Early-Stage Thinning for the Restoration of Young Redwood--Douglas-Fir Forests in Northern Coastal California, USA

Among forested parks and reserves of the Pacific Coast of the United States, the restoration of late-successional conditions to second-growth stands is a management priority. Some traditional silvicultural treatments may help achieve this objective. We evaluated early-stage thinning as a restoration treatment to facilitate the growth and development of young (33- to 45-year old), homogeneous, and second-growth stands of coast redwood (Sequoia sempervirens) and Douglas-fir (Pseudotsuga menziesii). Targeting both stand-level responses and dominant (focal) tree responses for analysis, we compared structural attributes of adjacent thinned and unthinned stands, 12–17 years after thinning. Thinned stands displayed enhanced metrics of tree vigor, growth, and mechanical stability, thereby improving response to future restoration treatments and broadening the range of potential stand conditions. We conclude that early-stage thinning has been successful as a preliminary restoration treatment because it accomplished many initial goals of forest restoration, while retaining sufficient tree numbers to buffer against possible attrition from future disturbances

Molecular dynamics simulations of the intrinsically disordered protein amelogenin

Amelogenin refers to a class of intrinsically disordered proteins that are the major constituents of enamel matrix derivative (EMD), an extract of porcine fetal teeth used in regenerative periodontal therapy. Modifications in molecular conformation induced by external stresses, such as changes in temperature or pH, are known to reduce the effectiveness of EMD. However, detailed descriptions of the conformational behavior of native amelogenin are lacking in the open literature. In the present work, a molecular model for the secondary and tertiary structure of the full-length major porcine amelogenin P173 was constructed from its primary sequence by replica exchange molecular dynamics (REMD) simulations. The REMD results for isolated amelogenin molecules at different temperatures were shown to be consistent with the available spectroscopic data. They therefore represent an important first step toward the simulation of the intra- and intermolecular interactions that mediate self-organization in amelogenin and its behavior in the presence of other EMD components under conditions representative of its therapeutic application

Semiaromatic polyamides with enhanced charge carrier mobility

The control of local order in polymer semiconductors using non-covalent interactions may be used to engineer materials with interesting combinations of mechanical and optoelectronic properties. To investigate the possibility of preparing n-type polymer semiconductors in which hydrogen bonding plays an important role in structural order and stability, we have used solution-phase polycondensation to incorporate dicyanoperylene bisimide repeat units into an aliphatic polyamide chain backbone. The morphology and thermomechanical characteristics of the resulting polyamides, in which the aliphatic spacer length was varied systematically, were comparable with those of existing semiaromatic engineering polyamides. At the same time, the charge carrier mobility as determined by pulse-radiolysis time-resolved microwave conductivity measurements was found to be about 10-2 cm2 V-1 s-1, which is similar to that reported for low molecular weight perylene bisimides. Our results hence demonstrate that it is possible to use hydrogen bonding interactions as a means to introduce promising optoelectronic properties into high-performance engineering polymers.Peer ReviewedPostprint (author's final draft

Thermal and dynamic mechanical properties of blends of bitumen with metallocene catalyzed polyolefins

A high penetration grade bitumen has been blended with up to 50 wt% of two different grades of metallocene catalyzed linear low density polyethylene (m-LLDPE) in order to investigate the potential of these and similar copolymers as a substitute for styrene butadiene styrene triblock copolymers in polymer-modified bitumens (PMB). A continuous polymer-rich phase was observed at m-LLDPE contents as low as 5-10 wt%, along with a significant decrease in the effective glass transition temperature of the PMBs with increasing polymer concentration, suggesting benefits for low temperature flexibility. The m-LLDPE-based PMBs also showed relatively low dynamic shear viscosities up to high polymer contents in the range of temperature and shear rate corresponding to typical PMB processing conditions. However, the presence of bitumen in the m-LLDPE-rich phase led to a significant reduction in the melting points of the m-LLDPE, and softening of the PMBs at temperatures as low as 40-50 degrees C, depending on the composition and the melting point of the pure polymer. PMBs based on the m-LLDPE with the higher melting point remained fully elastic in this temperature range, but at the expense of increased crystallinity and a higher glass transition temperature, which limit improvements in low temperature flexibility. On the other hand, the potentially broad composition and property windows associated with m-LLDPEs suggest considerable scope for the fine tuning of PMB properties by using combinations of different m-LLDPEs and/or other polyolefins as a means to optimize performance

Oncogenic Features in Histologically Normal Mucosa: Novel Insights Into Field Effect From a Mega-Analysis of Colorectal Transcriptomes

Introduction: Colorectal cancer is a common malignancy that can be cured when detected early, but recurrence among survivors is a persistent risk. A field effect of cancer in the colon has been reported and could have implications for surveillance, but studies to date have been limited. A joint analysis of pooled transcriptomic data from all available bulk RNA-sequencing data sets of healthy, histologically normal tumor-adjacent, and tumor tissues was performed to provide an unbiased assessment of field effect. Methods: A novel bulk RNA-sequencing data set from biopsies of nondiseased colon from screening colonoscopy along with published data sets from the Genomic Data Commons and Sequence Read Archive were considered for inclusion. Analyses were limited to samples with a quantified read depth of at least 10 million reads. Transcript abundance was estimated with Salmon, and downstream analysis was performed in R. Results: A total of 1,139 samples were analyzed in 3 cohorts. The primary cohort consisted of 834 independent samples from 8 independent data sets, including 462 healthy, 61 tumor-adjacent, and 311 tumor samples. Tumor-adjacent gene expression was found to represent an intermediate state between healthy and tumor expression. Among differentially expressed genes in tumor-adjacent samples, 1,143 were expressed in patterns similar to tumor samples, and these genes were enriched for cancer-associated pathways. Discussion: Novel insights into the field effect in colorectal cancer were generated in this mega-analysis of the colorectal transcriptome. Oncogenic features that might help explain metachronous lesions in cancer survivors and could be used for surveillance and risk stratification were identified

Biodegradable polylactide/hydroxyapatite nanocomposite foam scaffolds for bone tissue engineering applications

Supercritical carbon dioxide processing of poly--lactide (PLLA)/hydroxyapatite (nHA) nanocomposites was investigated as a means to prepare foams suitable as scaffolds in bone tissue engineering applications. For given foaming parameters, addition of nHA to the PLLA gave reduced cell sizes and improved homogeneity in the size distribution, but did not significantly affect the degree of crystallinity, which remained of the order of 50 wt% in all the foams. The compressive modulus and strength were primarily influenced by the porosity and there was no significant reinforcement of the matrix by the nHA. The mechanical properties of the foams were nevertheless comparable with those of trabecular bone, and by adjusting the saturation pressure and depressurization rate it was possible to generate porosities of about 85 %, an interconnected morphology and cell diameters in the range 200-400 mu m from PLLA containing 4.17 vol% nHA, satisfying established geometrical requirements for bone replacement scaffolds

Extracellular superoxide production by key microbes in the global ocean

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sutherland, K. M., Coe, A., Gast, R. J., Plummer, S., Suffridge, C. P., Diaz, J. M., Bowman, J. S., Wankel, S. D., & Hansel, C. M. Extracellular superoxide production by key microbes in the global ocean. Limnology and Oceanography, (2019), doi:10.1002/lno.11247.Bacteria and eukaryotes produce the reactive oxygen species superoxide both within and outside the cell. Although superoxide is typically associated with the detrimental and sometimes fatal effects of oxidative stress, it has also been shown to be involved in a range of essential biochemical processes, including cell signaling, growth, differentiation, and defense. Light‐independent extracellular superoxide production has been shown to be widespread among many marine heterotrophs and phytoplankton, but the extent to which this trait is relevant to marine microbial physiology and ecology throughout the global ocean is unknown. Here, we investigate the dark extracellular superoxide production of five groups of organisms that are geographically widespread and represent some of the most abundant organisms in the global ocean. These include Prochlorococcus, Synechococcus, Pelagibacter, Phaeocystis, and Geminigera. Cell‐normalized net extracellular superoxide production rates ranged seven orders of magnitude, from undetectable to 14,830 amol cell−1 h−1, with the cyanobacterium Prochlorococcus being the lowest producer and the cryptophyte Geminigera being the most prolific producer. Extracellular superoxide production exhibited a strong inverse relationship with cell number, pointing to a potential role in cell signaling. We demonstrate that rapid, cell‐number–dependent changes in the net superoxide production rate by Synechococcus and Pelagibacter arose primarily from changes in gross production of extracellular superoxide, not decay. These results expand the relevance of dark extracellular superoxide production to key marine microbes of the global ocean, suggesting that superoxide production in marine waters is regulated by a diverse suite of marine organisms in both dark and sunlit waters.The authors would like to acknowledge their funding sources including NASA NESSF NNX15AR62H (K.M.S.), NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., NSF‐OCE grant 1355720 to C.M.H., NSF‐OPP 1641019 (J.S.B), and Simons Foundation SCOPE Award ID 329108 (Sallie W. Chisholm). The authors would also like to thank the Harvey lab (Skidaway Institute of Oceanography) for use of their flow cytometer in this study. We thank Stephen Giovannoni and Sallie Chisholm for providing bacteria strains and laboratory facilities. Additional thanks to Marianne Acker, Rogier Braakman, and Aldo Arellano for assistance in lab and helpful conversations

Novel approach to observing system simulation experiments improves information gain of surface-atmosphere field measurements

The observing system design of multidisciplinary field measurements involves a variety of considerations on logistics, safety, and science objectives. Typically, this is done based on investigator intuition and designs of prior field measurements. However, there is potential for considerable increases in efficiency, safety, and scientific success by integrating numerical simulations in the design process. Here, we present a novel numerical simulation-environmental response function (NS-ERF) approach to observing system simulation experiments that aids surface-atmosphere synthesis at the interface of mesoscale and microscale meteorology. In a case study we demonstrate application of the NS-ERF approach to optimize the Chequamegon Heterogeneous Ecosystem Energy-balance Study Enabled by a High-density Extensive Array of Detectors 2019 (CHEESEHEAD19). During CHEESEHEAD19 pre-field simulation experiments, we considered the placement of 20 eddy covariance flux towers, operations for 72h of low-altitude flux aircraft measurements, and integration of various remote sensing data products. A 2h high-resolution large eddy simulation created a cloud-free virtual atmosphere for surface and meteorological conditions characteristic of the field campaign domain and period. To explore two specific design hypotheses we super-sampled this virtual atmosphere as observed by 13 different yet simultaneous observing system designs consisting of virtual ground, airborne, and satellite observations. We then analyzed these virtual observations through ERFs to yield an optimal aircraft flight strategy for augmenting a stratified random flux tower network in combination with satellite retrievals. We demonstrate how the novel NS-ERF approach doubled CHEESEHEAD19's potential to explore energy balance closure and spatial patterning science objectives while substantially simplifying logistics. Owing to its modular extensibility, NS-ERF lends itself to optimizing observing system designs also for natural climate solutions, emission inventory validation, urban air quality, industry leak detection, and multi-species applications, among other use cases. © 2021 Stefan Metzger et al

Consonance perception beyond the traditional existence region of pitch

Some theories posit that the perception of consonance is based on neural periodicity detection, which is dependent on accurate phase locking of auditory nerve fibers to features of the stimulus waveform. In the current study, 15 listeners were asked to rate the pleasantness of complex tone dyads (2 note chords) forming various harmonic intervals and bandpass filtered in a high-frequency region (all components >5.8 kHz), where phase locking to the rapid stimulus fine structure is thought to be severely degraded or absent. The two notes were presented to opposite ears. Consonant intervals (minor third and perfect fifth) received higher ratings than dissonant intervals (minor second and tritone). The results could not be explained in terms of phase locking to the slower waveform envelope because the preference for consonant intervals was higher when the stimuli were harmonic, compared to a condition in which they were made inharmonic by shifting their component frequencies by a constant offset, so as to preserve their envelope periodicity. Overall the results indicate that, if phase locking is indeed absent at frequencies greater than ∼5 kHz, neural periodicity detection is not necessary for the perception of consonance