Development of forest structure and leaf area in secondary forests regenerating on abandoned pastures in Central Amazonia

The area of secondary forest (SF) regenerating from pastures is increasing in the Amazon basin; however, the return of forest and canopy structure following abandonment is not well understood. This study examined the development of leaf area index (LAI), canopy cover, aboveground biomass, stem density, diameter at breast height (DBH), and basal area ( BA) by growth form and diameter class for 10 SFs regenerating from abandoned pastures. Biomass accrual was tree dominated, constituting >= 94% of the total measured biomass in all forests abandoned >= 4 to 6 yr. Vine biomass increased with forest age, but its relative contribution to total biomass decreased with time. The forests were dominated by the tree Vismia spp. (> 50%). Tree stem density peaked after 6 to 8 yr ( 10 320 stems per hectare) before declining by 42% in the 12- to 14-yr-old SFs. Small-diameter tree stems in the 1-5-cm size class composed > 58% of the total stems for all forests. After 12 to 14 yr, there was no significant leaf area below 150-cm height. Leaf area return (LAI = 3.2 after 12 to 14 yr) relative to biomass was slower than literature-reported recovery following slash-and-burn, where LAI can reach primary forest levels ( LAI = 4 - 6) in 5 yr. After 12 to 14 yr, the colonizing vegetation returned some components of forest structure to values reported for primary forest. Basal area and LAI were 50% - 60%, canopy cover and stem density were nearly 100%, and the rapid tree-dominated biomass accrual was 25% - 50% of values reported for primary forest. Biomass accumulation may reach an asymptote earlier than expected because of even-aged, monospecific, untiered stand structure. The very slow leaf area accumulation relative to biomass and to reported values for recovery following slash-and-burn indicates a different canopy development pathway that warrants further investigation of causes ( e. g., nutrient limitations, competition) and effects on processes such as evapotranspiration and soil water uptake, which would influence long-term recovery rates and have regional implications

Gesture analysis for physics education researchers

Systematic observations of student gestures can not only fill in gaps in students' verbal expressions, but can also offer valuable information about student ideas, including their source, their novelty to the speaker, and their construction in real time. This paper provides a review of the research in gesture analysis that is most relevant to physics education researchers and illustrates gesture analysis for the purpose of better understanding student thinking about physics.Comment: 14 page

Quantifying professionalism in peer review

Background The process of peer-review in academia has attracted criticism surrounding issues of bias, fairness, and professionalism; however, frequency of occurrence of such comments is unknown. Methods We evaluated 1491 sets of reviewer comments from the fields of “Ecology and Evolution” and “Behavioural Medicine,” of which 920 were retrieved from the online review repository Publons and 571 were obtained from six early career investigators. Comment sets were coded for the occurrence of “unprofessional comments” and “incomplete, inaccurate or unsubstantiated critiques” using an a-prior rubric based on our published research. Results are presented as absolute numbers and percentages. Results Overall, 12% (179) of comment sets included at least one unprofessional comment towards the author or their work, and 41% (611) contained incomplete, inaccurate of unsubstantiated critiques (IIUC). Conclusions The large number of unprofessional comments, and IIUCs observed could heighten psychological distress among investigators, particularly those at an early stage in their career. We suggest that development and adherence to a universally agreed upon reviewer code of conduct is necessary to improve the quality and professional experience of peer review.publishedVersio

An adaptive semi-Lagrangian advection model for transport of volcanic emissions in the atmosphere

The dispersion of volcanic emissions in the Earth atmosphere is of interest for climate research, air traffic control and human wellbeing. Current volcanic emission dispersion models rely on fixed-grid structures that often are not able to resolve the fine filamented structure of volcanic emissions being transported in the atmosphere. Here we extend an existing adaptive semi-Lagrangian advection model for volcanic emissions including the sedimentation of volcanic ash. The advection of volcanic emissions is driven by a precalculated wind field. For evaluation of the model, the explosive eruption of Mount Pinatubo in June 1991 is chosen, which was one of the largest eruptions in the 20th century. We compare our simulations of the climactic eruption on 15 June 1991 to satellite data of the Pinatubo ash cloud and evaluate different sets of input parameters. We could reproduce the general advection of the Pinatubo ash cloud and, owing to the adaptive mesh, simulations could be performed at a high local resolution while minimizing computational cost. Differences to the observed ash cloud are attributed to uncertainties in the input parameters and the course of Typhoon Yunya, which is probably not completely resolved in the wind data used to drive the model. The best results were achieved for simulations with multiple ash particle sizes

Pointing to visible and invisible targets

We investigated how the visibility of targets influenced the type of point used to provide directions. In Study 1 we asked 605 passersby in three localities for directions to well-known local landmarks. When that landmark was in plain view behind the requester, most respondents pointed with their index fingers, and few respondents pointed more than once. In contrast, when the landmark was not in view, respondents pointed initially with their index fingers, but often elaborated with a whole-hand point. In Study 2, we covertly filmed the responses from 157 passersby we approached for directions, capturing both verbal and gestural responses. As in Study 1, few respondents produced more than one gesture when the target was in plain view and initial points were most likely to be index finger points. Thus, in a Western geographical context in which pointing with the index finger is the dominant form of pointing, a slight change in circumstances elicited a preference for pointing with the whole hand when it was the second or third manual gesture in a sequence

Thresholds of riparian forest use by terrestrial mammals in a fragmented Amazonian deforestation frontier

Species persistence in fragmented landscapes is intimately related to the quality, structure, and context of remaining habitat remnants. Riparian vegetation is legally protected within private landholdings in Brazil, so we quantitatively assessed occupancy patterns of terrestrial mammals in these remnants, examining under which circumstances different species effectively use them. We selected 38 riparian forest patches and five comparable riparian sites within continuous forest, at which we installed four to five camera-traps per site (199 camera-trap stations). Terrestrial mammal assemblages were sampled for 60 days per station during the dry seasons of 2013 and 2014. We modelled species occupancy and detection probabilities within riparian forest remnants, and examined the effects of patch size, habitat quality, and landscape structure on occupancy probabilities. We then scaled-up modelled occupancies to all 1915 riparian patches throughout the study region to identify which remnants retain the greatest potential to work as habitat for terrestrial vertebrates. Of the ten species for which occupancy was modelled, six responded to forest quality (remnant degradation, cattle intrusion, palm aggregations, and understorey density) or structure (remnant width, isolation, length, and area of the patch from which it originates). Patch suitability was lower considering habitat quality than landscape structure, and virtually all riparian remnants were unsuitable to maintain a high occupancy probability for all species that responded to forest patch quality or structure. Beyond safeguarding legal compliance concerning riparian remnant amount, ensuring terrestrial vertebrate persistence in fragmented landscapes will require curbing the drivers of forest degradation within private landholdings

A rapid, non-invasive population assessment technique for marine burrowing macrofauna inhabiting soft sediments

Population assessment techniques for soft-sediment infauna (invertebrates within the substrate) requires excavation of specimens, damaging or killing the specimen and surrounding habitat, while being time-consuming and costly. Rapid population assessments of some marine burrowing decapods have been possible by counting burrow openings to estimate abundance, and while they may be used as indicator species, these decapods are not ubiquitous to environments requiring monitoring. Additionally, the presence of other burrowing macrofauna (invertebrates living in the sediment and retained on 1mm mesh such as clams or large worms) may reduce the efficacy of burrow openings in estimating macrofauna abundance. As such, we assessed mudflats along the north coast of British Columbia, Canada, during summer 2017 to determine if macrofauna abundances could be estimated from burrow openings on the sediment surface in regions of low (n = 1 species) and high (n = 8 species) biodiversity. Abundance could not be estimated at the low diversity sites where only one macrofaunal species created burrows. At the high diversity site, species-specific models estimating abundance from burrow openings could not be constructed; however, the total number of burrow openings observed was useful in estimating total infaunal community abundance. As such, burrow openings may not be an effective tool in assessing species-specific abundances, but may be appropriate to estimate overall community changes

Sediment geochemistry influences infaunal invertebrate community composition and population abundances

Infaunal invertebrate communities are structured by various factors, including predation, resource availability, and environmental conditions. Given that these invertebrates live within sediment, it is not surprising that sediment properties play a critical role in many infaunal behaviours. When models explaining spatial and temporal variation in infaunal community composition are constructed using physical, biophysical, environmental, and sediment properties (salinity, detrital cover, elevation, particle size distribution, organic and water content, redox conditions, and penetrability), a considerable portion of the variation in the data is typically unaccounted for. This suggests that we do not fully understand all the variables that influence infaunal invertebrate communities. One suite of under-explored variables is the elemental composition/concentration of the sediments themselves. As such, we evaluated if sediment geochemistry improved model performance of the spatial variation in infaunal invertebrate communities on three intertidal mudflats in northern British Columbia, Canada. We observed that models including geochemistry data outperformed models that only included physical, biophysical, and environmental properties. Our results therefore suggest that some of the observed, and previously unaccounted for spatial variation in infaunal community composition may be a product of variation in sediment geochemistry. As such, sediment geochemistry should be accounted for when studying infaunal communities and assessing human impacts upon intertidal systems

Assessment of sediment penetrability as an integrated in situ measure of intertidal soft-sediment conditions

Infauna have an intimate relationship with the sediments they inhabit, and any study conducted upon infauna must, at the very least, describe sediment conditions. Common sediment assessments in intertidal systems include particle size distribution, as well as water and organic matter contents. These measures require extracting and processing a sediment core, and this disturbance may result in data that do not necessarily reflect in situ conditions. Sediment penetrability measured in situ by using a penetrometer can circumvent this limitation. However, relationships between sediment penetrability and other sediment variables are poorly understood, especially in coastal systems. We evaluated the relationship between sediment penetrability and other variables – depth to the apparent redox potential discontinuity, mean particle size, organic matter content, and water content – on tidal flats along the Pacific and Atlantic coasts of Canada. We also assessed if adding penetrability into environmental models of the infaunal community 6 improved model performance. We observed that while penetrability is statistically related to other sediment variables, relationships to covariates were weak. Further, inclusion of 8 penetrability with other sediment variables improved the performance of models predicting infaunal community composition. Therefore, penetrability can be considered a separate variable, and contributes to an integrated assessment of environmental conditions experienced by biota. Finally, since we evaluated this method in different soft-sediment intertidal ecosystems (mudflats to sandflats), this method is applicable to a range of systems in other geographical areas.type of work: Research Articlepublication status: Accepted for publicatio

In vivo imaging of microenvironmental and anti-PD-L1-mediated dynamics in cancer using S100A8/S100A9 as an imaging biomarker

Purpose: As a promotor of tumor invasion and tumor microenvironment (TME) formation, the protein complex S100A8/S100A9 is associated with poor prognosis. Our aim was to further evaluate its origin and regulatory effects, and to establish an imaging biomarker for TME activity. Methods: S100A9−/−cells (ko) were created from syngeneic murine breast cancer 4T1 (high malignancy) and 67NR (low malignancy) wildtype (wt) cell lines and implanted into either female BALB/c wildtype or S100A9−/− mice (n = 10 each). Anti-S100A9-Cy5.5-targeted fluorescence reflectance imaging was performed at 0 h and 24 h after injection. Potential early changes of S100A9-presence under immune checkpoint inhibition (anti-PD-L1, n = 7 vs. rat IgG2b as isotype control, n = 3) were evaluated. Results: In S100A9−/−mice contrast-to-noise-ratios were significantly reduced for wt and S100A9−/−tumors. No significant differences were detected for 4T1 ko and 67NR ko cells as compared to wildtype cells. Under anti-PD-L1 treatment S100A9 presence significantly decreased compared with the control group. Conclusion: Our results confirm a secretion of S100A8/S100A9 by the TME, while tumor cells do not apparently release the protein. Under immune checkpoint inhibition S100A9-imaging reports an early decrease of TME activity. Therefore, S100A9-specific imaging may serve as an imaging biomarker for TME formation and activity