the use of anti-coreceptor antibodies in vivo for the establishment of immunological tolerance

A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring

Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables has rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as ‘‘Bison Pool’’ in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community.Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the composition of biomass and the environmental conditions

The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats

The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes

Multiscale modelling of ceramic nanoparticle interactions and their influence on the thermal conductivity of nanofluids

There is currently a lack of a reliable theory capable of making accurate predictions of the thermal enhancement in nanofluids (with relatively low solid volume fractions). The work described therefore assesses the thermal conductivity of nanoparticle suspensions in fluids using a Lagrangian particle tracking-based computational modelling technique. A 3D, multiphase fluid-solid model is developed which predicts the motion of suspended nanoparticles. The nanofluid is predicted using an Eulerian-Lagrangian hybrid approach with a constant timestep. This technique takes various multiscale forces into consideration in the calculations, whose characteristic scales are quite different, providing for the first time an analysis of all factors affecting the stability and thermal conductivity of nanofluids. The system considered consists of 71 nm diameter Al2O3 ceramic nanoparticles suspended in water, with homogeneous temperature distributions ranging from 25 °C to 85 °C, at various volume fractions between 1% and 5%. The results of the simulations demonstrate the effectiveness of the presented technique, with predictions elucidating the role of Brownian motion, fluid viscous drag, inter-particle collisions and DLVO attraction and repulsion forces on nanofluid stability. Results indicate that aggregated nanoparticles formed in the suspensions, at various particle concentrations, play an important role in the thermal behaviour of the nanofluids. Predictions are in agreement with theoretical and experimental results obtained in related studies. The thermal characteristics of nanofluids are also considered as a function of temperature, system chemistry and time (measured from an initially homogeneously dispersed state). The proven enhancement in the conductivity of fluids affected by the addition of nanoparticles has great potential to assist the development of commercial nanofluid technology aimed at energy efficient and sustainable processes

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

A pair of species within the genus Silene have evolved the largest known mitochondrial genomes, coinciding with extreme changes in mutation rate, recombination activity, and genome structure

Exploring Differences in Pain Beliefs Within and Between a Large Nonclinical (Workplace) Population and a Clinical (Chronic Low Back Pain) Population Using the Pain Beliefs Questionnaire

BACKGROUND: Beliefs, cognitions, and behaviors relating to pain can be associated with a range of negative outcomes. In patients, certain beliefs are associated with increased levels of pain and related disability. There are few data, however, showing the extent to which beliefs of patients differ from those of the general population. OBJECTIVE: This study explored pain beliefs in a large nonclinical population and a chronic low back pain (CLBP) sample using the Pain Beliefs Questionnaire (PBQ) to identify differences in scores and factor structures between and within the samples. DESIGN: This was a cross-sectional study. METHODS: The samples comprised patients attending a rehabilitation program and respondents to a workplace survey. Pain beliefs were assessed using the PBQ, which incorporates 2 scales: organic and psychological. Exploratory factor analysis was used to explore variations in factor structure within and between samples. The relationship between the 2 scales also was examined. RESULTS: Patients reported higher organic scores and lower psychological scores than the nonclinical sample. Within the nonclinical sample, those who reported frequent pain scored higher on the organic scale than those who did not. Factor analysis showed variations in relation to the presence of pain. The relationship between scales was stronger in those not reporting frequent pain. LIMITATIONS: This was a cross-sectional study; therefore, no causal inferences can be made. CONCLUSIONS: Patients experiencing CLBP adopt a more biomedical perspective on pain than nonpatients. The presence of pain is also associated with increased biomedical thinking in a nonclinical sample. However, the impact is not only on the strength of beliefs, but also on the relationship between elements of belief and the underlying belief structur