A New Field Protocol for Monitoring Forest Degradation

Forest degradation leads to the gradual reduction of forest carbon stocks, function, and biodiversity following anthropogenic disturbance. Whilst tropical degradation is a widespread problem, it is currently very under-studied and its magnitude and extent are largely unknown. This is due, at least in part, to the lack of developed and tested methods for monitoring degradation. Due to the relatively subtle and ongoing changes associated with degradation, which can include the removal of small trees for fuelwood or understory clearance for agricultural production, it is very hard to detect using Earth Observation. Furthermore, degrading activities are normally spatially heterogeneous and stochastic, and therefore conventional forest inventory plots distributed across a landscape do not act as suitable indicators: at best only a small proportion of plots (often zero) will actually be degraded in a landscape undergoing active degradation. This problem is compounded because the metal tree tags used in permanent forest inventory plots likely deter tree clearance, biasing inventories toward under-reporting change. We have therefore developed a new forest plot protocol designed to monitor forest degradation. This involves a plot that can be set up quickly, so a large number can be established across a landscape, and easily remeasured, even though it does not use tree tags or other obvious markers. We present data from a demonstration plot network set up in Jalisco, Mexico, which were measured twice between 2017 and 2018. The protocol was successful, with one plot detecting degradation under our definition (losing greater than 10% AGB but remaining forest), and a further plot being deforested for Avocado (Persea americana) production. Live AGB ranged from 8.4 Mg ha–1 to 140.8 Mg ha–1 in Census 1, and from 0 Mg ha–1 to 144.2 Mg ha–1 Census 2, with four of ten plots losing AGB, and the remainder staying stable or showing slight increases. We suggest this protocol has great potential for underpinning appropriate forest plot networks for degradation monitoring, potentially in combination with Earth Observation analysis, but also in isolation

An Extracellular Polysaccharide-Rich Organic Layer Contributes to Organization of the Coccosphere in Coccolithophores

This is the final version. Available from Frontiers Media via the DOI in this record.Coccolithophores are globally abundant marine microalgae characterized by their ability to form calcite platelets (coccoliths). The coccoliths are produced internally in a Golgi-derived vesicle. Mature coccoliths are extruded from the cell to form a protective covering on the cell surface, known as the coccosphere. Current evidence indicates that calcite precipitation in the coccolith vesicle (CV) is modulated by coccolith-associated polysaccharides (CAPs). Whilst previous research into CAPs has focussed on their roles in calcite precipitation within the CV, little is known of their extracellular roles. Using fluorescent lectins, we visualize the extracellular polysaccharide-rich organic layer associated with external coccoliths and demonstrate that it differs between species in structure and composition. Biochemical analysis of polysaccharide extracted from coccoliths indicated substantial differences between species in monosaccharide composition and uronic acid content. In Coccolithus braarudii our studies indicate that polysaccharide-rich material is extruded with the coccoliths, where it plays a role in the adhesion of the coccoliths to the cell surface and contributes to the overall organization of the coccosphere. Together, these results highlight the important extracellular roles of CAPs and their contribution to the dynamic nature of the coccosphere.The authors acknowledge funding from NERC SPITFIRE DTP studentship to CW. GW and CB acknowledge support from NERC (NE/N011708/1) and the European Research Council (ERC-ADG 670390). CW was additionally supported by the Gillings Graduate Exchange Programme (University of Southampton/University of North Carolina Wilmington). AT acknowledges NSF support (NSFGEO-NERC-1638838)

The Special Sauce of the Cancer Prevention and Control Research Network: 20 Years of Lessons Learned in Developing the Evidence Base, Building Community Capacity, and Translating Research into Practice

PURPOSE: The Cancer Prevention and Control Research Network (CPCRN) is a national network focused on accelerating the translation of cancer prevention and control research evidence into practice through collaborative, multicenter projects in partnership with diverse communities. From 2003 to 2022, the CPCRN included 613 members. METHODS: We: (1) characterize the extent and nature of collaborations through a bibliometric analysis of 20 years of Network publications; and (2) describe key features and functions of the CPCRN as related to organizational structure, productivity, impact, and focus on health equity, partnership development, and capacity building through analysis of 22 in-depth interviews and review of Network documentation. RESULTS: Searching Scopus for multicenter publications among the CPCRN members from their time of Network engagement yielded 1,074 collaborative publications involving two or more members. Both the overall number and content breadth of multicenter publications increased over time as the Network matured. Since 2004, members submitted 123 multicenter grant applications, of which 72 were funded (59%), totaling more than $77 million secured. Thematic analysis of interviews revealed that the CPCRN\u27s success-in terms of publication and grant productivity, as well as the breadth and depth of partnerships, subject matter expertise, and content area foci-is attributable to: (1) its people-the inclusion of members representing diverse content-area interests, multidisciplinary perspectives, and geographic contexts; (2) dedicated centralized structures and processes to enable and evaluate collaboration; and (3) focused attention to strategically adapting to change. CONCLUSION: CPCRN\u27s history highlights organizational, strategic, and practical lessons learned over two decades to optimize Network collaboration for enhanced collective impact in cancer prevention and control. These insights may be useful to others seeking to leverage collaborative networks to address public health problems

Active restoration accelerates the carbon recovery of human modified-tropical forests

More than half of all tropical forests are degraded by human impacts, leaving them threatened with conversion to agricultural plantations and risking substantial biodiversity and carbon losses. Restoration could accelerate recovery of aboveground carbon density (ACD), but adoption of restoration is constrained by cost and uncertainties over effectiveness. We report a long-term comparison of ACD recovery rates between naturally regenerating and actively restored logged tropical forests. Restoration enhanced decadal ACD recovery by more than 50%, from 2.9 to 4.4 megagrams per hectare per year. This magnitude of response, coupled with modal values of restoration costs globally, would require higher carbon prices to justify investment in restoration. However, carbon prices required to fulfill the 2016 Paris climate agreement [$40 to$80 (USD) per tonne carbon dioxide equivalent] would provide an economic justification for tropical forest restoration

Establishing a core outcome set for peritoneal dialysis : report of the SONG-PD (standardized outcomes in nephrology-peritoneal dialysis) consensus workshop

Outcomes reported in randomized controlled trials in peritoneal dialysis (PD) are diverse, are measured inconsistently, and may not be important to patients, families, and clinicians. The Standardized Outcomes in Nephrology-Peritoneal Dialysis (SONG-PD) initiative aims to establish a core outcome set for trials in PD based on the shared priorities of all stakeholders. We convened an international SONG-PD stakeholder consensus workshop in May 2018 in Vancouver, Canada. Nineteen patients/caregivers and 51 health professionals attended. Participants discussed core outcome domains and implementation in trials in PD. Four themes relating to the formation of core outcome domains were identified: life participation as a main goal of PD, impact of fatigue, empowerment for preparation and planning, and separation of contributing factors from core factors. Considerations for implementation were identified: standardizing patient-reported outcomes, requiring a validated and feasible measure, simplicity of binary outcomes, responsiveness to interventions, and using positive terminology. All stakeholders supported inclusion of PD-related infection, cardiovascular disease, mortality, technique survival, and life participation as the core outcome domains for PD

Risks to carbon storage from land-use change revealed by peat thickness maps of Peru

This work was funded by NERC (grant ref. NE/R000751/1) to I.T.L., A.H., K.H.R., E.T.A.M., C.M.A., T.R.B., G.D. and E.C.D.G.; Leverhulme Trust (grant ref. RPG-2018-306) to K.H.R., L.E.S.C. and C.E.W.; Gordon and Betty Moore Foundation (grant no. 5439, MonANPeru network) to T.R.B., E.N.H.C. and G.F.; Wildlife Conservation Society to E.N.H.C.; Concytec/British Council/Embajada Británica Lima/Newton Fund (grant ref. 220–2018) to E.N.H.C. and J.D.; Concytec/NERC/Embajada Británica Lima/Newton Fund (grant ref. 001–2019) to E.N.H.C. and N.D.; the governments of the United States (grant no. MTO-069018) and Norway (grant agreement no. QZA-12/0882) to K.H.; and NERC Knowledge Exchange Fellowship (grant ref no. NE/V018760/1) to E.N.H.C.Tropical peatlands are among the most carbon-dense ecosystems but land-use change has led to the loss of large peatland areas, associated with substantial greenhouse gas emissions. To design effective conservation and restoration policies, maps of the location and carbon storage of tropical peatlands are vital. This is especially so in countries such as Peru where the distribution of its large, hydrologically intact peatlands is poorly known. Here field and remote sensing data support the model development of peatland extent and thickness for lowland Peruvian Amazonia. We estimate a peatland area of 62,714 km2 (5th and 95th confidence interval percentiles of 58,325 and 67,102 km2, respectively) and carbon stock of 5.4 (2.6–10.6) PgC, a value approaching the entire above-ground carbon stock of Peru but contained within just 5% of its land area. Combining the map of peatland extent with national land-cover data we reveal small but growing areas of deforestation and associated CO2 emissions from peat decomposition due to conversion to mining, urban areas and agriculture. The emissions from peatland areas classified as forest in 2000 represent 1–4% of Peruvian CO2 forest emissions between 2000 and 2016. We suggest that bespoke monitoring, protection and sustainable management of tropical peatlands are required to avoid further degradation and CO2 emissions.PostprintPeer reviewe

Deficits in neurite density underlie white matter structure abnormalities in first-episode psychosis

Background: Structural abnormalities across multiple white matter tracts are recognised in people with early psychosis, consistent with dysconnectivity as a neuropathological account of symptom expression. We applied advanced neuroimaging techniques to characterise microstructural white matter abnormalities for a deeper understanding of the developmental aetiology of psychosis. Methods: Thirty-five first-episode psychosis patients, and 19 healthy controls, participated in a quantitative neuroimaging study using Neurite Orientation Dispersion and Density Imaging (NODDI), a multi-shell diffusion-weighted MRI technique that distinguishes white matter fibre arrangement and geometry from changes in neurite density. Fractional anisotropy (FA) and mean diffusivity images were also derived. Tract-based spatial statistics compared white matter structure between patients and controls and tested associations with age, symptom severity and medication. Results: Patients with first-episode psychosis had lower regional FA in multiple commissural, corticospinal, and association tracts. These abnormalities predominantly colocalized with regions of reduced neurite density, rather than aberrant fibre bundle arrangement (orientation dispersion index). There was no direct relationship with active symptomatology. FA decreased and orientation dispersion index increased with age in patients, but not controls, suggesting accelerated effects of white matter geometry change. Conclusions: Deficits in neurite density appear fundamental to abnormalities in white matter integrity in early psychosis. In the first application of NODDI in psychosis, we found that processes compromising axonal fibre number, density, and myelination, rather than processes leading to spatial disruption of fibre organisation, are implicated in the aetiology of the disorder. This accords with a neurodevelopmental origin of aberrant brain-wide structural connectivity predisposing individuals to psychosis

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.We thank the DKFZ Genomics and Proteomics Core Facility and the OICR Genome Technologies Platform for provision of sequencing services. Financial support was provided by the consortium projects READNA under grant agreement FP7 Health-F4-2008-201418, ESGI under grant agreement 262055, GEUVADIS under grant agreement 261123 of the European Commission Framework Programme 7, ICGC-CLL through the Spanish Ministry of Science and Innovation (MICINN), the Instituto de Salud Carlos III (ISCIII) and the Generalitat de Catalunya. Additional financial support was provided by the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF, grants #01KU1201A, MedSys #0315416C and NGFNplus #01GS0883; the Ontario Institute for Cancer Research to PCB and JDM through funding provided by the Government of Ontario, Ministry of Research and Innovation; Genome Canada; the Canada Foundation for Innovation and Prostate Cancer Canada with funding from the Movember Foundation (PCB). PCB was also supported by a Terry Fox Research Institute New Investigator Award, a CIHR New Investigator Award and a Genome Canada Large-Scale Applied Project Contract. The Synergie Lyon Cancer platform has received support from the French National Institute of Cancer (INCa) and from the ABS4NGS ANR project (ANR-11-BINF-0001-06). The ICGC RIKEN study was supported partially by RIKEN President’s Fund 2011, and the supercomputing resource for the RIKEN study was provided by the Human Genome Center, University of Tokyo. MDE, LB, AGL and CLA were supported by Cancer Research UK, the University of Cambridge and Hutchison-Whampoa Limited. SD is supported by the Torres Quevedo subprogram (MI CINN) under grant agreement PTQ-12-05391. EH is supported by the Research Council of Norway under grant agreements 221580 and 218241 and by the Norwegian Cancer Society under grant agreement 71220-PR-2006-0433. Very special thanks go to Jennifer Jennings for administrating the activity of the ICGC Verification Working Group and Anna Borrell for administrative support.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1000