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opencc-zeroDec 2016View details →

Data from: Foraging sparrows exhibit individual differences but not a syndrome when responding to multiple types of novelty

Differences between individuals in correlated responses across contexts have both functional and mechanistic implications. Such syndromes may have either beneficial or harmful consequences when novel changes in the environment occur. We used wild-caught house sparrows, Passer domesticus, to test in functionally relevant circumstances, whether neophobia (initial fear of novelty), habituation, and the learning of novel cues (discriminant learning) were linked by a common underlying mechanism or reflected separate processes. We repeatedly measured individual latencies to approach and also to feed from a familiar feeding site in three contexts: a baseline control for mild disturbance, in the presence of a novel object, and to a novel cue indicating hidden food. House sparrows on average exhibited neophobia, habituated to novel objects, and learned to associate new cues to a reward. We also found evidence for consistent individual differences in in both latencies within most contexts, but there was no evidence of individual differences in plasticity with repeated trials within either the novel object (habituation) or novel cue (learning) contexts. There was also little or no correlation between the two latencies within individuals within contexts. Individual differences in latencies to arrive at the food station exhibited strong correlations across contexts, but latencies to feed were weaker. These results suggest a personality trait that exists regardless of novelty, but no syndrome affecting reactions to different forms of novelty. House sparrows appear strongly plastic when responding to novel environments. Such plasticity is likely favored by the varied consequences of novelty across environments.

opencc-zeroNov 2019View details →

Data from: Type Maastrichtian gastropod faunas evidencing rapid ecosystem recovery following the Cretaceous-Palaeogene boundary

The study of the global mass extinction event at the Cretaceous–Palaeogene (K/Pg) boundary can aid in understanding patterns of selective extinction and survival, and dynamics of ecosystem recovery. Outcrops in the Maastrichtian type area (southeast Netherlands, northeast Belgium) comprise an exceptionally expanded K/Pg boundary succession that offers a unique opportunity to study marine ecosystem recovery within the first thousands of years following the mass extinction event. A quantitative analyses was performed on systematically sampled macrofossils of the topmost Maastrichtian and lowermost Danian strata at the former Curfs-Ankerpoort quarry (Geulhem), which represent 'snapshots' of the latest Cretaceous and earliest Palaeogene marine ecosystems, respectively. Molluscs in particular are diverse and abundant in the studied succession. Regional ecosystem changes across the K/Pg boundary are relatively minor, showing a decline in suspension feeders, accompanied by an ecological shift to endobenthic molluscs. The earliest Paleocene gastropod assemblage retains many 'Maastrichtian' features and documents a fauna that temporarily survived into the Danian. The shallow, oligotrophic carbonate platform in this area was inhabited by taxa that were adapted to low nutrient levels and resistant to starvation. As a result, the local taxa were less affected by the short-lived detrimental conditions related to K/Pg boundary perturbations, such as darkness, cooling, starvation and ocean acidification. This resulted in relatively high survival rates, which enabled rapid recolonization and recovery of marine faunas in the Maastrichtian type area.

opencc-zeroDec 2017View details →

Data from: Resilience of seed production to a severe El Niño‐induced drought across functional groups and dispersal types

More frequent and severe El Niño Southern Oscillations (ENSO) are causing episodic periods of decreased rainfall. Although the effects of these ENSO-induced droughts on tree growth and mortality have been well studied, the impacts on other demographic rates such as reproduction are less well known. We use a four-year seed rain dataset encompassing the most severe ENSO-induced drought in more than 30 years to assess the resilience (i.e. resistance and recovery) of the seed composition and abundance of three forest types in a tropical dry forest. We found that forest types showed distinct differences in the timing, duration and intensity of drought during the ENSO event, which likely mediated seed composition shifts and resilience. Drought-deciduous species were particularly sensitive to the drought with overall poor resilience of seed production, whereby seed abundance of this functional group failed to recover to pre-drought levels even two years after the drought. Liana and wind-dispersed species were able to maintain seed production both during and after drought suggesting that ENSO events promote early successional species or species with a colonization strategy. Combined, these results suggest that ENSO-induced drought mediates the establishment of functional groups and dispersal types suited for early successional conditions with more open canopies and reduced competition among plants. The effects of the ENSO-induced drought on seed composition and abundance were still evident two years after the event suggesting the recovery of seed production requires multiple years that may lead to shifts in forest composition and structure in the long-term, with potential consequences for higher trophic levels like frugivores.

opencc-zeroMay 2020View details →

Data from: Pest control potential of adjacent agri-environment schemes varies with crop type and is shaped by landscape context and within-field position

<ol> <li>Increasing natural pest control in agricultural fields is an important aim of ecological intensification. Combined effects of landscape context and local placement of agri-environmental schemes on natural pest control and within field distance functions of natural pest control agents have rarely been addressed but might affect the distribution of biocontrol providers. Importantly, it is currently unknown whether ecosystem services provided by adjacent agri-environmental schemes (AES) are consistent for different crop types during crop rotation.</li> <li>In this study, we assessed whether crop rotation from oilseed rape to cereals altered within-field distance functions of ground dwelling predators from adjacent agri-environmental fields along a gradient in landscape context. Additionally we recorded crop pests, predation rates, parasitoids as well as crop yields on a total of 30 study sites.</li> <li>Distance functions varied between trophic levels: Carabid richness decreased while densities of carabid beetles, staphylinid beetles as well as crop yields increased towards the field centres. Distance functions of parasitoids and pests were modulated by the amount of semi-natural habitat in the surrounding landscape, while the effects of adjacent AES were limited.</li> <li>Distance decay functions found for ground dwelling predators in oilseed rape in the previous year were not always present in cereals. Increasing distance to the field edge also increased effects of crop rotation on carabid beetle assemblages, indicating a source habitat function of field edges.</li> <li>Synthesis and applications. Distance functions of natural pest control are not universal and the effects of agri-environmental schemes (AES) in different adjacent crops during crop rotation vary and depends on ecological contrasts. A network of semi-natural habitats and spatially optimised AES habitats can benefit pest control in agricultural landscapes, but constraints as a result of crop type need to be addressed by annually targeted, spatially shifting AES schemes for different crops.</li> </ol> <div> </div>

opencc-by-4.0Jun 2021View details →

Exploratory analysis using machine learning of predictive factors for falls in persons with type 2 diabetes: A Longitudinal Study

The risk of falls in elderly individuals with diabetes was reported to be 1.5 - 3 times higher than in those without diabetes. However, it is not clear what risk factors are strongly related to falls in those with diabetes. In this study, we aimed to investigate the status of falls and to identify important risk factors for falls in persons with type 2 diabetes (T2D) including the non-elderly. Participants were 316 persons with T2D who were admitted to the University of Tsukuba Hospital for treatment of diabetes. They were assessed for medical history, laboratory data and physical capabilities during the hospitalization and were given a questionnaire on falls one year after discharge. Two different statistical models, logistic regression and random forest classifier, were used to investigate important predictors of falls. The response rate to the survey was 72%; of the 226 respondents, there were 129 males and 97 females (median age 62 years). The fall rate during the first year after discharge was 19% and increased with age; fall rates were 17% for those <60 years, 20% for those aged 60 – 69 years and 24% for those ≥70 years. Logistic regression revealed that knee extension strength (β= -0.698, P = 0.002), fasting C-peptide (F-CPR) level (β= 0.492, P = 0.009) and dorsiflexion strength (β= -0.432, P = 0.047) were independent predictors of falls. The random forest classifier placed knee extension strength (covariate importance = 0.304), grip strength (0.234), F-CPR level (0.232) and dorsiflexion strength (0.230) in the top 4 important variables for falls. The rate of falls in persons with T2D was high even in middle age. Lower extremity muscle weakness as well as elevated F-CPR levels and reduced grip strength were shown to be important risk factors for falls in T2D.

opencc-zeroApr 2020View details →

Data from: Entropic bonding of the type 1 pilus from experiment and simulation

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations [A. Alonso-Caballero et al., Nature Commun. 9, 2758 (2018)]. In this work we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature.

opencc-zeroMar 2020View details →

Liana communities exhibit different species composition, diversity and community structure across forest types in the Congo Basin

Lianas are poorly characterized for central African forests. We quantify variation in liana composition, diversity and community structure in different forest types in the Yangambi Man and Biosphere Reserve, Democratic Republic of Congo. These attributes of liana assemblages were examined in 12 1-ha plots, randomly demarcated within regrowth forest, old-growth monodominant forest, old-growth mixed forest and old-growth edge forest. Using a combination of multivariate and univariate community analyses, we visualize the patterns of these liana assemblage attributes and/or test for their significant differences across forest types. The combined 12 1-ha area contains 2,638 lianas (≥ 2 cm diameter) representing 105 species, 49 genera and 22 families. Liana species composition differed significantly across forest types. Taxonomic diversity was higher in old-growth mixed forests compared to old-growth monodominant and regrowth forests. Trait diversity was higher than expected in the regrowth forest as opposed to the rest of forest types. Similarly, the regrowth forest differed from the rest of forest types in the pattern of liana species ecological traits and diameter frequency distribution. The regrowth forest was also less densely populated in lianas, and had lower liana total basal area than the rest of forest types. We speculate that the mechanism of liana competitive exclusion by dominant tree species is mainly responsible for the lower liana species diversity in monodominant compared to mixed forests. We attribute variation in liana community structure between regrowth and old-growth forests mostly to short development time of size hierarchies.

opencc-zeroDec 2016View details →

Data from: Biogenic silica accumulation varies across tussock tundra plant functional type

1. Silica (SiO2) accumulation by terrestrial vegetation is an important component of the biological silica cycle because it improves overall plant fitness and influences export rates of silica from terrestrial to marine systems. However, most research on silica in plants has focused on agricultural and forested ecosystems, and knowledge of terrestrial silica cycling in the Arctic, as well as the potential impacts of climate change on the silica cycle is severely lacking. 2. We quantified biogenic silica (BSi) accumulation in above and belowground portions of three moist acidic tundra (MAT) sites spanning a 300 km latitudinal gradient in central and northern Alaska, USA. We also examined plant silica accumulation across three main tundra types found in the Arctic (MAT, moist non-acidic tundra (MNT), and wet sedge tundra (WST)). 3. BSi concentrations in live Eriophorum vaginatum, a tussock-forming sedge that is the foundation species of tussock tundra, were not significantly (p<0.05) different across the three main sites. Concentrations of BSi in live aboveground tissue were highest in the graminoid species (0.55 ± 0.07 % BSi in sedges from WST, and 0.27 ± 0.01% in E. vaginatum across the three MAT sites). Both inter-tussock tundra species and shrubs contained substantially lower BSi concentrations than E. vaginatum. 4. Our results have implications for how shifts in vegetation cover associated with climatic warming may alter silica storage in tussock tundra vegetation. Our calculations suggest that shrub expansion via warming will increase BSi storage in Arctic land plants due to the higher biomass associated with shrub tundra, whereas conversion of tussock tundra to WST via permafrost thaw would produce the opposite effect in the terrestrial plant BSi pool. Such changes in the size of the terrestrial vegetation silica reservoir could have direct consequences for the rates and timing of silica delivery to receiving waters in the Arctic.

opencc-zeroDec 2019View details →

The contribution of semi-natural habitats to biological control is dependent on sentinel prey type

<ol> <li>It is widely recognized that landscape factors affect the biological control of weed seeds and insect pests in arable crops, but landscape effects have been found to be inconsistent between studies.</li> <li>Here, we compare six different types of sentinels (surrogate prey that was either live insects or seeds) to measure the effects of semi-natural habitats at field to landscape scales on levels of biological control in winter wheat in the UK. Sentinels were located in fields adjacent to three boundary types: grassy margin, hedgerows or woodland to study local scale effects and in landscapes of varying heterogeneity in study areas of 1 km radius. </li> <li> Overall mean levels of predation were higher for most insect prey (60.8%) located on the ground compared to the crop (12.2%) and was lower for seeds (5.8%). Predation of sentinels on the ground was attributed to generalist predators. <a name="_Hlk24705886">Semi-natural habitats had both positive and negative effects at field and landscape scales, but the response varied with the sentinel type.</a><a name="_Hlk12869057"> Herbaceous linear semi-natural habitats had positive effects at local scales for Calliphora vomitoria and Sitobion avenae sentinels and provides </a>evidence that farmers can introduce linear herbaceous features to benefit biological control. In contrast our distance weighted kernel models identified a positive relationship between woody habitats and the predation of Caliphora vomitoria and Chenopodium album. Natural aphid infestations were lower in landscapes with more semi-natural habitat. </li> <li> Synthesis and applications. Sentinels may be sensitive enough to detect variation in levels of biological control influenced by semi-natural habitats, but this study confirms that landscape effects differ for different types of sentinel prey. This implies that it may not be possible to categorize landscapes as pest suppressive using a single sentinel type. Future studies should therefore consider using multiple sentinels to give a better perspective on predation intensity. The resulting recommendations for farm management include planting woodland adjacent wheat fields infested with seed predators and positioning herbaceous linear habitats adjacent wheat fields infested with Sitobion Avenae, particularly if fields are bordered by woody liner habitats due to their association with decreased Sitobion Avenae predation. </li> </ol>

opencc-zeroAug 2019View details →

Data from: Effects of soil type and light on height growth, biomass partitioning, and nitrogen dynamics on 22 species of tropical dry forest tree seedlings: comparisons between legumes and nonlegumes

PREMISE OF THE STUDY: The seedling stage is particularly vulnerable to resource limitation, with potential consequences for community composition. We investigated how light and soil variation affected early growth, biomass partitioning, morphology, and physiology of 22 tree species common in tropical dry forest, including eight legumes. Our hypothesis was that legume seedlings are better at taking advantage of increased resource availability, which contributes to their successful regeneration in tropical dry forests. METHODS: We grew seedlings in a full-factorial design under two light levels in two soil types that differed in nutrient concentrations and soil moisture. We measured height biweekly and, at final harvest, biomass partitioning, internode segments, leaf carbon, nitrogen, δ 13 C, and δ 15 N. KEY RESULTS: Legumes initially grew taller and maintained that height advantage over time under all experimental conditions. Legumes also had the highest final total biomass and water-use efficiency in the high-light and high-resource soil. For nitrogen-fixing legumes, the amount of nitrogen derived from fixation was highest in the richer soil. Although seed mass tended to be larger in legumes, seed size alone did not account for all the differences between legumes and nonlegumes. Both belowground and aboveground resources were limiting to early seedling growth and function. CONCLUSIONS: Legumes may have a different regeneration niche, in that they germinate rapidly and grow taller than other species immediately after germination, maximizing their performance when light and belowground resources are readily available, and potentially permitting them to take advantage of high light, nutrient, and water availability at the beginning of the wet season.

opencc-zeroMar 2020View details →

Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

Context Cardiovascular disease (CVD) is a major cause of mortality in adults with type 1 diabetes. Objective We prospectively evaluated CVD risk factors in a large, contemporary cohort of adults with type 1 diabetes living in the United States. Design Observational study of CVD and CVD risk factors over a median of 5.3 years. Setting The T1D Exchange clinic network. Patients Adults (age ≥18 years) with type 1 diabetes and without known CVD diagnosed before or at enrollment. Main Outcome Measure Associations between CVD risk factors and incident CVD were assessed by multivariable logistic regression. Results The study included 8,727 participants (53% female, 88% non-Hispanic white, median age 33 years [IQR=21, 48], type 1 diabetes duration 16 years [IQR=9, 26]). At enrollment, median HbA1c was 7.6% (66 mmol/mol) [IQR=6.9 (52), 8.6 (70)], 33% used a statin, and 37% used blood pressure medication. Over a mean follow-up of 4.6 years, 325 (3.7%) participants developed incident CVD. Ischemic heart disease was the most common CVD event. Increasing age, BMI, HbA1c, presence of hypertension and dyslipidemia, increasing duration of diabetes, and diabetic nephropathy were associated with increased risk for CVD. There were no significant gender differences in CVD risk. Conclusion HbA1c, hypertension, dyslipidemia and diabetic nephropathy are important risk factors for CVD in adults with type 1 diabetes. A longer follow-up is likely required to assess the impact of other traditional CVD risk factors on incident CVD in the current era.

opencc-zeroDec 2016View details →

Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen

The breve species group includes closely related Bembidion Latreille ground beetles commonly found at high elevation in the mountains of western North America. For several decades, the group has been considered to consist of two species. Here, we present evidence from morphological, molecular and geographic data that the group contains nine species: Bembidion ampliatum, B. breve, B. geopearlis, B. laxatum, B. lividulum, B. oromaia, B. saturatum, B. testatum and B. vulcanix. We describe three species (B. geopearlis, B. oromaia and B. vulcanix) as new and resurrect four previously synonymized names (B. ampliatum, B. lividulum, B. saturatum and B. testatum). Species diversity is highest throughout the Cascades in Oregon and Washington, and Sierra Nevada of California, where up to seven species can occur in sympatry. We resolved challenging nomenclatural issues through analysis of sequences obtained from century-old type specimens by using a novel application of rDNA copy number analysis – an approach that may prove useful for other historical specimens.

opencc-zeroFeb 2020View details →

Barn Swallow (Hirundo rustica) fledglings use crop habitat more frequently in relation to its availability than pasture and other habitat types

Populations of birds that forage on aerial insects have been declining across North America for several decades, but the main causes of and reasons for geographical variation in these declines remains unclear. We examined the habitat use and survival of post-fledging Barn Swallows (Hirundo rustica), near Vancouver, BC, Canada using VHF radio telemetry. We predicted that fledgling Barn Swallows hatched in higher quality natal habitat (pasture) would fledge at higher quality, stay closest to the nest, disproportionately use higher-quality habitat during the post-fledge stage and have higher survival rates in the region. Contrary to our predictions, we found that natal habitat (crop, pasture or non-agriculture) had no effect on fledgling quality or movement distance. Barn Swallow fledglings used crop habitat more frequently in relation to its availability than other habitat types, including pasture. Barn Swallows had low post-fledging survival rates (0.44; 95% CI: 0.35-0.57), which could negatively influence the population trend of the species in this region. While natal habitat had only minor effects, crop habitat appears to be important for fledgling Barn Swallows and therefore a decline in this habitat type could have further negative implications for an already declining species.

opencc-by-4.0Jun 2021View details →

Probabilistic Reconstruction of Type Ia Supernova SN 2002bo

SN2002bo_emulator_paper_data <ul> <li>The TARDIS configuration YAML file used as a template for the training spectra.</li> <li>HDF5 file of posterior samples of model parameters and their associated weights from the nested sampler.</li> </ul> SN2002bo_emulator_paper_spectra <ul> <li>Input grid of model parameters and corresponding spectra produced by TARDIS used to generate the training grid of the emulator.</li> </ul>

Figure 9 in Illustrated catalogue of type specimens of Megalopodidae (Coleoptera) deposited at the Museu de Zoologia da Universidade de São Paulo

Figure 9. Megalopodidae type specimens, habitus and labels. (A-C) Mastostethus semirufus Guérin, 1943, holotype; (D-F) Megalopus bicolor Guérin, 1943, holotype; (G-I) Megalopus jacobyi var. apicalis Monrós, 1947, syntype.

Figure 8 in Illustrated catalogue of type specimens of Megalopodidae (Coleoptera) deposited at the Museu de Zoologia da Universidade de São Paulo

Figure 8. Megalopodidae type specimens, habitus and labels. (A-C) Mastostethus nigripes Guérin, 1945, holotype; (D-F) Mastostethus pallidus Guérin, 1943, holotype; (G-I) Mastostethus punctatus Guérin, 1952, paratype.

Figure 5 in Illustrated catalogue of type specimens of Megalopodidae (Coleoptera) deposited at the Museu de Zoologia da Universidade de São Paulo

Figure 5. Megalopodidae type specimens, habitus and labels. (A-C) Mastostethus duodecimpunctatus Guérin, 1945, holotype; (D-F) Mastostethus elongatus Guérin, 1944, holotype; (G-I) Mastostethus haematomelas unicolor Guérin, 1943, holotype.

Figure 2 in Illustrated catalogue of type specimens of Megalopodidae (Coleoptera) deposited at the Museu de Zoologia da Universidade de São Paulo

Figure 2. Megalopodidae type specimens, habitus and labels. (A-C) Agathomerus hieroglyphicus Guérin, 1945, holotype; (D-F) Agathomerus nobilis cyaneonotatus Guérin, 1943 (= Agathomerus basalis Pic, 1916), holotype. (G-I) Agathomerus nicki Guérin, 1948, holotype (not "allotype");

Figure 1 in Illustrated catalogue of type specimens of Megalopodidae (Coleoptera) deposited at the Museu de Zoologia da Universidade de São Paulo

Figure 1. Megalopodidae type specimens, habitus and labels. (A-C) Agathomerus almeidai Guérin, 1946, holotype; (D-F) Agathomerus bifasciatus nigrapex Guérin, 1949, holotype; (G-I) Agathomerus elegans humerinotatus Guérin, 1943, holotype.

Figure 4 in Illustrated catalogue of type specimens of Megalopodidae (Coleoptera) deposited at the Museu de Zoologia da Universidade de São Paulo

Figure 4. Megalopodidae type specimens, habitus and labels. (A-C) Mastostethus cordatus Guérin, 1943, holotype; (D-F) Mastostethus costaricensis Guérin, 1948, holotype; (G-I) Mastostethus decoratus Guérin, 1944, holotype.