Evolving Through the Looking Glass: Learning Improved Search Spaces with Variational Autoencoders

Nature has spent billions of years perfecting our genetic representations, making them evolvable and expressive. Generative machine learning offers a shortcut: learn an evolvable latent space with implicit biases towards better solutions. We present SOLVE: Search space Optimization with Latent Variable Evolution, which creates a dataset of solutions that satisfy extra problem criteria or heuristics, generates a new latent search space, and uses a genetic algorithm to search within this new space to find solutions that meet the overall objective. We investigate SOLVE on five sets of criteria designed to detrimentally affect the search space and explain how this approach can be easily extended as the problems become more complex. We show that, compared to an identical GA using a standard representation, SOLVE with its learned latent representation can meet extra criteria and find solutions with distance to optimal up to two orders of magnitude closer. We demonstrate that SOLVE achieves its results by creating better search spaces that focus on desirable regions, reduce discontinuities, and enable improved search by the genetic algorithm. Fig. 1.Search space Optimization with Latent Variable Evolution (SOLVE). An optimizer produces a dataset of random solutions satisfying an extra criterion (e.g., constraint or secondary objective). A variational autoencoder learns this dataset and produces a learned latent representation biased towards the desired region of the search space. This learned representation is then used by a genetic algorithm to find solutions that meet the objective and extra criterion together

Myxomycetes recorded from three lowland tropical forests in Vietnam

Abstract The first report of myxomycetes from Vietnam was in 2009 by van Hooff, who listed 23 species, including one (Cribraria tecta) new to science, from moist chamber cultures prepared with samples of dead leaves, lychee husks, woody twigs and herbaceous stems. Two other species, both new to science, were reported in a recent paper. The project reported herein investigated the occurrence of myxomycetes in moist chamber cultures prepared with samples of various types of dead plant material collected in three lowland tropical forests in Vietnam. These samples were randomly collected from Cuc Phuong, Bu Gia Map and Nam Cat Tien national parks in the late dry season or between the dry season and the rainy season during 2012 and 2013. From 360 moist chambers, 43 species of myxomycetes representing 19 genera were recorded. The most abundant species were Arcyria cinerea, Collaria arcyrionema, Cribraria microcarpa, Cribraria violacea, Perichaena chrysosperma and Perichaena depressa. The taxonomic composition of the assemblage of species associated with the three study areas was found to be similar to what has been reported from Laos, Myanmar and Thailand, the other regions of SE Asia for which comparable studies have been carried out. In brief, the present project added 32 new records of myxomycetes for Vietnam, increasing the total number of species known from the country to 57

Phytophthora antagonism of endophytic bacteria isolated from roots of black pepper (Piper nigrum L.).

[[abstract]]Abstract: In this study, 90 root samples were collected from 30 black pepper farms in three provinces in the Central Highlands of Vietnam. A total of 352 endophytic bacteria were isolated and their morphology described. An in vitro assay on the ntifungal activity of these isolates was then conducted and 47 isolates were found to have antagonistic activity on Phytophthora fungi. The antifungal activity of the 47 isolates was evaluated in vivo by shoot assay. Among these 47 isolates, 6 were selected for further investigation. The six isolates were classified and identified by sequencing the 16S RNA gene and phylogeny. The results showed that all six endophytic bacteria belong to the following species of Bacillus genus: B. siamensis, B. amyloliquefaciens, B. velezenis, and B. methylotrophiycus. Enzymatic activity related to the antifungal activity of the six potent isolates was determined; it showed that they possessed high chitinase and protease activities. These isolates were applied for black pepper seedlings in greenhouse. The results showed three promising isolates: B. siamensis EB.CP6, B. velezensis EB.KN12, and B. methylotrophycus EB.KN13. Black pepper seedlings treated with the promising bacteria had the lowest rate of root disease (8.45–11.21%) and lower fatal rate (11.11–15.55%) compared to the control group (24.81% and 24.44%). In addition, the three promising isolates strongly affected the growth of the black pepper seedlings in greenhouse. The plant height, length of roots, and fresh biomass of the seedlings in the treated plots were higher than those in the control plots. Thus, the endophytic bacterial isolates have the potential to act as biocontrol agent for the sustainable production of black pepper.[[sponsorship]]科技部[[notice]]補正完

Oxidation kinetics of hercynite spinels for solar thermochemical fuel production

The development of an economically viable solar thermochemical fuel production process relies largely on identifying redox active materials with optimized thermodynamic and kinetic properties. Iron aluminate (FeAl2O4, hercynite) and cobalt-iron aluminate (CoxFe1-xAl2O4) have both been demonstrated as viable redox-active materials for this process. However, doping with cobalt creates a tradeoff between the thermodynamics and kinetics of H2 production mediated by hercynite in which the kinetics are improved at the expense of lowering the yield. In this work, we evaluate four spinel aluminate materials with varying cobalt contents (FeAl2O4, Co0.05Fe0.95Al2O4, Co0.25Fe0.75Al2O4, and Co0.40Fe0.60Al2O4) to better understand the role of cobalt in the redox mediating properties of these materials and to quantify its effect on the thermodynamic and kinetic properties for CO2 reduction. A solid-state kinetic analysis was performed on each sample to model its CO2 reduction kinetics at temperatures ranging from 1200 °C to 1350 °C. An F1 model representative of first-order reaction kinetics was found to most accurately represent the experimental data for all materials evaluated. The computed rate constants, activation energies, and pre-exponential factors all increase with increasing cobalt content. High temperature in-situ XPS was utilized to characterize the spinel surfaces and indicated the presence of metallic states of the reduced cobalt-iron spinel, which are not present in un-doped hercynite. These species provide a new site for the CO2 reduction reaction and enhance its rate through an increased pre-exponential factor

Trypan Blue Dye Enters Viable Cells Incubated with the Pore-Forming Toxin HlyII of Bacillus cereus

Trypan blue is a dye that has been widely used for selective staining of dead tissues or cells. Here, we show that the pore-forming toxin HlyII of Bacillus cereus allows trypan blue staining of macrophage cells, despite the cells remaining viable and metabolically active. These findings suggest that the dye enters viable cells through the pores. To our knowledge, this is the first demonstration that trypan blue may enter viable cells. Consequently, the use of trypan blue staining as a marker of vital status should be interpreted with caution. The blue coloration does not necessarily indicate cell lysis, but may rather indicate pore formation in the cell membranes and more generally increased membrane permeability

Conversion of shrimp head waste for production of a thermotolerant, detergent-stable, alkaline protease by Paenibacillus sp.

[[abstract]]Fishery processing by-products have been of great interest to researchers due to their beneficial applications in many fields. In this study, five types of marine by-products, including demineralized crab shell, demineralized shrimp shell, shrimp head, shrimp shell, and squid pen, provided sources of carbon and nitrogen nutrition by producing a protease from Paenibacillus sp. TKU047. Strain TKU047 demonstrated the highest protease productivity (2.98 U/mL) when cultured for two days on a medium containing 0.5% of shrimp head powder (SHP). The mass of TKU047 protease was determined to be 32 kDa (approximately). TKU047 protease displayed optimal activity at 70–80 °C and pH 9, with a pH range of stability from 6 to 11. TKU047 protease also showed stability in solutions containing surfactants and detergents. Based on its excellent properties, Paenibacillus sp. TKU047 protease may be a feasible candidate for inclusion in laundry detergents.[[sponsorship]]MOST[[notice]]補正完

Distant X-ray Galaxies: Insights from the Local Population

A full understanding of the origin of the hard X-ray background requires a complete and accurate census of the distant galaxies that produce it. Unfortunately, distant X-ray galaxies tend to be very faint at all wavelengths, which hinders efforts to perform this census. This chapter discusses the insights that can be obtained through comparison of the distant population to local X-ray galaxies, whose properties are well characterized. Such comparisons will ultimately aid investigations into the cosmic evolution of supermassive black holes and their environments.Comment: 19 pages, 10 figures, to appear as Chapter 7 in "Supermassive Black Holes in the Distant Universe" (2004), ed. A. J. Barger, Kluwer Academic Publishers, in pres

An exochitinase with N-acetyl-β-glucosaminidase activity from shrimp heads conversion by Streptomyces speibonae and its application in hydrolyzing β-chitin powder to produce N-acetyl-d-glucosamine

[[abstract]]Marine chitinous byproducts possess significant applications in many fields. In this research, different kinds of fishery chitin-containing byproducts from shrimp (shrimp head powder (SHP) and demineralized shrimp shell powder), crab (demineralized crab shell powder), as well as squid (squid pen powder) were used to provide both carbon and nitrogen (C/N) nutrients for the production of an exochitinase via Streptomyces speibonae TKU048, a chitinolytic bacterium isolated from Taiwanese soils. S. speibonae TKU048 expressed the highest exochitinase productivity (45.668 U/mL) on 1.5% SHP-containing medium at 37 °C for 2 days. Molecular weight determination analysis basing on polyacrylamide gel electrophoresis revealed the mass of TKU048 exochitinase was approximately 21 kDa. The characterized exochitinase expressed some interesting properties, for example acidic pH optima (pH 3 and pH 5–7) and a higher temperature optimum (60 °C). Furthermore, the main hydrolysis mechanism of TKU048 exochitinase was N-acetyl-β-glucosaminidase-like activity; its most suitable substrate was β-chitin powder. The hydrolysis experiment revealed that TKU048 exochitinase was efficient in the cleavage of β-chitin powder, thereby releasing N-acetyl-d-glucosamine (GlcNAc, monomer unit of chitin structure) as the major product with 0.335 mg/mL of GlcNAc concentration and a yield of 73.64% after 96 h of incubation time. Thus, TKU048 exochitinase may have potential in GlcNAc production due to its N-acetyl-β-glucosaminidase-like activity.[[sponsorship]]科技部[[notice]]補正完

A massive, quiescent galaxy at redshift of z=3.717

In the early Universe finding massive galaxies that have stopped forming stars present an observational challenge as their rest-frame ultraviolet emission is negligible and they can only be reliably identified by extremely deep near-infrared surveys. These have revealed the presence of massive, quiescent early-type galaxies appearing in the universe as early as z$\sim$2, an epoch 3 Gyr after the Big Bang. Their age and formation processes have now been explained by an improved generation of galaxy formation models where they form rapidly at z$\sim$3-4, consistent with the typical masses and ages derived from their observations. Deeper surveys have now reported evidence for populations of massive, quiescent galaxies at even higher redshifts and earlier times, however the evidence for their existence, and redshift, has relied entirely on coarsely sampled photometry. These early massive, quiescent galaxies are not predicted by the latest generation of theoretical models. Here, we report the spectroscopic confirmation of one of these galaxies at redshift z=3.717 with a stellar mass of 1.7$\times$10$^{11}$ M$_\odot$ whose absorption line spectrum shows no current star-formation and which has a derived age of nearly half the age of the Universe at this redshift. The observations demonstrates that the galaxy must have quickly formed the majority of its stars within the first billion years of cosmic history in an extreme and short starburst. This ancestral event is similar to those starting to be found by sub-mm wavelength surveys pointing to a possible connection between these two populations. Early formation of such massive systems is likely to require significant revisions to our picture of early galaxy assembly.Comment: 6 pages, 7 figures. This is the final preprint corresponding closely to the published version. Uploaded 6 months after publication in accordance with Nature polic

Unbalanced Hybrid AOA/RSSI Localization for Simplified Wireless Sensor Networks

Source positioning using hybrid angle-of-arrival (AOA) estimation and received signal strength indicator (RSSI) is attractive because no synchronization is required among unknown nodes and anchors. Conventionally, hybrid AOA/RSSI localization combines the same number of these measurements to estimate the agents’ locations. However, since AOA estimation requires anchors to be equipped with large antenna arrays and complicated signal processing, this conventional combination makes the wireless sensor network (WSN) complicated. This paper proposes an unbalanced integration of the two measurements, called 1AOA/nRSSI, to simplify the WSN. Instead of using many anchors with large antenna arrays, the proposed method only requires one master anchor to provide one AOA estimation, while other anchors are simple single-antenna transceivers. By simply transforming the 1AOA/1RSSI information into two corresponding virtual anchors, the problem of integrating one AOA and N RSSI measurements is solved using the least square and subspace methods. The solutions are then evaluated to characterize the impact of angular and distance measurement errors. Simulation results show that the proposed network achieves the same level of precision as in a fully hybrid nAOA/nRSSI network with a slightly higher number of simple anchors