Comparison of metagenomic samples using sequence signatures

BACKGROUND: Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. RESULTS: We studied several dissimilarity measures, including d(2), d(2)(*) and d(2)(S) recently developed from our group, a measure (hereinafter noted as Hao) used in CVTree developed from Hao’s group (Qi et al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009), as well as standard l(p) measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d(2)(S) can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature. CONCLUSIONS: Sequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. The d(2)(S) dissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths

Spatio-Temporal Change of LakeWater Extent in Wuhan Urban Agglomeration Based on Landsat Images from 1987 to 2015

Urban lakes play an important role in urban development and environmental protection for the Wuhan urban agglomeration. Under the impacts of urbanization and climate change, understanding urban lake-water extent dynamics is significant. However, few studies on the lake-water extent changes for the Wuhan urban agglomeration exist. This research employed 1375 seasonally continuous Landsat TM/ETM+/OLI data scenes to evaluate the lake-water extent changes from 1987 to 2015. The random forest model was used to extract water bodies based on eleven feature variables, including six remote-sensing spectral bands and five spectral indices. An accuracy assessment yielded a mean classification accuracy of 93.11%, with a standard deviation of 2.26%. The calculated results revealed the following: (1) The average maximum lake-water area of the Wuhan urban agglomeration was 2262.17 km2 from 1987 to 2002, and it decreased to 2020.78 km2 from 2005 to 2015, with a loss of 241.39 km2 (10.67%). (2) The lake-water areas of loss of Wuhan, Huanggang, Xianning, and Xiaogan cities, were 114.83 km2, 44.40 km2, 45.39 km2, and 31.18 km2, respectively, with percentages of loss of 14.30%, 11.83%, 13.16%, and 23.05%, respectively. (3) The lake-water areas in the Wuhan urban agglomeration were 226.29 km2, 322.71 km2, 460.35 km2, 400.79 km2, 535.51 km2, and 635.42 km2 under water inundation frequencies of 5%–10%, 10%–20%, 20%–40%, 40%–60%, 60%–80%, and 80%–100%, respectively. The Wuhan urban agglomeration was approved as the pilot area for national comprehensive reform, for promoting resource-saving and environmentally friendly developments. This study could be used as guidance for lake protection and water resource management

Coherent phonon Rabi oscillations with a high frequency carbon nanotube phonon cavity

Phonon-cavity electromechanics allows the manipulation of mechanical oscillations similar to photon-cavity systems. Many advances on this subject have been achieved in various materials. In addition, the coherent phonon transfer (phonon Rabi oscillations) between the phonon cavity mode and another oscillation mode has attracted many interest in nano-science. Here we demonstrate coherent phonon transfer in a carbon nanotube phonon-cavity system with two mechanical modes exhibiting strong dynamical coupling. The gate-tunable phonon oscillation modes are manipulated and detected by extending the red-detuned pump idea of photonic cavity electromechanics. The first- and second-order coherent phonon transfers are observed with Rabi frequencies 591 kHz and 125 kHz, respectively. The frequency quality factor product fQ_m~2=10^12 Hz achieved here is larger thank k_B T_base/h, which may enable the future realization of Rabi oscillations in the quantum regime

Strongly-coupled nanotube electromechanical resonators

Coupling an electromechanical resonator with carbon-nanotube quantum dots is a significant method to control both the electronic charge and the spin quantum states. By exploiting a novel micro-transfer technique, we fabricate two strongly-coupled and electrically-tunable mechanical resonators on a single carbon nanotube for the first time. The frequency of the two resonators can be individually tuned by the bottom gates, and strong coupling is observed between the electron charge and phonon modes of each resonator. Furthermore, the conductance of either resonator can be nonlocally modulated by the phonon modes in the other resonator. Strong coupling is observed between the phonon modes of the two resonators, which provides an effective long distance electron-electron interaction. The generation of phonon-mediated-spin entanglement is also theoretically analyzed for the two resonators. This strongly-coupled nanotube electromechanical resonator array provides an experimental platform for future studies of the coherent electron-phonon interaction, the phonon mediated long-distance electron interaction, and entanglement state generation

Scenario-Based Analysis on the Structural Change of Land Uses in China

Land Use/Land Cover change (LUCC) is a key aspect of global environmental change, which has a significant impact on climate change. In the background of increasing global warming resulting from greenhouse effect, to understand the impact of land use change on climate change is necessary and meaningful. In this study, we choose China as the study area and explore the possible land use change trends based on the AgLU module and ERB module of global change assessment model (GCAM model and Global Change Assessment Model). We design three scenarios based on socioeconomic development and simulated the corresponding structure change of land use according to the three scenarios with different parameters. Then we simulate the different emission of CO2 under different scenarios based on the simulation results of structure change of land use. At last, we choose the most suitable scenario that could control the emission of CO2 best and obtain the relatively better land use structure change for adaption of climate change. Through this research we can provide a theoretical basis for the future land use planning to adapt to climate change

Construction and Validation of a Geometry-based Mathematical Model for Hard X-ray Imager

Quantitative and analytical analysis of modulation process of the collimator is a great challenge, and is also of great value to the design and development of Fourier transform imaging telescopes. The Hard X-ray Imager (HXI), as one of the three payloads onboard the Advanced Space-based Solar Observatory(ASO-S) mission, adopts modulating Fourier-Transformation imaging technique and will be used to explore mechanism of energy release and transmission in solar flare activities. In this paper, a mathematical model is developed to analyze the modulation function under a simplified condition first. Then its behavior under six degrees of freedom is calculated after adding the rotation matrix and translation change to the model. In addition, unparalleled light and extended sources also are considered so that our model can be used to analyze the X-ray beam experiment. Next, applied to the practical HXI conditions, the model has been confirmed not only by Geant4 simulations but also by some verification experiments. Furthermore, how this model will help to improve the image reconstruction process after the launch of ASO-S is also presented