Eighty years of food-web response to interannual variation in discharge recorded in river diatom frustules from an ocean sediment core.

Little is known about the importance of food-web processes as controls of river primary production due to the paucity of both long-term studies and of depositional environments which would allow retrospective fossil analysis. To investigate how freshwater algal production in the Eel River, northern California, varied over eight decades, we quantified siliceous shells (frustules) of freshwater diatoms from a well-dated undisturbed sediment core in a nearshore marine environment. Abundances of freshwater diatom frustules exported to Eel Canyon sediment from 1988 to 2001 were positively correlated with annual biomass of Cladophora surveyed over these years in upper portions of the Eel basin. Over 28 years of contemporary field research, peak algal biomass was generally higher in summers following bankfull, bed-scouring winter floods. Field surveys and experiments suggested that bed-mobilizing floods scour away overwintering grazers, releasing algae from spring and early summer grazing. During wet years, growth conditions for algae could also be enhanced by increased nutrient loading from the watershed, or by sustained summer base flows. Total annual rainfall and frustule densities in laminae over a longer 83-year record were weakly and negatively correlated, however, suggesting that positive effects of floods on annual algal production were primarily mediated by "top-down" (consumer release) rather than "bottom-up" (growth promoting) controls

Linking Scales in Stream Ecology

The hierarchical structure of natural systems can be useful in designing ecological studies that are informative at multiple spatial scales. Although stream systems have long been recognized as having a hierarchical spatial structure, there is a need for more empirical research that exploits this structure to generate an understanding of population biology, community ecology, and species-ecosystem linkages across spatial scales. We review studies that link pattern and process across multiple scales of stream-habitat organization, highlighting the insight derived from this multiscale approach and the role that mechanistic hypotheses play in its successful application. We also describe afrontier in stream research that relies on this multiscale approach: assessing the consequences and mechanisms of ecological processes occurring at the network scale. Broader use of this approach will advance many goals in applied stream ecology, including the design of reserves to protect stream biodiversity and the conservation of freshwater resources and services

Preparedness for eHealth: Health sciences students' knowledge, skills, and confidence

There is increasing recognition of the role eHealth will play in the effective and efficient delivery of healthcare. This research challenges the assumption that students enter university as digital natives, able to confidently and competently adapt their use of information and communication technology (ICT) to new contexts. This study explored health sciences students' preparedness for working, and leading change, in eHealth-enabled environments. Using a cross-sectional study design, 420 undergraduate and postgraduate students participated in an online survey investigating their understanding of and attitude towards eHealth, frequency of online activities and software usage, confidence learning and using ICTs, and perceived learning needs. Although students reported that they regularly engaged with a wide range of online activities and software and were confident learning new ICT skills especially where they have sufficient time or support, their understanding of eHealth was uncertain or limited. Poor understanding of and difficulty translating skills learned in personal contexts to the professional context may impair graduates ability to confidently engage in the eHealth-enabled workplace. These results suggest educators need to scaf-fold the learning experience to ensure students build on their ICT knowledge to transfer this to their future workplaces

HTA: A Scalable High-Throughput Accelerator for Irregular HPC Workloads

We propose a new architecture called HTA for high throughput irregular HPC applications with little data reuse. HTA reduces the contention within the memory system with the help of a partitioned memory controller that is amenable for 2.5D implementation using Silicon Photonics. In terms of scalability, HTA supports 4 × higher number of compute units compared to the state-of-the-art GPU systems. Our simulation-based evaluation on a representative set of HPC benchmarks shows that the proposed design reduces the queuing latency by 10% to 30%, and improves the variability in memory access latency by 10% to 60%. Our results show that the HTA improves the L1 miss penalty by 2.3 × to 5 × over GPUs. When compared to a multi-GPU system with the same number of compute units, our simulation results show that the HTA can provide up to 2 × speedup

Degradation of the plant defense signal salicylic acid protects Ralstonia solanacearum from toxicity and enhances virulence on tobacco

Plants use the signaling molecule salicylic acid (SA) to trigger defenses against diverse pathogens, including the bacterial wilt pathogen Ralstonia solanacearum. SA can also inhibit microbial growth. Most sequenced strains of the heterogeneous R. solanacearum species complex can degrade SA via gentisic acid to pyruvate and fumarate. R. solanacearum strain GMI1000 expresses this SA degradation pathway during tomato pathogenesis. Transcriptional analysis revealed that subinhibitory SA levels induced expression of the SA degradation pathway, toxin efflux pumps, and some general stress responses. Interestingly, SA treatment repressed expression of virulence factors, including the type III secretion system, suggesting that this pathogen may suppress virulence functions when stressed. A GMI1000 mutant lacking SA degradation activity was much more susceptible to SA toxicity but retained the wild-type colonization ability and virulence on tomato. This may be because SA is less important than gentisic acid in tomato defense signaling. However, another host, tobacco, responds strongly to SA. To test the hypothesis that SA degradation contributes to virulence on tobacco, we measured the effect of adding this pathway to the tobacco-pathogenic R. solanacearum strain K60, which lacks SA degradation genes. Ectopic addition of the GMI1000 SA degradation locus, including adjacent genes encoding two porins and a LysR-type transcriptional regulator, significantly increased the virulence of strain K60 on tobacco. Together, these results suggest that R. solanacearum degrades plant SA to protect itself from inhibitory levels of this compound and also to enhance its virulence on plant hosts like tobacco that use SA as a defense signal molecule. (Résumé d'auteur

A generation of junior faculty is at risk from the impacts of COVID-19

For junior investigators starting their independent careers, the challenges of the Coronavirus Disease 2019 (COVID-19) pandemic extend beyond lost time and are career threatening. Without intervention, academic science could lose a generation of talent

Implications for oxidative stress and astrocytes following 26S proteasomal depletion in mouse forebrain neurones

Neurodegenerative diseases are characterized by progressive degeneration of selective neurones in the nervous system, but the underlying mechanisms involved in neuroprotection and neurodegeneration remain unclear. Dysfunction of the ubiquitin proteasome system is one of the proposed hypotheses for the cause and progression of neuronal loss. We have performed quantitative two-dimensional fluorescence difference in-gel electrophoresis combined with peptide mass fingerprinting to reveal proteome changes associated with neurodegeneration following 26S proteasomal depletion in mouse forebrain neurones. Differentially expressed proteins were validated by Western blotting, biochemical assays and immunohistochemistry. Of significance was increased expression of the antioxidant enzyme peroxiredoxin 6 (PRDX6) in astrocytes, associated with oxidative stress. Interestingly, PRDX6 is a bifunctional enzyme with antioxidant peroxidase and phospholipase A2 (PLA2) activities. The PLA2 activity of PRDX6 was also increased following 26S proteasomal depletion and may be involved in neuroprotective or neurodegenerative mechanisms. This is the first in vivo report of oxidative stress caused directly by neuronal proteasome dysfunction in the mammalian brain. The results contribute to understanding neuronal–glial interactions in disease pathogenesis, provide an in vivo link between prominent disease hypotheses and importantly, are of relevance to a heterogeneous spectrum of neurodegenerative diseases

LLM: Realizing Low-Latency Memory by Exploiting Embedded Silicon Photonics for Irregular Workloads

As emerging workloads exhibit irregular memory access patterns with poor data reuse and locality, they would benefit from a DRAM that achieves low latency without sacrificing bandwidth and energy efficiency. We propose LLM (Low Latency Memory), a codesign of the DRAM microarchitecture, the memory controller and the LLC/DRAM interconnect by leveraging embedded silicon photonics in 2.5D/3D integrated system on chip. LLM relies on Wavelength Division Multiplexing (WDM)-based photonic interconnects to reduce the contention throughout the memory subsystem. LLM also increases the bank-level parallelism, eliminates bus conflicts by using dedicated optical data paths, and reduces the access energy per bit with shorter global bitlines and smaller row buffers. We evaluate the design space of LLM for a variety of synthetic benchmarks and representative graph workloads on a full-system simulator (gem5). LLM exhibits low memory access latency for traffics with both regular and irregular access patterns. For irregular traffic, LLM achieves high bandwidth utilization (over 80% peak throughput compared to 20% of HBM2.0). For real workloads, LLM achieves 3 × and 1.8 × lower execution time compared to HBM2.0 and a state-of-the-art memory system with high memory level parallelism, respectively. This study also demonstrates that by reducing queuing on the data path, LLM can achieve on average 3.4 × lower memory latency variation compared to HBM2.0

Forecasting tillage and soil warming effects on earthworm populations

1. Healthy soils are crucial for sustainable food production, but tillage limits the biological regulation of essential ecosystem services. Better understanding of the mechanisms driving management effects on soil ecosystem engineers is needed to support sustainable management under environmental change. 2. This paper presents the EEEworm (Energy–Environment–Earthworm) model, a mechanistic individual-based model (IBM) of Lumbricus terrestris populations. L. terrestris is a dominant earthworm species in undisturbed habitats and is closely associated with numerous ecosystem services such as water flow regulation, soil structure and crop production. In reduced tillage agriculture a decline in mechanical disturbance allows for L. terrestris proliferation, whilst the activities of L. terrestris can replace many of the soil functions provided by tillage. 3. Extensive EEEworm validation with eight published studies (average R2 = 0.84) demonstrates a mechanistic approach which can extrapolate between diverse soil, management and weather conditions. EEEworm simulation experiments elucidate that a combination of direct and indirect tillage effects lead to population declines in tilled fields, with litter removal from the soil surface being the main driver. 4. We investigate the effects of different tillage intensities under historical and projected soil warming conditions, and find that future warmer and drier soils in our simulation exacerbate the effects of deep ploughing on L. terrestris population declines. These effects result from warmer and drier soil conditions increasing individual metabolic rates and tillage reducing food availability to meet energy demands. 5. Synthesis and applications. Pre-emptive strategies to mitigate climate change impacts on soil health in agroecosystems should focus on decreasing tillage intensity and retention of crop residues following tillage. EEEworm has the potential to benefit land managers, policy makers, risk assessors and regulators by providing a tool to forecast how soil systems respond to combinations of land management and environmental change. To allow better cost-benefit analysis of contrasting land management systems a future aim of mechanistic models like EEEworm is to incorporate the links between earthworm populations, soil functions and ecosystem services