Improving the taxonomy of fossil pollen using convolutional neural networks and superresolution microscopy.

Taxonomic resolution is a major challenge in palynology, largely limiting the ecological and evolutionary interpretations possible with deep-time fossil pollen data. We present an approach for fossil pollen analysis that uses optical superresolution microscopy and machine learning to create a quantitative and higher throughput workflow for producing palynological identifications and hypotheses of biological affinity. We developed three convolutional neural network (CNN) classification models: maximum projection (MPM), multislice (MSM), and fused (FM). We trained the models on the pollen of 16 genera of the legume tribe Amherstieae, and then used these models to constrain the biological classifications of 48 fossil Striatopollis specimens from the Paleocene, Eocene, and Miocene of western Africa and northern South America. All models achieved average accuracies of 83 to 90% in the classification of the extant genera, and the majority of fossil identifications (86%) showed consensus among at least two of the three models. Our fossil identifications support the paleobiogeographic hypothesis that Amherstieae originated in Paleocene Africa and dispersed to South America during the Paleocene-Eocene Thermal Maximum (56 Ma). They also raise the possibility that at least three Amherstieae genera (Crudia, Berlinia, and Anthonotha) may have diverged earlier in the Cenozoic than predicted by molecular phylogenies.

An integrated modeling approach for estimating hydrologic responses to future urbanization and climate changes in a mixed-use midwestern watershed.

Future urban development and climatic changes are likely to affect hydrologic regimes in many watersheds. Quantifying potential water regime changes caused by these stressors is therefore crucial for enabling decision makers to develop viable environmental management strategies. This study presents an approach that integrates mid-21st century impervious surface growth estimates derived from the Imperviousness Change Analysis Tool with downscaled climate model projections and a hydrologic model Soil and Water Assessment Tool to characterize potential water regime changes in a mixed-use watershed in central Missouri, USA. Results for the climate change only scenario showed annual streamflow and runoff decreases (-10.7% and -9.2%) and evapotranspiration increases (+6.8%), while results from the urbanization only scenario showed streamflow and runoff increases (+3.8% and +9.3%) and evapotranspiration decreases (-2.4%). Results for the combined impacts scenario suggested that climatic changes could have a larger impact than urbanization on annual streamflow, (overall decrease of -6.1%), and could largely negate surface runoff increases caused by urbanization. For the same scenario, climatic changes exerted a stronger influence on annual evapotranspiration than urbanization (+3.9%). Seasonal results indicated that the relative influences of urbanization and climatic changes vary seasonally. Climatic changes most greatly influenced streamflow and runoff during winter and summer, and evapotranspiration during summer. During some seasons the directional change for hydrologic processes matched for both stressors. This work presented a practicable approach for investigating the relative influences of mid-21st century urbanization and climatic changes on the hydrology of a representative mixed-use watershed, adding to a limited body of research on this topic. This was done using a transferrable approach that can be adapted for watersheds in other regions.

A late-Quaternary perspective, on atmospheric pCO2, climate, and fire as drivers of C4-grass abundance.

Various environmental factors, including atmospheric CO2 (pCO2), regional climate, and fire, have been invoked as primary drivers of long-term variation in C4 grass abundance. Evaluating these hypotheses has been difficult because available paleorecords often lack information on past C4 grass abundance or potential environmental drivers. We analyzed carbon isotope ratios (delta13C) of individual grains of grass pollen in the sediments of two East African lakes to infer changes in the relative abundance of C3 vs. C4 grasses during the past 25 000 years. Results were compared with concurrent changes in pCO2, temperature, moisture balance, and fire activity. Our grass-pollen delta13C analysis reveals a dynamic history of grass-dominated vegetation in equatorial East Africa: C4 grasses have not consistently dominated lowland areas, and high-elevation grasses have not always been predominantly C3. On millennial timescales, C4 grass abundance does not correlate with charcoal influx at either site, suggesting that fire was not a major proximate control of the competitive balance between C3 and C4 grasses. Above the present-day treeline on Mt. Kenya, C4 grass abundance declined from an average of approximately 90% during the glacial period to less than approximately 60% throughout the Holocene, coincident with increases in pCO2 and temperature, and shifts in moisture balance. In the lowland savanna southeast of Mt. Kilimanjaro, C4 grass abundance showed no such directional trend, but fluctuated markedly in association with variation in rainfall amount and seasonal-drought severity. These results underscore spatiotemporal variability in the relative influence of pCO2 and climate on the interplay of C3 and C4 grasses and shed light on an emerging conceptual model regarding the expansion of C4-dominated grasslands in Earth's history. They also suggest that future changes in the C3/C4 composition of grass-dominated ecosystems will likely exhibit striking spatiotemporal variability as a result of varying combinations of environmental controls.

Watch-sized 12 Tesla all-high-temperature-superconducting magnet.

We demonstrate the construction of 7 Tesla and 12 Tesla all high-temperature-superconducting (HTS) magnets, small enough to fit on your wrist. The size of the magnet reduces the cost of fabrication, decreases the fringe field to permit facile siting of magnets, and decreases the stored energy of high field magnets. These small HTS-based magnets are being developed for gyrotron microwave sources for use in high-field nuclear magnetic resonance applications. The 7 Tesla and 12 Tesla magnets employ a no-insulation winding technique and are cooled to 4.2 Kelvin in a liquid helium cryostat. The 7 Tesla magnet is a single pancake coil, made of only 9.4 m of HTS tape, with an inner diameter of 8 mm and an outer diameter of 24 mm. This magnet was charged up to 1168 Amperes, generating a field of 7.3 Tesla. The 12 Tesla magnet is comprised of two pancake coils (inner diameter of 10 mm and outer diameter of 27 mm) connected in series. This magnet reached its maximum field at a current of 850 Amperes.

Long-term variability and rainfall control of savanna fire regimes in equatorial East Africa.

Fires burning the vast grasslands and savannas of Africa significantly influence the global carbon cycle. Projecting the impacts of future climate change on fire-mediated biogeochemical processes in these dry tropical ecosystems requires understanding of how various climate factors influence regional fire regimes. To examine climate-vegetation-fire linkages in dry savanna, we conducted macroscopic and microscopic charcoal analysis on the sediments of the past 25 000 years from Lake Challa, a deep crater lake in equatorial East Africa. The charcoal-inferred shifts in local and regional fire regimes were compared with previously published reconstructions of temperature, rainfall, seasonal drought severity, and vegetation dynamics to evaluate millennial-scale drivers of fire occurrence. Our charcoal data indicate that fire in the dry lowland savanna of southeastern Kenya was not fuel-limited during the Last Glacial Maximum (LGM) and Late Glacial, in contrast to many other regions throughout the world. Fire activity remained high at Lake Challa probably because the relatively high mean-annual temperature (~22 °C) allowed productive C4 grasses with high water-use efficiency to dominate the landscape. From the LGM through the middle Holocene, the relative importance of savanna burning in the region varied primarily in response to changes in rainfall and dry-season length, which were controlled by orbital insolation forcing of tropical monsoon dynamics. The fuel limitation that characterizes the region's fire regime today appears to have begun around 5000-6000 years ago, when warmer interglacial conditions coincided with prolonged seasonal drought. Thus, insolation-driven variation in the amount and seasonality of rainfall during the past 25 000 years altered the immediate controls on fire occurrence in the grass-dominated savannas of eastern equatorial Africa. These results show that climatic impacts on dry-savanna burning are heterogeneous through time, with important implications for efforts to anticipate future shifts in fire-mediated ecosystem processes.

Improving the sensitivity of MAS spheres using a 9.5 mm spherical shell with 219 µL sample volume spinning in a spherical solenoid coil.

Spherical rotors in magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments have potential advantages relative to cylindrical rotors in terms of ease of fabrication, low risk of rotor crash, easy sample exchange, and better microwave access. However, one major disadvantage so far of spherical rotors is poor NMR filling factor due to the small sample volume and large cylindrical radiofrequency (RF) coil. Here we present a novel NMR coil geometry in the form of a spherical coil. The spherical coil best fits the spherical sample to maximize sensitivity, while also providing excellent RF homogeneity. We further improve NMR sensitivity by employing a spherical shell as the rotor, thereby maximizing sample volume (219 µL in this case of 9.5 mm outer diameter spheres). The spinning gas is supplied by a 3D-printed ring stator external to the coil, thereby introducing a simplified form of MAS stators. In this apparatus, the RF field generated along the coil axis is perpendicular to the external magnetic field, regardless of rotor orientation. We observe a linear increase in sensitivity with increasing sample volume. We also simulate the RF performance of spherical and cylindrical solenoid coils with constant or variable pitch for spherical and cylindrical rotors, respectively. The simulation results show that spherical solenoid coils generate comparable B1 field intensities but have better homogeneity than cylindrical solenoid coils do.

Cuticle and subsurface ornamentation of intact plant leaf epidermis under confocal and superresolution microscopy.

Plant cuticle micromorphology is an invaluable tool in modern ecology and paleoecology. It has expanded our knowledge of systematic relationships among diverse plant groups and can be used to identify fossil plants. Furthermore, fossil plant leaf micromorphology is used for reconstructing past environments, most notably for estimating atmospheric CO2 concentration. Here we outline a new protocol for imaging plant cuticle for archival and paleoecological applications. Traditionally, both modern reference and fossil samples undergo maceration with subsequent imaging via environmental SEM, widefield fluorescence, or light microscopy. In this paper, we demonstrate the capabilities of alternative preparation and imaging methods using confocal and superresolution microscopy with intact leaf samples. This method produces detailed three-dimensional images of surficial and subsurface structures of the intact leaf. Multiple layers are captured simultaneously, which previously required independent maceration and microtome steps. We compared clearing agents (chloral hydrate, KOH, and Visikol); mounting media (Eukitt and Hoyer's); fluorescent stains (periodic acid Schiff, propidium iodide); and confocal vs. superresolution microscopes. We conclude that Eukitt is the best medium for long-term preservation and imaging. Because of nontoxicity and ease of procurement, Visikol made for the best clearing agent. Staining improves contrast and under most circumstances PAS provided the clearest images. Supperresolution produced higher clarity images than traditional confocal, but the information gained was minimal. This new protocol provides the botanical and paleobotanical community an alternative to traditional techniques. Our proposed workflow has the net benefit of being more efficient than traditional methods, which only capture the surface of the plant epidermis. Microsc. Res. Tech. 81:129-140, 2018. © 2016 Wiley Periodicals, Inc.

Comparative performance of airyscan and structured illumination superresolution microscopy in the study of the surface texture and 3D shape of pollen.

The visualization of taxonomically diagnostic features of individual pollen grains can be a challenge for many ecologically and phylogenetically important pollen types. The resolution of traditional optical microscopy is limited by the diffraction of light (250 nm), while high resolution tools such as electron microscopy are limited by laborious preparation and imaging workflows. Airyscan confocal superresolution and structured illumination superresolution (SR-SIM) microscopy are powerful new tools for the study of nanoscale pollen morphology and three-dimensional structure that can overcome these basic limitations. This study demonstrates their utility in capturing morphological details below the diffraction limit of light. Using three distinct pollen morphotypes (Croton hirtus, Dactylis glomerata, and Helianthus sp.) and contrast-enhancing fluorescent staining, we were able to assess the effectiveness of the Airyscan and SR-SIM. We further demonstrate that these new superresolution methods can be easily applied to the study of fossil pollen material.

Perceptions of wood in rivers and challenges for stream restoration in the United States.

This article reports a study of the public perception of large wood in rivers and streams in the United States. Large wood is an element of freshwater aquatic ecosystems that has attracted much scientific interest in recent years because of its value in biological and geomorphological processes. At the heart of the issue is the nature of the relationship between scientific recognition of the ecological and geomorphological benefits of wood in rivers, management practices utilizing wood for river remediation progress, and public perceptions of in-channel wood. Surveys of students' perceptions of riverscapes with and without large wood in the states of Colorado, Connecticut, Georgia, Illinois, Iowa, Missouri, Oregon, and Texas suggest that many individuals in the United States adhere to traditionally negative views of wood. Except for students in Oregon, most respondents considered photographs of riverscapes with wood to be less aesthetically pleasing and needing more improvement than rivers without wood. Analysis of reasons given for improvement needs suggest that Oregon students are concerned with improving channels without wood for fauna habitat, whereas respondents elsewhere focused on the need for cleaning wood-rich channels for flood risk management. These results underscore the importance of public education to increase awareness of the geomorphological and ecological significance of wood in stream systems. This awareness should foster more positive attitudes toward wood. An integrated program of research, education, and policy is advocated to bridge the gap between scientific knowledge and public perception for effective management and restoration of river systems with wood.