Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the ...target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines.
The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/.
luo_weijun@yahoo.com
Supplementary data are available at Bioinformatics online.
Single cell RNA sequencing (scRNA-Seq) is being widely used in biomedical research and generated enormous volume and diversity of data. The raw data contain multiple types of noise and technical ...artifacts, which need thorough cleaning. Existing denoising and imputation methods largely focus on a single type of noise (i.e., dropouts) and have strong distribution assumptions which greatly limit their performance and application. Here we design and develop the AutoClass model, integrating two deep neural network components, an autoencoder, and a classifier, as to maximize both noise removal and signal retention. AutoClass is distribution agnostic as it makes no assumption on specific data distributions, hence can effectively clean a wide range of noise and artifacts. AutoClass outperforms the state-of-art methods in multiple types of scRNA-Seq data analyses, including data recovery, differential expression analysis, clustering analysis, and batch effect removal. Importantly, AutoClass is robust on key hyperparameter settings including bottleneck layer size, pre-clustering number and classifier weight. We have made AutoClass open source at: https://github.com/datapplab/AutoClass .
Neural network forms the foundation of deep learning and numerous AI applications. Classical neural networks are fully connected, expensive to train and prone to overfitting. Sparse networks tend to ...have convoluted structure search, suboptimal performance and limited usage. We proposed the novel uniform sparse network (USN) with even and sparse connectivity within each layer. USN has one striking property that its performance is independent of the substantial topology variation and enormous model space, thus offers a search-free solution to all above mentioned issues of neural networks. USN consistently and substantially outperforms the state-of-the-art sparse network models in prediction accuracy, speed and robustness. It even achieves higher prediction accuracy than the fully connected network with only 0.55% parameters and 1/4 computing time and resources. Importantly, USN is conceptually simple as a natural generalization of fully connected network with multiple improvements in accuracy, robustness and scalability. USN can replace the latter in a range of applications, data types and deep learning architectures. We have made USN open source at https://github.com/datapplab/sparsenet.
Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over ...individual gene analyses, including greater robustness, sensitivity and biological relevance. However, previous GSA methods have limited usage as they cannot handle datasets of different sample sizes or experimental designs.
To address these limitations, we present a new GSA method called Generally Applicable Gene-set Enrichment (GAGE). We successfully apply GAGE to multiple microarray datasets with different sample sizes, experimental designs and profiling techniques. GAGE shows significantly better results when compared to two other commonly used GSA methods of GSEA and PAGE. We demonstrate this improvement in the following three aspects: (1) consistency across repeated studies/experiments; (2) sensitivity and specificity; (3) biological relevance of the regulatory mechanisms inferred.GAGE reveals novel and relevant regulatory mechanisms from both published and previously unpublished microarray studies. From two published lung cancer data sets, GAGE derived a more cohesive and predictive mechanistic scheme underlying lung cancer progress and metastasis. For a previously unpublished BMP6 study, GAGE predicted novel regulatory mechanisms for BMP6 induced osteoblast differentiation, including the canonical BMP-TGF beta signaling, JAK-STAT signaling, Wnt signaling, and estrogen signaling pathways-all of which are supported by the experimental literature.
GAGE is generally applicable to gene expression datasets with different sample sizes and experimental designs. GAGE consistently outperformed two most frequently used GSA methods and inferred statistically and biologically more relevant regulatory pathways. The GAGE method is implemented in R in the "gage" package, available under the GNU GPL from http://sysbio.engin.umich.edu/~luow/downloads.php.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The need for a high‐frequency and high‐efficiency gallium nitride (GaN)‐based buck converter that can be controlled directly by a low swing pulse width‐modulated (PWM) signal, without the need for ...additional buffers or preamplifiers, poses a significant challenge in the field of power conversion and dynamically power supply applications. To solve this problem, this letter presents a monolithic two‐phase synchronous buck converter, fabricated using a 0.25‐um GaN‐on‐Si process, integrated both the drivers and power stage transistors, without requiring additional buffers or preamplifiers. So, the proposed converter can be directly controlled by a PWM signal with a swing of only 1 V (−0.5 to 0.5 V). At a 100‐MHz switching frequency, the converter achieves a maximum output power of 12 W with a power stage efficiency of 82%. The converter includes two identical half‐bridge Monolithic Microwave Integrated Circuit (MMICs), and with the frequency multiplication property of multi‐phase topology, the equivalent switching frequency can reach 200 MHz in the open‐loop operating mode. The experimental results show that the converter can track a 40‐MHz bandwidth envelope signal (256 QAM, 6 dB PAPR) with 80.1% efficiency.
The need for a high‐frequency and high‐efficiency GaN‐based buck converter that can be controlled directly by a low swing PWM signal, without the need for additional buffers or preamplifiers, poses a significant challenge in the field of power conversion and dynamically power supply applications. To solve this problem, this letter presents a monolithic two‐phase synchronous buck converter, fabricated using a 0.25um GaN‐on‐Si process, integrated both the drivers and power stage transistors, without requiring additional buffers or preamplifiers. So, the proposed converter can be directly controlled by a PWM (Pulse Width Modulated) signal with a swing of only 1V (‐0.5V‐0.5V).
The thick Cenozoic sedimentary sequence of the Linxia Basin contains abundant well-preserved mammalian fossils, which provide significant information on the paleoenvironmental processes and mammalian ...evolution associated with the uplift and expansion of the Tibetan Plateau. Ambiguous age estimations have been made for some coarse-grained sedimentary units in the basin, which have led to the misinterpretation of biostratigraphic and magnetostratigraphic age models. To resolve these issues, we present radiometric dating of three late Cenozoic sedimentary units (“Liushu”, Hewangjia, and Jishi formations) in the eastern Linxia Basin using cosmogenic 26Al/10Be and 10Be/21Ne burial methods. isotope measurements for the upper “Liushu” Formation indicate a 10Be/21Ne burial age of 11.70 ± 0.17 Ma. This age is older than, but not contrary to, recently revised bio-magnetostratigraphic work. The 26Al/10Be burial age of the Hewangjia Formation is 3.06 (+0.36/−0.31) Ma and had been underestimated by post-burial muon production possibility, while the 26Al/10Be burial age of the Jishi Formation is 2.50 (+0.20/−0.18) Ma and had been overestimated due to inherited cosmogenic nuclides from recycled deposits. The new age from the Jishi Formation delays the initial deposition of conglomerates in the Linxia Basin to no earlier than 2.5 Ma and constrains an important episode of tectonic uplift of the northeastern Tibetan Plateau to 2.5–3.1 Ma. The age of the Equus fauna of Longdan is revised to the Early Quaternary (ca. 2.1–1.9 Ma). Our new age determinations significantly refine the terrestrial sequence chronology of the Linxia Basin and associated mammalian faunas of the late Miocene to the early Pleistocene.
•Cosmogenic nuclide burial dating is applied in the Linxia Basin.•A 26Al/10Be age for the Jishi Formation is 2.50 (+0.20/−0.18) Ma.•A 26Al/10Be age Hewangjia Formation estimate is 3.06 (+0.36/−0.31) Ma.•A 21Ne/10Be age for the “Liushu” Formation is 11.70 ± 0.17 Ma.•Tectonic uplift of the northeastern Tibetan Plateau occurred ∼2.5–3.1 Ma.
This study presents new stable isotope data for precipitation (δ18Op) and drip water (δ18Od) from eight cave sites in the monsoon regions of China (MRC), with monthly to bi-monthly sampling intervals ...from May-2011 to April-2014, to investigate the regional-scale climate forcing on δ18Op and how the isotopic signals are transmitted to various drip sites.
The monthly δ18Op values show negative correlation with surface air temperature at all the cave sites except Shihua Cave, which is opposite to that expected from the temperature effect. In addition, although the monthly δ18Op values are negatively correlated with precipitation at all the cave sites, only three sites are significant at the 95% level. These indicate that, due to the various vapor sources, a large portion of variability in δ18Op in the MRC cannot be explained simply by either temperature or precipitation alone.
All the thirty-four drip sites are classified into three types based on the δ18Od variability. About 82% of them are static drips with little discernable variation in δ18Od through the whole study period, but the drip rates of these drips are not necessary constant. Their discharge modes are site-specific and the oxygen isotopic composition of the stalagmites growing from them may record the average of multi-year climatic signals, which are modulated by the seasonality of recharge and potential effects of evaporation, and in some cases infiltration from large rainfall events. About 12% of the thirty-four drip sites are seasonal drips, although the amplitude of δ18Od is narrower than that of δ18Op, the monthly response of δ18Od to coeval precipitation is not completely damped, and some of them follow the seasonal trend of δ18Op very well. These drips may be mainly recharged by present-day precipitation, mixing with some stored water. Thus, the stalagmites growing under them may record portions of the seasonal climatic signals embedded in δ18Op. About 6% of the thirty-four drip sites are medium-variability drips, with constant and relatively low δ18Od values in the wet season, but with variable and relatively high δ18Od values in the dry season, reflecting flow switching in the karst or evaporation inside the cave.
•A karstic surface atop basal Ediacaran Doushantuo cap dolostone in South China.•Abundant speleothems in sheet-cavities of Doushantuo cap dolostone in South China.•An active soil-microbial ecosystem ...facilitated Ediacaran speleothem formation.
Cryogenian snowball Earth glaciations may have had disastrous impacts on the biosphere, particularly the terrestrial ecosystem. However, how the terrestrial ecosystem responded to and recovered from these glaciations remains poorly understood. Speleothems offer important insights into terrestrial life because their formation is critically dependent on soil CO2 derived from microbial respiration. Here we report the wide distribution of miniature paleo-speleothems from the ∼ 635 Ma Doushantuo cap dolostone in South China and assess their implications for the recovery of terrestrial life after the terminal Cryogenian Marinoan glaciation. The ∼ 3-m-thick cap dolostone was deposited during the initial transgression following deglaciation but subsequently experienced subaerial exposure due to post-glacial rebound, which resulted in the development of extensive sheet-cavities in the cap dolostone and a widespread karstic surface atop the cap dolostone. The sheet-cavities were filled with multiple generations of minerals, including isopachous dolomite interpreted to have formed in the phreatic zone, speleothems consisting of fibrous calcite interpreted to have formed in the vadose zone, as well as later phases (i.e., isopachous radial chalcedony, crystalline quartz, and blocky calcite). The Doushantuo speleothems are millimeter-to-centimeter in size and include gravitational speleothems (stalactites and stalagmites) and non-gravitational speleothems (helictites, moonmilk, botryoids, and flat crusts). Some of them were secondarily silicified by hydrothermal fluids before a renewed transgression in which ∼ 632 Ma shales overlying the cap dolostone were deposited. The wide distribution of Doushantuo speleothems and the preservation of microfossils in these speleothems indicate the presence of an active soil-microbial ecosystem in the earliest Ediacaran Period and the rapid recovery of terrestrial life after the Marinoan snowball Earth.
•The rock-soil fabrics affects the surface evaporation.•There are significant differences in surface evaporation between different rock exposure rate after rainfall of different intensities.•The ...evaporation from rock maybe is an important part of surface evaporation.•The leakage coefficients with and without cracks varied greatly.•The amount of leakage and the time to reach the peak flow varied greatly among the different rock-soil fabrics.
Karst water is an extremely important resource and can respond to precipitation events quickly due to the high rock exposure rate, shallow and uneven soil layers, and various crack sizes. The impacts of this special rock–soil structure type on hydrological processes are difficult to quantify,mainlybecause the karst subsurface structure is very complex. In this study, lysimeters representing four rock–soil structures with two rock exposure rates (50% and 80%) and two soil thicknesses (5 cm and 20 cm) were constructed at the Puding Karst Ecosystem Research Station, Chinese Academy of Sciences. The following results were obtained by observing the evaporation and leakage from September 2019 to August 2020. 1) Over a year, the evaporation of the 80% rock exposure lysimeter was approximately 8% less than that of the 50% rock exposure lysimeter, while the two lysimeters with different soil thicknesses had only a 2% difference in evaporation. 2) The surface evaporation of different rock exposure rates varies greatly after different rainfall intensities. However, there was no significant change in surface evaporation between different soil thicknesses after rainfall of different intensities. 3) Generally, with the increase in the rock exposure rate, the infiltration coefficient nonlinearly increased. The leakage coefficients for cracks of different sizes and different soil thicknesses were approximately 0.67 and 0.57, respectively. 4) The amount of leakage and the time to reach the peak flow varied greatly among different rock–soil structures and were also affected by the antecedent rainfall. Thus, rock exposure has a great impact on surface evaporation after rainfall, and the influence of cracks on subsurface hydrological processes was greater than that of soil thickness. These findings can provide a scientific reference for water use and management practices in karst areas.
PdSe2, an emerging 2D material with a novel anisotropic puckered pentagonal structure, has attracted growing interest due to its layer‐dependent electronic bandgap, high carrier mobility, and good ...air stability. Herein, a detailed Raman spectroscopic study of few‐layer PdSe2 (two to five layers) under the in‐plane uniaxial tensile strain up to 3.33% is performed. Two of the prominent PdSe2 Raman peaks are influenced differently depending on the direction of strain application. The Ag1 mode redshifts more than the Ag3 mode when the strain is applied along the a‐axis of the crystal, while the Ag3 mode redshifts more than the Ag1 mode when the strain is applied along the b‐axis. Such an anisotropic phonon response to strain indicates directionally dependent mechanical and thermal properties of PdSe2 and also allows the identification of the crystal axes. The results are further supported using first‐principles density‐functional theory. Interestingly, the near‐zero Poisson’s ratios for few‐layer PdSe2 are found, suggesting that the uniaxial tensile strain can easily be applied to few‐layer PdSe2 without significantly altering their dimensions at the perpendicular directions, which is a major contributing factor to the observed distinct phonon behavior. The findings pave the way for further development of 2D PdSe2‐based flexible electronics.
The distinct anisotropic phonon response of strained few‐layer PdSe2 (two to five layers) is investigated via Raman spectroscopy. Density‐functional theory calculations reveal the near‐zero Poisson’s ratios of few‐layer (one to three layers) PdSe2. The experimental and theoretical findings are expected to facilitate further understanding of the mechanical, thermal, optical, and electronic properties of PdSe2 for future flexible electronics.
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