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Efficacy and safety of semaglutide for type 2 diabetes by race and ethnicity: a post hoc analysis of the SUSTAIN trials
<p class="CxSpFirst"><b>Context:</b> Variations in the prevalence and aetiology of type 2 diabetes (T2D) across race and ethnicity may affect treatment responses. Semaglutide is a glucagon-like peptide-1 (GLP-1) analog approved for once–weekly, subcutaneous (s.c.) treatment of T2D.</p> <p class="CxSpFirst"><b>Objective:</b> To compare semaglutide efficacy and safety in race and ethnicity subgroups across the SUSTAIN trials.</p> <p class="CxSpMiddle"><b>Design:</b> <i>Post hoc </i>analysis of data from phase 3 randomized SUSTAIN 1–5 and 7 (pooled) and SUSTAIN 6 trials.</p> <p class="CxSpMiddle"><b>Participants:</b> 3,074 subjects (SUSTAIN 1–5 and 7); 1,648 subjects (SUSTAIN 6).</p> <p class="CxSpMiddle"><b>Interventions:</b> Semaglutide 0.5 or 1.0 mg, placebo or active comparator (sitagliptin 100 mg, exenatide extended release 2.0 mg, insulin glargine 100IU/ml and dulaglutide 0.75 or 1.5 mg).</p> <p class="CxSpFirst"><b>Main Outcome Measures:</b> Change in HbA<sub>1c</sub> and body weight from baseline to week 30/40/104, other efficacy and safety endpoints.</p> <p class="CxSpMiddle"><b>Results:</b> HbA<sub>1c</sub> was reduced from baseline by 1.0–1.5%-points and 1.3–2.0%-points, and body weight by 2.3–4.7 kg and 3.6–6.1 kg with semaglutide 0.5 and 1.0 mg, respectively, across race and ethnicity subgroups. Minor changes in blood pressure and lipid profiles were observed. Adverse events (AEs) were reported in similar proportions of subjects across trials. More Asian vs other race subgroups discontinued treatment prematurely due to AEs. The most commonly reported AEs were gastrointestinal disorders.</p> <p class="CxSpMiddle"><b>Conclusion(s):</b> In this SUSTAIN trials <i>post hoc</i> analysis, semaglutide was associated with consistent and clinically relevant reductions in HbA<sub>1c</sub> and body weight in subjects with T2D, with minor variations in efficacy and safety outcomes associated with race or ethnicity.</p>
Data from: Equilibrium and non-equilibrium phases in the radiation of Hakea and the drivers of diversity in Mediterranean-Type Ecosystems
Mediterranean-Type ecosystems (MTEs) contain exceptional plant diversity. Explanations for this diversity are usually classed as either "equilibrium", with elevated MTE diversity resulting from greater ecological carrying capacities, or "non-equilibrium", with MTEs having a greater accumulation of diversity over time. These models have typically been considered as mutually exclusive. Here we present a trait-based explanatory framework that incorporates both equilibrium and non-equilibrium dynamics. Using a large continental Australian plant radiation (Hakea) as a case study, we identify traits associated with niche partitioning in co-occurring species (α traits) and with environmental filtering (β traits), and reconstruct the mode and relative timing of diversification of these traits. Our results point to a radiation with an early, non-equilibrium phase marked by divergence of β traits as Hakea diversified exponentially and expanded from the southwest Australian MTE into biomes across the Australian continent. This was followed from 7Mya by an equilibrium phase, marked by diversification of α traits and a slowdown in lineage diversification as the MTE niches became saturated. These results suggest that processes consistent with both equilibrium and non-equilibrium models have been important during different stages of the radiation of Hakea, and together they provide a richer explanation of present-day diversity patterns.
Cost-effectiveness analysis of cetuximab combined with chemotherapy as a first-line treatment for RAS wild-type metastatic colorectal cancer patients based on the TAILOR trial
<p><b>Objectives</b> Cetuximab plus leucovorin, fluorouracil, and oxaliplatin (FOLFOX-4) is superior to FOLFOX-4 alone as a first-line treatment for patients with RAS wild-type metastatic colorectal cancer (wt mCRC), with significantly improved survival benefit by TAILOR, an open-label, randomized, multicentre, phase III trial. Nevertheless, the cost-effectiveness of these two regimens remains uncertain. The following study aims to determine whether cetuximab combined with FOLFOX-4 is a cost-effective strategy for specific RAS wt mCRC patients in China.</p> <p><b>Design</b> A combined decision tree and Markov model with three health states (stable, progressive and dead) was constructed to simulate a hypothetical cohort of patients with RAS wt mCRC. The health outcomes and utility scores were derived from the TAILOR trial and previously published sources, respectively. Costs were calculated with reference to the Chinese societal perspective. A lifetime horizon was used. Univariate and probabilistic sensitivity analyses were carried out to test the robustness of the model results.</p> <p><b>Participants</b> The included patients were newly diagnosed Chinese patients with fully RAS wt mCRC. <b>Interventions</b> Either cetuximab plus FOLFOX-4 or FOLFOX-4 alone as a first-line treatment.</p> <p><b>Main outcome measures</b> The primary outcomes are costs, quality-adjusted life-years (QALYs) and incremental cost-effectiveness ratios (ICERs).</p> <p><b>Results</b> Baseline analysis showed that the addition of cetuximab increased the QALYs by 0.383, while an increase of $62,947 was observed in relation to FOLFOX-4 chemotherapy. This led to an incremental cost-effectiveness ratio (ICER) of $164,044/QALY. Sensitivity analysis showed that across the wide variation in parameters, the ICER exceeded the willingness-to-pay threshold of $28,106/QALY, which was three times the per capita GDP in China.</p> <p><b>Conclusions</b> Despite the survival benefit, cetuximab combined with FOLFOX-4 is not a cost-effective treatment for the first line treatment of patients with RAS wt mCRC in China.</p>
Data from: Effect of ecological momentary assessment, goal-setting and personalized phone-calls on adherence to interval walking training using the InterWalk application among patients with type 2 diabetes – a pilot randomized controlled trial
Objectives: The objective was to investigate the feasibility and usability of structured text-messages, goal-setting and phone-calls on adherence to a 12-week self-conducted interval walking training (IWT) program, delivered by the InterWalk smartphone among patients with type 2 diabetes (T2D). Methods: In a two-arm pilot randomized controlled trial (Denmark, March 2014 to February 2015), patients with T2D (18-80 years with a Body Mass Index of 18 and 40 kg/m2) were randomly allocated to 12 weeks of IWT with (intervention) or without additional support (control). The primary outcome was the difference between groups in accumulated time of interval walking training across 12 weeks. All patients were encouraged to use the InterWalk application to perform IWT for ≥90 minute/week. Patients in the intervention group made individual goals regarding lifestyle change, received automated text-messages once a week, inquiring about exercise adherence. In case of consistent non-adherence, the patients would receive a phone-call inquiring about the reason for non-adherence. The control group did not receive additional support. Information about training adherence was assessed objectively. Usability of structured text-messages was assessed based on response rates and self-reported satisfaction after 12-weeks. Results: Thirty-seven patients with T2D (66 years, 65% female, hemoglobin 1Ac 50.3 mmol/mol) where included (n=18 and n=19 in intervention and control group, respectively). The retention rate was 83%. The intervention group accumulated [95%CI] 345 -7, 698 minutes of IWT more than the control group. The response rate for the text-messages was 83% (68% for males and 90% for females). Forty-one percent of the intervention and 25% of the control group were very satisfied with their participation. Conclusion: The combination of structured text-messages, goal-setting with the possibility of follow-up phone calls are considered feasible interventions to attain training adherence when using the InterWalk app during a 12-week period in patients with T2D. Some uncertainty about the effect size of adherence remains.
Data from: Soil types select for plants with matching nutrient‐acquisition and ‐use traits in hyperdiverse and severely nutrient‐impoverished campos rupestres and cerrado in Central Brazil
1. Understanding the mechanisms that underlie the generation of beta-diversity remains a challenge in ecology. Underground plant adaptations to environmental gradients have received relatively little attention. 2. We studied plant nutrient-acquisition strategies and nutrient-use efficiency at three stages of pedogenesis in infertile soils from campos rupestres and on less infertile soil from cerrado sensu stricto in Brazil. All soils support very high plant diversity with high species turnover between soil types at small spatial scales (meters). We expected that differences in nutrient–acquisition and –use strategies would be associated with this high species turnover. With severely decreasing phosphorus (P) availability, we expected the effectiveness of arbuscular mycorrhizal (AM) symbioses for plant P acquisition to decrease, and reliance on non-mycorrhizal strategies (NM) to increase, while maintaining efficient nutrient-use. 3. Concentrations of total soil P and nitrogen (N) were greater in soils in cerrado than in those from campos rupestres, and the more weathered soils from campos rupestres were severely P– and N–impoverished. The proportion of the root length colonised by AM fungi was 71% in the soils from the cerrado and campos rupestres. Conversely, the proportion of species with non-mycorrhizal P-acquisition strategies such as rhizosheaths was greater in the most P-impoverished soils. Leaf [P] and [N] were very low and decreased with decreasing soil [P] and [N]. Leaf N: P ratios suggest P-limitation of plant productivity in the campos rupestres but N-P co-limitation in the cerrado. Photosynthetic rates decreased with increasing P-impoverishment, but photosynthetic P-use efficiency was very high and photosynthetic N-use efficiency moderately high on all soils. Most species had very high P-remobilisation efficiency during leaf senescence (>70%), but only moderate N-remobilisation efficiency (~50%). 4. Synthesis. We observed very high P-use efficiency and moderately high N-use efficiency in campos rupestres and cerrado species, consistent with plant productivity being more strongly limited by P than by N. Our findings demonstrate that different soil characteristics (nutrient availability and soil texture) select for species differing in nutrient-acquisition and -use strategies (especially belowground traits) which is likely key for the very high species turnover at a very small scale between soil types (i.e. beta-diversity) in campos rupestres and cerrado.
Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype
Breeding has transformed wild plant species into modern crops, increasing the allocation of their photosynthetic assimilate into grain, fiber, and other products for human use. Despite progress in increasing the harvest index, much of the biomass of crop plants is not utilized. Potential uses for the large amounts of agricultural residues that accumulate are animal fodder or bioenergy, though these may not be economically viable without additional efforts such as targeted breeding or improved processing. We characterized leaf and stem tissue from a diverse set of rice genotypes (varieties) grown in two environments (greenhouse and field) and report bioenergy-related traits across these variables. Among the 16 traits measured, cellulose, hemicelluloses, lignin, ash, total glucose, and glucose yield changed across environments, irrespective of the genotypes. Stem and leaf tissue composition differed for most traits, consistent with their unique functional contributions and suggesting that they are under separate genetic control. Plant variety had the least influence on the measured traits. High glucose yield was associated with high total glucose and hemicelluloses, but low lignin and ash content. Bioenergy yield of greenhouse-grown biomass was higher than field-grown biomass, suggesting that greenhouse studies overestimate bioenergy potential. Nevertheless, glucose yield in the greenhouse predicts glucose yield in the field (ρ = 0.85, p < 0.01) and could be used to optimize greenhouse (GH) and field breeding trials. Overall, efforts to improve cell wall composition for bioenergy require consideration of production environment, tissue type, and variety.
Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages
Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121 populations in the two river drainages. An index of genetic differentiation, FST, over all populations and loci was 0.087, with individual locus values ranging from 0.031 to 0.172. Standardized to an ecotype sample size of 275 individuals, the least genetically diverse ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee displayed the greatest number of alleles (260 alleles), with lake-type Sockeye Salmon intermediate (241 alleles). Kokanee populations from the Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson River (a major Fraser River tributary) drainage populations, and the mid-Fraser River populations all clustered together in a neighbor-joining analysis, indicative of a monophyletic origin of the Kokanee ecotype in these regions, likely reflecting the origin of salmon radiating from a refuge after the last glaciation period. However, upstream of the mid-Fraser River populations, there were closer relationships between the lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of the Kokanee ecotype evolving independently from the lake-type Sockeye Salmon ecotype in parallel radiation. Kokanee population structure within the entire Fraser River drainage suggested a polyphyletic origin of the ecotype within the drainage. Studies employing geographically restricted population sampling may not outline accurately the phylogenetic history of salmonid ecotypes.
Data from: Structural complexity and large-sized trees explain shifting species richness and carbon relationship across vegetation types
<p>1. It is prominently claimed that enhancing forest diversity would play a dual role of nature conservation and climate regulation. While the idea is intuitively appealing, studies show that species richness effects on aboveground carbon (AGC) are not always positive, but instead unpredictable especially across scales and complex terrestrial systems having large-diameter and tall-stature trees. Previous studies have further considered structural complexity and larger trees as determinants of AGC. Yet it remains unclear what drives differential diversity-AGC relationships across vegetation types.</p> <p>2. Here, we test whether structural complexity and large-sized trees play an influential role in explaining shifting diversity-AGC relationships across vegetation types, using a 22.3 ha sampled dataset of 124 inventory plots in woodlands, gallery forests, tree/shrub savannahs and mixed plantations in West Africa.</p> <p>3. Natural vegetation had greater species richness and structural complexity than mixed plantations, as expected. In addition, AGC was highest in gallery forests and mixed plantations, which is consistent with favorable environmental conditions in the former and high stocking densities and presence of fast-growing species in the latter. Significant interaction effects of species richness and vegetation on AGC revealed a vegetation-dependent species richness-AGC relationship: consistently, we found positive species richness-AGC relationship in both mixed plantations and woodlands, and nonsignificant patterns in gallery forests and tree/shrub savannah. Further, there was a vegetation-dependent mediation of structural complexity in linking species richness to AGC, with stronger positive structural complexity effects where species richness-AGC relationships were positive, and stronger positive large-sized trees' effect where species richness-AGC relationships were neutral.</p> <p>4. Our study provides strong evidence of vegetation-dependent species richness-AGC relationships, which operated through differential mediation by structural complexity of the species richness and large trees' effects. We conclude that even higher species richness in diversified ecosystems may not always relate positively with AGC, and that neutral pattern may arise possibly as a result of larger dominant individual trees imposing a slow stand dynamic flux and overruling species richness effects.</p>
Data from: Patterns and limitations of urban human mobility resilience under the influence of multiple types of natural disaster
Natural disasters pose serious threats to large urban areas, therefore understanding and predicting human movements is critical for evaluating a population's vulnerability and resilience and developing plans for disaster evacuation, response and relief. However, only limited research has been conducted into the effect of natural disasters on human mobility. This study examines how natural disasters influence human mobility patterns in urban populations using individuals' movement data collected from Twitter. We selected fifteen destructive cases across five types of natural disaster and analyzed the human movement data before, during, and after each event, comparing the perturbed and steady state movement data. The results suggest that the power-law can describe human mobility in most cases and that human mobility patterns observed in steady states are often correlated with those in perturbed states, highlighting their inherent resilience. However, the quantitative analysis shows that this resilience has its limits and can fail in more powerful natural disasters. The findings from this study will deepen our understanding of the interaction between urban dwellers and civil infrastructure, improve our ability to predict human movement patterns during natural disasters, and facilitate contingency planning by policymakers.
Data from: Effects of arbuscular mycorrhizal fungi on aboveground tri-trophic interactions are contingent upon plant genetic effects of cross type in the perennial herb Ruellia nudiflora
1.- Recent work has improved our understanding of the linkages between above- and below-ground interactions mediated by plants. However, relatively few of the studies conducted thus far have focused on muli-trophic interactions (i.e. beyond two trophic levels) and the influence of plant genetic intra-specific variation on these dynamics has rarely been addressed. 2.- We tested the effect of arbuscular mycorrhizal fungi (AMF) on above-ground tri-trophic interactions associated with the canopy of the perennial herb <i></i>Ruellia nudiflora<i></i>, and further determined whether genetic effects due to cross type (i.e. wether a plant originated from from self- or cross-pollination) influenced these interactions. 3.- We propagated plants originating from self- or cross-pollination, and within each category inoculated half of the plants with AMF. We subsequently established a common garden where plants were exposed to naturally occurring seed-eating caterpillars and their parasitoids. We measured plant growth, fruit output, calculated the proportion of attacked fruits by the caterpillar and the proportion of parasitized caterpillars, and also estimated the proportion of "rescued" seeds by parasitoids representing an indirect positive effect of the third trophic level on the plant by reducing caterpillar consumption. 4.- AMF drove 18% and 15% increases in plant growth and fruit output respectively, and drove a 25% reduction in caterpillar fruit attack, but did not influence parasitism or parasitoid seed "rescue". In contrast, cross type did not influence growth, fruit number, herbivore attack, parasitism, or seed rescue. More importantly, however, we found a significant AMF by cross type interaction on caterpillar attack where AMF significantly reduced fruit attack (by 30%) in progeny from cross-pollination but did not influence herbivory in progeny from self-pollination. 5.- Synthesis. Results indicate that AMF effects on above-ground interactions are contingent upon plant intra-specific variation originating from cross type, which is likely a common source of variation in associated interactions for plants with mixed mating systems. Further studies examining plant-mediated below- and aboveground interactions should consider the influence of specific sources of plant genetic variation, as well as address the consequences of such dynamics for interactions beyond two trophic levels.
Data from: CO2 enrichment and soil type additively regulate grassland productivity
Atmospheric CO2 enrichment usually increases aboveground productivity (ANPP) of grassland vegetation, but the magnitude of the ANPP-CO2 response differs among ecosystems. Soil properties affect ANPP via multiple mechanisms and vary over topographic to geographic gradients, but have received little attention as potential modifiers of the ANPP-CO2 response. We assessed effects of three soil types, sandy loam, silty clay, and clay, on the ANPP response of perennial C3/C4 grassland communities to a subambient to elevated CO2 gradient over 10 years in Texas, USA. We predicted an interactive, rather than additive, effect of CO2 and soil type on ANPP. Contrary to prediction, CO2 and soil additively influenced grassland ANPP. Increasing CO2 by 250 μL L-1 increased ANPP by 170 g m-2 across soil types. Increased clay content from 10% to 50% among soils reduced ANPP by 50 g m-2. CO2 enrichment increased ANPP via a predominant direct effect accompanied by a smaller indirect effect mediated by successional shift to increased dominance of the C4 tallgrass Sorghastrum nutans. Our results indicate a large, positive influence of CO2 enrichment on grassland productivity that resulted from direct physiological benefits of CO2 augmented by species succession and was expressed similarly across soils of differing physical properties.
Data from: Matrix type and landscape attributes modulate avian taxonomic and functional spillover across habitat boundaries in the Brazilian Atlantic Forest
Land use intensification drives biodiversity loss worldwide. In heterogeneous landscape mosaics, both overall forest area and anthropogenic matrix structure induce changes in biological communities in primary habitat remnants. However, community changes via cross-habitat spillover processes along forest-matrix interfaces remain poorly understood. Moreover, information on how landscape attributes affect spillover processes across habitat boundaries are embryonic. Here, we quantify avian and β-diversity (as proxies of spillover rates) across two dominant types of forest-matrix interfaces (forest-pasture and forest-eucalyptus plantation) within the Atlantic Forest biodiversity hotspot in southeast Brazil. We also assess the effects of anthropogenic matrix type and landscape attributes (forest cover, edge density and land-use diversity) on bird taxonomic and functional β-diversity across forest-matrix boundaries. Alpha taxonomic richness was higher in forest edges than within both matrix types, but between matrix types, it was higher in pastures than in eucalyptus plantations. Although significantly higher in forests edges than in the adjacent eucalyptus, bird functional richness did not differ between forest edges and adjacent pastures. Community changes (β-diversity) related to species and functional replacements (turnover component) were higher across forest-pasture boundaries, whereas changes related to species and functional loss (nested component) were higher across forest-eucalyptus boundaries. Forest edges adjacent to eucalyptus had significant higher species and functional replacements than forest edges adjacent to pastures. Forest cover negatively influenced functional β-diversity across both forest-pasture and forest-eucalyptus interfaces. We show the importance of matrix type and the structure of surrounding landscapes (mainly forest cover) on rates of bird assemblage spillover across forest-matrix boundaries, which has profound implications to biological fluxes, ecosystem functioning and land-use management in human-modified landscapes.
Data from: Mechanisms and implications of a type IV functional response for short-term intake rate of dry matter in large mammalian herbivores
1. The functional response (i.e. the relationship between consumers' intake rate and resource density) is central in plant-herbivore interactions. Its shape and the biological processes leading to it have significant implications for both foraging theory and ecology of grazing systems. 2. A type IV functional response (i.e. dome-shaped relationship) of short-term intake rate of dry matter (intake while grazing) has rarely been reported for large herbivores and the conditions that can lead to it are poorly understood. 3. We report a type IV functional response observed in heifers grazing monocultures of Cynodon sp. and Avena strigosa. The mechanisms and consequences of this type of functional response for grazed system dynamics are discussed. 4. Intake rate was higher at intermediate than at short or tall sward heights in both grass species. The type IV functional response resulted from changes in bite mass instead of a longer time needed to encounter and process bites. Thus, the decrease of intake rate of dry matter in tall swards is not explained by a shift from process 3 (potential bites are concentrated and apparent) to process 2 (potential bites are apparent but dispersed, Spalinger & Hobbs 1992). Bite mass was smaller in tall than in intermediate swards due to a reduction of bite volume possibly caused by the greater proportion of stem and sheath acting as a physical barrier to bite formation. 5. It is generally accepted that potential bites are abundant and apparent in most grassland and meadow systems, as they were in the present experiments. Therefore, a type IV response of intake rate not directly related to digestive constraints may determine the dynamics of intake and defoliation under a much larger set of conditions than previously thought. These results have implications for foraging theory and stability of grazing systems. For example, if animals prefer patches of intermediate stature that yield the highest intake rate, grazing should lead to the widely observed bimodal distribution of plant mass per unit area, even when tall patches are not of significantly lower digestive quality than the pasture average.
The role of environmental vs. biotic filtering in the structure of European ant communities: a matter of trait type and spatial scale
<p>Functional trait-based approaches are increasingly used for studying the processes underlying community assembly. The relative influence of different assembly rules might depend on the spatial scale of analysis, the environmental context and the type of functional traits considered. By using a functional trait-based approach, we aim to disentangle the relative role of environmental filtering and interspecific competition on the structure of European ant communities according to the spatial scale and the type of trait considered. We used a large database on ant species composition that encompasses 361 ant communities distributed across the five biogeographic regions of Europe; these communities were composed of 155 ant species, which were characterized by 6 functional traits. We then analysed the relationship between functional divergence and co-occurrence between species pairs across different spatial scales (European, biogeographic region and local) and considering different types of traits (ecological tolerance and niche traits). Three different patterns emerged: negative, positive and non-significant regression coefficients suggest that environmental filtering, competition and neutrality are at work, respectively. We found that environmental filtering is important for structuring European ant communities at large spatial scales, particularly at the scale of Europe and most biogeographic regions. Competition could play a certain role at intermediate spatial scales where temperatures are more favourable for ant productivity (i.e. the Mediterranean region), while neutrality might be especially relevant in spatially discontinuous regions (i.e. the Alpine region). We found that no ecological mechanism (environmental filtering or competition) prevails at the local scale. The type of trait is especially important when looking for different assembly rules, and multi-trait grouping works well for traits associated with environmental responses (tolerance traits), but not for traits related to resource exploitation (niche traits). The spatial scale of analysis, the environmental context and the chosen traits merit special attention in trait-based analyses of community assembly mechanisms.</p>
Data from: Relationship type affects the reliability of dispersal distance estimated using pedigree inferences in partially sampled populations: a case study involving invasive American mink in Scotland
Estimating dispersal—a key parameter for population ecology and management—is notoriously difficult. The use of pedigree assignments, aided by likelihood-based software, has become popular to estimate dispersal rate and distance. However, the partial sampling of populations may produce false assignments. Further, it is unknown how the accuracy of assignment is affected by the genealogical relationships of individuals and is reflected by software-derived assignment probabilities. Inspired by a project managing invasive American mink (Neovison vison), we estimated individual dispersal distances using inferred pairwise relationships of culled individuals. Additionally, we simulated scenarios to investigate the accuracy of pairwise inferences. Estimates of dispersal distance varied greatly when derived from different inferred pairwise relationships, with mother–offspring relationship being the shortest (average = 21 km) and the most accurate. Pairs assigned as maternal half-siblings were inaccurate, with 64%–97% falsely assigned, implying that estimates for these relationships in the wild population were unreliable. The false assignment rate was unrelated to the software-derived assignment probabilities at high dispersal rates. Assignments were more accurate when the inferred parents were older and immigrants and when dispersal rates between subpopulations were low (1% and 2%). Using 30 instead of 15 loci increased pairwise reliability, but half-sibling assignments were still inaccurate (>59% falsely assigned). The most reliable approach when using inferred pairwise relationships in polygamous species would be not to use half-sibling relationship types. Our simulation approach provides guidance for the application of pedigree inferences under partial sampling and is applicable to other systems where pedigree assignments are used for ecological inference.
Substrate quality drives fungal necromass decay and decomposer community structure under contrasting vegetation types
<p>1. Fungal mycelium is increasingly recognized as a central component of soil biogeochemical cycling, yet our current understanding of the ecological controls on fungal necromass decomposition is limited to single sites and vegetation types.</p> <p>2. By deploying common fungal necromass substrates in a temperate oak savannah and hardwood forest in the midwestern USA, we assessed the generality of the rate at which high- and low-quality fungal necromass decomposes; further, we investigated how the decomposer 'necrobiome' varies both across and within sites under vegetation types dominated by either arbuscular (AM) or ectomycorrhizal (EM) plants.</p> <p>3. The effects of necromass quality on decay rate were robust to site and vegetation type differences, with high-quality fungal necromass decomposing, on average, 2.5 times faster during the initial stages of decay. Across vegetation types, bacterial and fungal communities present on decaying necromass differed from bulk soil microbial communities and were influenced by necromass quality. Moulds, yeasts and copiotrophic bacteria consistently dominated the necrobiome of high-quality fungal substrates.</p> <p>4. Synthesis: We show that regardless of differences in decay environments, high-quality fungal substrates decompose faster and support different types of decomposer microorganisms when compared with low-quality fungal tissues. These findings help to refine our theoretical understanding of the dominant factors affecting fast cycling components of soil organic matter (SOM) and the microbial communities associated with rapid decay.</p>
Data from: The importance of delineating networks by activity type in bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida
Network analysis has proved to be a valuable tool for studying the behavioural patterns of complex social animals. Often such studies either do not distinguish between different behavioural states of the organisms or simply focus attention on a single behavioural state to the exclusion of all others. In either of these approaches it is impossible to ascertain how the behavioural patterns of individuals depend on the type of activity they are engaged in. Here we report on a network-based analysis of the behavioural associations in a population of bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida. We consider three distinct behavioural states—socializing, travelling and foraging—and analyse the association networks corresponding to each activity. Moreover, in constructing the different activity networks we do not simply record a spatial association between two individuals as being either present or absent, but rather quantify the degree of any association, thus allowing us to construct weighted networks describing each activity. The results of these weighted activity networks indicate that networks can reveal detailed patterns of bottlenose dolphins at the population level; dolphins socialize in large groups with preferential associations; travel in small groups with preferential associates; and spread out to forage in very small, weakly connected groups. There is some overlap in the socialize and travel networks but little overlap between the forage and other networks. This indicates that the social bonds maintained in other activities are less important as they forage on dispersed, solitary prey. The overall network, not sorted by activity, does not accurately represent any of these patterns.
Data from: Effects of experimental warming on biodiversity depend on ecosystem type and local species composition
Climatic warming is a primary driver of change in ecosystems worldwide. Here, we synthesize responses of species richness and evenness from 187 experimental warming studies in a quantitative meta-analysis. We asked 1) whether effects of warming on diversity were detectable and consistent across terrestrial, freshwater and marine ecosystems, 2) if effects on diversity correlated with intensity, duration, and experimental unit size of temperature change manipulations, and 3) whether these experimental effects on diversity interacted with ecosystem types. Using multilevel mixed linear models and model averaging, we also tested the relative importance of variables that described uncontrolled environmental variation and attributes of experimental units. Overall, experimental warming reduced richness across ecosystems (mean log-response ratio = –0.091, 95% bootstrapped CI: –0.13, –0.05) representing an 8.9% decline relative to ambient temperature treatments. Richness did not change in response to warming in freshwater systems, but was more strongly negative in terrestrial (–11.8%) and marine (–10.5%) experiments. In contrast, warming impacts on evenness were neutral overall and in aquatic systems, but weakly negative on land (7.6%). Intensity and duration of experimental warming did not explain variation in diversity responses, but negative effects on richness were stronger in smaller experimental units, particularly in marine systems. Model-averaged parameter estimation confirmed these main effects while accounting for variation in latitude, ambient temperature at the sites of manipulations, venue (field versus lab), community trophic type, and whether experiments were open or closed to colonization. These analyses synthesize extensive experimental evidence showing declines in local richness with increased temperature, particularly in terrestrial and marine communities. However, the more variable effects of warming on evenness were better explained by the random effect of site identity, suggesting that effects on species' relative abundances were contingent on local species composition.
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment.
Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
Background: In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods: Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results: Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.