Testing Ecological Theory with Lianas

Lianas constitute a diverse polyphyletic plant group that is advancing our understanding of ecological theory. Specifically, lianas are providing new insights into the mechanisms that control plant distribution and diversity maintenance. For example, there is now evidence that a single, scalable mechanism may explain local, regional, and pan‐tropical distribution of lianas, as well as the maintenance of liana species diversity. The ability to outcompete trees under dry, stressful conditions in seasonal forests provides lianas a growth advantage that, over time, results in relatively high abundance in seasonal forests and low abundance in aseasonal forests. Lianas may also gain a similar growth advantage following disturbance, thus explaining why liana density and diversity peak following disturbance at the local, forest scale. The study of ecology, however, is more than the effect of the environment on organisms; it also includes the effects of organisms on the environment. Considerable empirical evidence now indicates that lianas substantially alter their environment by consuming resources, suppressing tree performance, and influencing emergent properties of forests, such as ecosystem functioning, plant and animal diversity, and community composition. These recent studies using lianas are transcending classical tropical ecology research and are now providing novel insights into fundamental ecological theory

Comparison and relative utility of inequality measurements: as applied to Scotland’s child dental health

This study compared and assessed the utility of tests of inequality on a series of very large population caries datasets. National cross-sectional caries datasets for Scotland’s 5-year-olds in 1993/94 (n = 5,078); 1995/96 (n = 6,240); 1997/98 (n = 6,584); 1999/00 (n = 6,781); 2002/03 (n = 9,747); 2003/04 (n = 10,956); 2005/06 (n = 10,945) and 2007/08 (n = 12,067) were obtained. Outcomes were based on the d3mft metric (i.e. the number of decayed, missing and filled teeth). An area-based deprivation category (DepCat) measured the subjects’ socioeconomic status (SES). Simple absolute and relative inequality, Odds Ratios and the Significant Caries Index (SIC) as advocated by the World Health Organization were calculated. The measures of complex inequality applied to data were: the Slope Index of Inequality (absolute) and a variety of relative inequality tests i.e. Gini coefficient; Relative Index of Inequality; concentration curve; Koolman and Doorslaer’s transformed Concentration Index; Receiver Operator Curve and Population Attributable Risk (PAR). Additional tests used were plots of SIC deciles (SIC10) and a Scottish Caries Inequality Metric (SCIM10). Over the period, mean d3mft improved from 3.1(95%CI 3.0–3.2) to 1.9(95%CI 1.8–1.9) and d3mft = 0% from 41.1(95%CI 39.8–42.3) to 58.3(95%CI 57.8–59.7). Absolute simple and complex inequality decreased. Relative simple and complex inequality remained comparatively stable. Our results support the use of the SII and RII to measure complex absolute and relative SES inequalities alongside additional tests of complex relative inequality such as PAR and Koolman and Doorslaer’s transformed CI. The latter two have clear interpretations which may influence policy makers. Specialised dental metrics (i.e. SIC, SIC10 and SCIM10) permit the exploration of other important inequalities not determined by SES, and could be applied to many other types of disease where ranking of morbidity is possible e.g. obesity. More generally, the approaches described may be applied to study patterns of health inequality affecting worldwide populations

Reproducibility of experiments in recommender systems evaluation

© IFIP International Federation for Information Processing 2018 Published by Springer International Publishing AG 2018. All Rights Reserved. Recommender systems evaluation is usually based on predictive accuracy metrics with better scores meaning recommendations of higher quality. However, the comparison of results is becoming increasingly difficult, since there are different recommendation frameworks and different settings in the design and implementation of the experiments. Furthermore, there might be minor differences on algorithm implementation among the different frameworks. In this paper, we compare well known recommendation algorithms, using the same dataset, metrics and overall settings, the results of which point to result differences across frameworks with the exact same settings. Hence, we propose the use of standards that should be followed as guidelines to ensure the replication of experiments and the reproducibility of the results

Future fire risk under climate change and deforestation scenarios in tropical Borneo

This is the final version. Available from IOP Publishing via the DOI in this record. Data availability statement: The data that support the findings of this study are available upon reasonable request from the authors.Fire in the tropical peatland forests of Borneo is an environmental issue with interactions with climate change and deforestation, and the consequences have local and global implications. While research has shown that fire severity and frequency are expected to increase with climate change, there is conflicting model and observational data as to the effect of deforestation on precipitation, which is a key metric for fire risk. To better understand the changes in fire risk from deforestation and climate change we ran simulations of the climate scenario RCP8.5 with and without total deforestation using regional climate model RegCM4. The output was then used for calculations of the Fire Weather Index. We find that annual temperature change from deforestation at elevations above 500m is 53% of the change over the 21st Century in RCP8.5. Fire risk is significantly affected by both climate change and deforestation, despite some increases in precipitation from deforestation. While the multi model dry season (June-August) mean increases in fire risk are larger from elevated atmospheric carbon dioxide, the increases in maximum fire risk are larger from deforestation. The altitude is a good predictor of fire risk change, with larger increases at more densely populated lower elevations where the peatlands are concentrated and smaller increases at higher elevations. Therefore, while deforestation generally causes a smaller increase in climate-related fire risk than climate change, its local control and heterogeneous effects compared to global carbon emissions makes it critical for climate mitigation policy. These high-resolution simulations provide a guide to the most vulnerable areas of Borneo from climatic increases in fire risk.Natural Environment Research Council (NERC

Quantifying causal teleconnections to drought and fire risks in Indonesian Borneo

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: Datasets for this research are openly available in the in-text citations. For observational estimates (ERA5, CHIRPS, Hadley SST, etc.), readers are referred to Tables S1 and S2 for details. Climate model data used in this study are available from the CMIP6 archive at https://esgf-index1.ceda.ac.uk/search/cmip6-ceda/Fires occurring over the peatlands in Indonesian Borneo accompanied by droughts have posed devastating impacts on human health, livelihoods, economy and the natural environment, and their prevention requires comprehensive understanding of climate-associated risk. Although it is widely known that the droughts are associated with El Niño events, the onset process of El Niño and thus the drought precursors and their possible changes under the future climate are not clearly understood. Here, we use a causal network approach to quantify the strength of teleconnections to droughts at a seasonal timescale shown in observations and climate models. We portray two drivers of June-July-August (JJA) droughts identified through literature review and causal analysis, namely Niño 3.4 sea surface temperature (SST) in JJA (El Niño Southern Oscillation [abbreviated as ENSO]) and SST anomaly over the eastern North Pacific to the east of the Hawaiian Islands (abbreviated as Pacific SST) in March-April-May (MAM) period. We argue that the droughts are strongly linked to ENSO variability, with drier years corresponding to El Niño conditions. The droughts can be predicted with a lead time of 3 months based on their associations with Pacific SST, with higher SST preceding drier conditions. We find that under the SSP585 scenario, the Coupled Model Intercomparison Phase 6 (CMIP6) multi-model ensembles show significant increase in both the maximum number of consecutive dry days in the Indonesian Borneo region in JJA (p = 0.006) and its linear association with Pacific SST in MAM (p = 0.001) from year 2061 to 2100 compared with the historical baseline. Some models are showing unrealistic amounts of JJA rainfall and underestimate drought risks in Indonesian Borneo and their teleconnections, owing to the underestimation of ENSO amplitude and overestimation of local convections. Our study strengthens the possibility of early warning triggers of fires and stresses the need for taking enhanced climate risk into consideration when formulating long-term policies to eliminate fires.Engineering and Physical Sciences Research Council (EPSRC

Scallop swimming kinematics and muscle performance: modelling the effects of "within-animal" variation in temperature sensitivity

Escape behaviour was investigated in Queen scallops (Aequipecten opercularis) acclimated to 5, 10 or 15 degrees C and tested at their acclimation temperature. Scallops are active molluscs, able to escape from predators by jet-propelled swimming using a striated muscle working in opposition to an elastic hinge ligament. The first cycle of the escape response was recorded using high-speed video ( 250 Hz) and whole-animal velocity and acceleration determined. Muscle shortening velocity, force and power output were calculated using measurements of valve movement and jet area, and a simple biomechanical model. The average shortening speed of the adductor muscle had a Q(10) of 2.04, significantly reducing the duration of the jetting phase of the cycle with increased temperature. Muscle lengthening velocity and the overall duration of the clap cycle were changed little over the range 5 - 15 degrees C, as these parameters were controlled by the relatively temperature-insensitive, hinge ligament. Improvements in the average power output of the adductor muscle over the first clap cycle ( 222 vs. 139 W kg(-1) wet mass at 15 and 5 degrees C respectively) were not translated into proportional increases in overall swimming velocity, which was only 32% higher at 15 degrees C ( 0.37m s(-1)) than 5 degrees C (0.28 m s(-1))

Kaposi’s sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs

Historically, ribosomes were viewed as unchanged homogeneous macromolecular machines with no regulatory capacity for mRNA translation. An emerging concept is that heterogeneity of ribosomal composition exists, exerting a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct specialised ribosomes that actively regulate mRNA translation. Viruses lack their own translational machinery and impose high translational demands on the host during replication. We explore the possibility that KSHV manipulates ribosome biogenesis producing specialised ribosomes which preferentially translate viral transcripts. Quantitative proteomic analysis identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic replication. We demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and the KSHV ORF11 protein, with small ribosomal subunit precursor complexes during lytic replication. BUD23 depletion resulted in significantly reduced viral gene expression, culminating in dramatic reduction of infectious virion production. Ribosome profiling demonstrated BUD23 is essential for reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the downstream coding sequence. Results provide mechanistic insights into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialised ribosomes facilitating efficient translation of viral mRNAs