Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2, 3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Urbanisation affects ecosystem functioning more than structure in tropical streams

Urbanisation poses a clear threat to tropical freshwater streams, yet fundamental knowledge gaps hinder our ability to effectively conserve stream biodiversity and preserve ecosystem functioning. Here, we studied the impact of urbanisation on structural and functional ecosystem responses in low-order streams in Singapore, a tropical city with a mosaic landscape of protected natural forests, managed buffer zones (between forest and open-country habitats), and built-up urban areas. We quantified an urbanisation gradient based on landscape, in-stream, and riparian conditions, and found an association between urbanisation and pollution-tolerant macroinvertebrates (e.g. freshwater snail and worm species) in litter bags. We also found greater macroinvertebrate abundance (mean individuals bag−1; forest: 30.3, buffer: 70.1, urban: 109.0) and richness (mean taxa bag−1; forest: 4.53, buffer: 4.75, urban: 7.50) in urban streams, but similar diversity across habitats. Higher levels of primary productivity (measured from algal accrual on ceramic tiles) and microbial decomposition (measured from litter-mass loss in mesh bags) at urban sites indicate rapid microbial activity at higher light, temperature, and nutrient levels. We found that urbanisation affected function 32% more than structure in the studied tropical streams, likely driven by greater algal growth in urban streams. These changes in ecological processes (i.e. ecosystem functioning) possibly lead to a loss of ecosystem services, which would negatively affect ecology, society, and economy. Our results point to possible management strategies (e.g. increasing vegetation density through buffer park creation) to reduce the impacts of urbanisation, restore vital ecosystem functions in tropical streams, and create habitat niches for native species

KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis.

Whole-exome and targeted sequencing of 13 individuals from 10 unrelated families with overlapping clinical manifestations identified loss-of-function and missense variants in KIAA1109 allowing delineation of an autosomal-recessive multi-system syndrome, which we suggest to name Alkuraya-Kučinskas syndrome (MIM 617822). Shared phenotypic features representing the cardinal characteristics of this syndrome combine brain atrophy with clubfoot and arthrogryposis. Affected individuals present with cerebral parenchymal underdevelopment, ranging from major cerebral parenchymal thinning with lissencephalic aspect to moderate parenchymal rarefaction, severe to mild ventriculomegaly, cerebellar hypoplasia with brainstem dysgenesis, and cardiac and ophthalmologic anomalies, such as microphthalmia and cataract. Severe loss-of-function cases were incompatible with life, whereas those individuals with milder missense variants presented with severe global developmental delay, syndactyly of 2nd and 3rd toes, and severe muscle hypotonia resulting in incapacity to stand without support. Consistent with a causative role for KIAA1109 loss-of-function/hypomorphic variants in this syndrome, knockdowns of the zebrafish orthologous gene resulted in embryos with hydrocephaly and abnormally curved notochords and overall body shape, whereas published knockouts of the fruit fly and mouse orthologous genes resulted in lethality or severe neurological defects reminiscent of the probands' features.This article is freely available via Open Access. Click on the Additional Link above to access the full-text via the publisher's site

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

<p>This repository hosts the supplementary data associated with the manuscript entitled "Genome-resolved diversity and biosynthetic potential of the coral reef microbiome".</p&gt

Endobronchial Ultrasound-Guided Transbronchial Forceps Biopsy: A Retrospective Bicentric Study Using the Olympus 1.5 mm Mini-Forceps

When evaluating mediastinal/hilar lymphadenopathy (LAD) or masses, guidelines recommend endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) as an initial technique for tissue analysis and diagnosis. However, owing to the small sample size obtained by needle aspiration, its diagnostic yield (DY) is limited. EBUS transbronchial forceps biopsy (TBFB) used as a complimentary technique to EBUS-TBNA might allow for better histopathological evaluation, thus improving DY. In this retrospective bicentric study, we assessed the DY and safety of an EBUS-guided 1.5 mm mini-forceps biopsy combined with EBUS-TBNA for the diagnosis of mediastinal/hilar LAD or masses compared to EBUS-TBNA alone. In total, 105 patients were enrolled. The overall DY was 61.9% and 85.7% for TBNA alone and EBUS-TBNA combined with EBUS-TBFB, respectively (p < 0.001). While the combined approach was associated with a significantly higher DY for lung cancer diagnosis (97.1% vs. 76.5%, p = 0.016) and sarcoidosis (85.2% vs. 44.4%, p = 0.001), no significant differences in DY were calculated for subgroups with smaller sample sizes such as lymphoma. No major adverse events were observed. Using a 1.5 mm mini-forceps is a safe and feasible technique for biopsy of mediastinal or hilar LAD or masses with superior overall DY compared to EBUS-TBNA as a standalone technique

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Thresholds for adding degraded tropical forest to the conservation estate.

Acknowledgements: This study was supported by funding to the Stability of Altered Forest Ecosystems Project by the Sime Darby Foundation. Research permission and site access were provided by the Maliau Basin Management Committee, the Sabah Foundation, Benta Wawasan, Sabah Softwoods, the Innoprise Foundation, the Sabah Forestry Department and the Sabah Biodiversity Centre. R.M.E. is supported by the NOMIS Foundation. Data collection was financed by Australian Research Council grant DP140101541; Bat Conservation International; the British Council Newton-Ungku Omar Fund 216433953; British Ecological Society grant 3256/4035; the Cambridge Trust; the Cambridge University Commonwealth Fund; the Czech Science Foundation (14-32302S); the European Research Council (281986); the European Social Fund and the Czech Republic (CZ.1.07/2.3.00/20.0064); the Fundamental Research Grant Scheme (FRG0302-STWN-1/ 2011), Ministry of Higher Education, Malaysia; FFWS CZU (IGA number A_26_22); the Jardine Foundation; Malaysia Industry Group for High Technology (216433953); the Ministry of Education, Youth and Sports of the Czech Republic (INTER-TRANSFER LTT19018); the Panton Trust; the Primate Society of Great Britain; ProForest; Royal Society of London grant RG130793; the Sime Darby Foundation; the S. T. Lee Fund; the Sir Philip Reckitt Educational Trust; the Tim Whitmore Fund; the Universiti Malaysia Sabah; the University of East Anglia; the University of Kent; the University of Florida Institute of Food and Agricultural Sciences; UK Research and Innovation Natural Environment Research Council grants NE/H011307/1, NE/K016253/1, NE/K016407/1, NE/K016148/1, NE/K0106261/1, NE/K015377/1, NE/L002515/1, NE/L002582/1 and NE/P00363X/1 and studentship 1122589; the Varley Gradwell Travelling Fellowship; and the World Wildlife Fund for Nature. Data collection was supported by R. Adzhar, A. Afendy, N. Arumugam, S. Benedick, V. Bignet, S. Butler, K. Graves, H. E. Hah, H. Heroin, A. Kendall, H. H. Mahsol, D. Mann, J. Miller, S. Milne, J. Mumford, D. Norman, H. Rossleykho, D. Shapiro, K. Sieving, J. Sugau, B. Udell, B. E. Yahya and M. A. Zakaria.Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked