Neurogenesis Deep Learning

Neural machine learning methods, such as deep neural networks (DNN), have achieved remarkable success in a number of complex data processing tasks. These methods have arguably had their strongest impact on tasks such as image and audio processing - data processing domains in which humans have long held clear advantages over conventional algorithms. In contrast to biological neural systems, which are capable of learning continuously, deep artificial networks have a limited ability for incorporating new information in an already trained network. As a result, methods for continuous learning are potentially highly impactful in enabling the application of deep networks to dynamic data sets. Here, inspired by the process of adult neurogenesis in the hippocampus, we explore the potential for adding new neurons to deep layers of artificial neural networks in order to facilitate their acquisition of novel information while preserving previously trained data representations. Our results on the MNIST handwritten digit dataset and the NIST SD 19 dataset, which includes lower and upper case letters and digits, demonstrate that neurogenesis is well suited for addressing the stability-plasticity dilemma that has long challenged adaptive machine learning algorithms.Comment: 8 pages, 8 figures, Accepted to 2017 International Joint Conference on Neural Networks (IJCNN 2017

Set‐Based Design and the Ship to Shore Connector

The Ship to Shore Connector (SSC), a replacement for the Landing Craft, Air Cushion (LCAC), is the first government‐led design of a ship in over 15 years. This paper will discuss the changes that a government‐led design presents to the design approach, including schedule, organization structure, and design methodology. While presenting challenges, a government‐led design also afforded the opportunity to implement a new technique for assessing various systems and ship alternatives, set‐based design (SBD). The necessity for implementing SBD was the desire to design SSC from a blank sheet of paper and the need for a replacement craft in a short time frame. That is, the LCACs need to be replaced and consequently the preliminary design phase of the SSC program will only be 12 months. This paper will describe SBD and how it was applied to the SSC, the challenges that the program faced, and an assessment of the new methodology, along with recommendations that future design programs should consider when adopting this approach.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90054/1/j.1559-3584.2011.00332.x.pd

Different carboxyl-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Liu, S., Parsons, R., Opalk, K., Baetge, N., Giovannoni, S., Bolanos, L. M., Kujawinski, E. B., Longnecker, K., Lu, Y., Halewood, E., & Carlson, C. A. Different carboxyl-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea. Limnology and Oceanography, (2020), doi:10.1002/lno.11405.Marine dissolved organic matter (DOM) varies in its recalcitrance to rapid microbial degradation. DOM of varying recalcitrance can be exported from the ocean surface to depth by subduction or convective mixing and oxidized over months to decades in deeper seawater. Carboxyl‐rich alicyclic molecules (CRAM) are characterized as a major component of recalcitrant DOM throughout the oceanic water column. The oxidation of CRAM‐like compounds may depend on specific bacterioplankton lineages with oxidative enzymes capable of catabolizing complex molecular structures like long‐chain aliphatics, cyclic alkanes, and carboxylic acids. To investigate the interaction between bacteria and CRAM‐like compounds, we conducted microbial remineralization experiments using several compounds rich in carboxyl groups and/or alicyclic rings, including deoxycholate, humic acid, lignin, and benzoic acid, as proxies for CRAM. Mesopelagic seawater (200 m) from the northwest Sargasso Sea was used as media and inoculum and incubated over 28 d. All amendments demonstrated significant DOC removal (2–11 μmol C L−1) compared to controls. Bacterioplankton abundance increased significantly in the deoxycholate and benzoic acid treatments relative to controls, with fast‐growing Spongiibacteracea, Euryarcheaota, and slow‐growing SAR11 enriched in the deoxycholate treatment and fast‐growing Alteromonas, Euryarcheaota, and Thaumarcheaota enriched in the benzoic acid treatment. In contrast, bacterioplankton grew slower in the lignin and humic acid treatments, with oligotrophic SAR202 becoming significantly enriched in the lignin treatment. Our results indicate that the character of the CRAM proxy compounds resulted in distinct bacterioplankton removal rates of DOM and affected specific lineages of bacterioplankton capable of responding.We thank Z. Landry for the inspiring idea of SAR202 catabolism of CRAM. We thank the University of California, Santa Barbara Marine Science Institute Analytical Laboratory for analyzing inorganic nutrient samples. We thank C. Johnson for her help in FISH sample processing and BATS group in supporting our project. We thank N. K. Rubin‐Saika and R. Padula for their help with amino acid sample preparation. We thank Z. Liu, J. Xue, K. Lu, and Y. Shen for their help with amino acid protocol development and validation. We thank B. Stephens for his help on microscopic image analysis. We thank M. Dasenko and the staff of the CGRB at Oregon State University for amplicon library preparation and DNA sequencing. We are grateful for the help provided by the officers and crews of the R/V Atlantic Explorer. Bermuda Institute of Ocean Sciences (BIOS) provides us tremendous support in terms of facilities and lab space. We thank Bermuda government for its allowance of our water sampling and sample export (export permit number SP160904, issued 07 October 2016 under the Fisheries Act, 1972). This project was supported by Simons Foundation International's BIOS‐SCOPE program

A Digital Neuromorphic Architecture Efficiently Facilitating Complex Synaptic Response Functions Applied to Liquid State Machines

Information in neural networks is represented as weighted connections, or synapses, between neurons. This poses a problem as the primary computational bottleneck for neural networks is the vector-matrix multiply when inputs are multiplied by the neural network weights. Conventional processing architectures are not well suited for simulating neural networks, often requiring large amounts of energy and time. Additionally, synapses in biological neural networks are not binary connections, but exhibit a nonlinear response function as neurotransmitters are emitted and diffuse between neurons. Inspired by neuroscience principles, we present a digital neuromorphic architecture, the Spiking Temporal Processing Unit (STPU), capable of modeling arbitrary complex synaptic response functions without requiring additional hardware components. We consider the paradigm of spiking neurons with temporally coded information as opposed to non-spiking rate coded neurons used in most neural networks. In this paradigm we examine liquid state machines applied to speech recognition and show how a liquid state machine with temporal dynamics maps onto the STPU-demonstrating the flexibility and efficiency of the STPU for instantiating neural algorithms.Comment: 8 pages, 4 Figures, Preprint of 2017 IJCN

Seasonality of the Microbial Community Composition in the North Atlantic

Planktonic communities constitute the basis of life in marine environments and have profound impacts in geochemical cycles. In the North Atlantic, seasonality drives annual transitions in the ecology of the water column. Phytoplankton bloom annually in spring as a result of these transitions, creating one of the major biological pulses in productivity on earth. The timing and geographical distribution of the spring bloom as well as the resulting biomass accumulation have largely been studied using the global capacity of satellite imaging. However, fine-scale variability in the taxonomic composition, spatial distribution, seasonal shifts, and ecological interactions with heterotrophic bacterioplankton has remained largely uncharacterized. The North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) conducted four meridional transects to characterize plankton ecosystems in the context of the annual bloom cycle. Using 16S rRNA gene-based community profiles we analyzed the temporal and spatial variation in plankton communities. Seasonality in phytoplankton and bacterioplankton composition was apparent throughout the water column, with changes dependent on the hydrographic origin. From winter to spring in the subtropic and subpolar subregions, phytoplankton shifted from the predominance of cyanobacteria and picoeukaryotic green algae to diverse photosynthetic eukaryotes. By autumn, the subtropics were dominated by cyanobacteria, while a diverse array of eukaryotes dominated the subpolar subregions. Bacterioplankton were also strongly influenced by geographical subregions. SAR11, the most abundant bacteria in the surface ocean, displayed higher richness in the subtropics than the subpolar subregions. SAR11 subclades were differentially distributed between the two subregions. Subclades Ia.1 and Ia.3 co-occurred in the subpolar subregion, while Ia.1 dominated the subtropics. In the subtropical subregion during the winter, the relative abundance of SAR11 subclades "II" and 1c.1 were elevated in the upper mesopelagic. In the winter, SAR202 subclades generally prevalent in the bathypelagic were also dominant members in the upper mesopelagic zones. Co-varying network analysis confirmed the large-scale geographical organization of the plankton communities and provided insights into the vertical distribution of bacterioplankton. This study represents the most comprehensive survey of microbial profiles in the western North Atlantic to date, revealing stark seasonal differences in composition and richness delimited by the biogeographical distribution of the planktonic communities

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).

Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci

Efficacy of tetroxoprim/sulphadiazine in the treatment of Pneumocystis cannii pneumonitis in rats

Pneumocystis carinii pneumonitis was induced using dexamethasone in male Sprague-Dawley rats. After the first death due to Pn. carinii occurred, nine rats received 50mg/kg/day tetroxoprim and 120mg/kg/day sulphadiazdne. Four additional rats were given no therapy and served as a positive control. All the surviving rats including five negative controls were sacrificed four weeks after the last positive control rat died. All four rats in the positive control group and two of nine in the treated group developed Pn. carinii pneumonitis, whereas none of the five negative controls had evidence of Pn. carinii infection. The difference between the treated and untreated rats was significant (P=0-05). These results suggest that combination therapy with tetroxoprim/sulphadiazine is effective in the treatment of Pn. carinii pneumonitis in this animal model

Migratory zooplankton excreta and its influence on prokaryotic communities

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Maas, A. E., Liu, S., Bolanos, L. M., Widner, B., Parsons, R., Kujawinski, E. B., Blanco-Bercial, L., & Carlson, C. A. Migratory zooplankton excreta and its influence on prokaryotic communities. Frontiers in Marine Science, 7, (2020): 573268, doi:10.3389/fmars.2020.573268.Particulate organic matter (POM) (fecal pellets) from zooplankton has been demonstrated to be an important nutrient source for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12–16 h of incubation. We measured bulk dissolved organic carbon (DOC), dissolved free amino acids (DFAA) via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins, and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200 m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16S rRNA gene amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.Funding for this research was provided by Simons Foundation International as part of the BIOS-SCOPE project to AM, LB-B, CC, and EK

The Seasonal Flux and Fate of Dissolved Organic Carbon Through Bacterioplankton in the Western North Atlantic

The oceans teem with heterotrophic bacterioplankton that play an appreciable role in the uptake of dissolved organic carbon (DOC) derived from phytoplankton net primary production (NPP). As such, bacterioplankton carbon demand (BCD), or gross heterotrophic production, represents a major carbon pathway that influences the seasonal accumulation of DOC in the surface ocean and, subsequently, the potential vertical or horizontal export of seasonally accumulated DOC. Here, we examine the contributions of bacterioplankton and DOM to ecological and biogeochemical carbon flow pathways, including those of the microbial loop and the biological carbon pump, in the Western North Atlantic Ocean (∼39–54°N along ∼40°W) over a composite annual phytoplankton bloom cycle. Combining field observations with data collected from corresponding DOC remineralization experiments, we estimate the efficiency at which bacterioplankton utilize DOC, demonstrate seasonality in the fraction of NPP that supports BCD, and provide evidence for shifts in the bioavailability and persistence of the seasonally accumulated DOC. Our results indicate that while the portion of DOC flux through bacterioplankton relative to NPP increased as seasons transitioned from high to low productivity, there was a fraction of the DOM production that accumulated and persisted. This persistent DOM is potentially an important pool of organic carbon available for export to the deep ocean via convective mixing, thus representing an important export term of the biological carbon pump

Singlet Portal to the Hidden Sector

Ultraviolet physics typically induces a kinetic mixing between gauge singlets which is marginal and hence non-decoupling in the infrared. In singlet extensions of the minimal supersymmetric standard model, e.g. the next-to-minimal supersymmetric standard model, this furnishes a well motivated and distinctive portal connecting the visible sector to any hidden sector which contains a singlet chiral superfield. In the presence of singlet kinetic mixing, the hidden sector automatically acquires a light mass scale in the range 0.1 - 100 GeV induced by electroweak symmetry breaking. In theories with R-parity conservation, superparticles produced at the LHC invariably cascade decay into hidden sector particles. Since the hidden sector singlet couples to the visible sector via the Higgs sector, these cascades necessarily produce a Higgs boson in an order 0.01 - 1 fraction of events. Furthermore, supersymmetric cascades typically produce highly boosted, low-mass hidden sector singlets decaying visibly, albeit with displacement, into the heaviest standard model particles which are kinematically accessible. We study experimental constraints on this broad class of theories, as well as the role of singlet kinetic mixing in direct detection of hidden sector dark matter. We also present related theories in which a hidden sector singlet interacts with the visible sector through kinetic mixing with right-handed neutrinos.Comment: 12 pages, 5 figure