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"Liu, Xiaonan"
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Public budgeting reform in China : theory and practice
This book introduces the theory and practice of Chinese public budget reform, including the manner and implications of public budget reform, the role and status of central government and local governments in budget reform, as well as the latest achievements of China?s local government public budget reform. The authors of this book are all researchers who have witnessed Chinese public budget reform.
Book
Tunable Diode Laser Absorption Spectroscopy Based Temperature Measurement with a Single Diode Laser Near 1.4 μm
The rapidly changing and wide dynamic range of combustion temperature in scramjet engines presents a major challenge to existing test techniques. Tunable diode laser absorption spectroscopy (TDLAS) based temperature measurement has the advantages of high sensitivity, fast response, and compact structure. In this invited paper, a temperature measurement method based on the TDLAS technique with a single diode laser was demonstrated. A continuous-wave (CW), distributed feedback (DFB) diode laser with an emission wavelength near 1.4 ?m was used for temperature measurement, which could cover two water vapor (H2O) absorption lines located at 7153.749 cm?1 and 7154.354 cm?1 simultaneously. The output wavelength of the diode laser was calibrated according to the two absorption peaks in the time domain. Using this strategy, the TDLAS system has the advantageous of immunization to laser wavelength shift, simple system structure, reduced cost, and increased system robustness. The line intensity of the two target absorption lines under room temperature was about one-thousandth of that under high temperature, which avoided the measuring error caused by H2O in the environment. The system was tested on a McKenna flat flame burner and a scramjet model engine, respectively. It was found that, compared to the results measured by CARS technique and theoretical calculation, this TDLAS system had less than 4% temperature error when the McKenna flat flame burner was used. When a scramjet model engine was adopted, the measured results showed that such TDLAS system had an excellent dynamic range and fast response. The TDLAS system reported here could be used in real engine in the future.
Journal Article
Secular Trends in the Incidence of and Mortality Due to Alzheimer’s Disease and Other Forms of Dementia in China From 1990 to 2019: An Age-Period-Cohort Study and Joinpoint Analysis
The number of individuals with dementia is increasing, which negatively affects families, communities, and health care systems worldwide. The changes in the incidence of and mortality due to Alzheimer's disease and other forms of dementia at the national level in China have remained unknown over the past three decades.
Following the general analytical strategy used in the Global Burden of Disease Study (GBD) 2019, the age- and sex-specific incidence and mortality rates for dementia in China were analyzed. Trends in the incidence of and mortality due to dementia from 1990 to 2019 were assessed by joinpoint regression analysis. The effects of age, period and cohort on the incidence of and mortality due to dementia were estimated by an age-period-cohort model.
The age-standardized incidence and mortality rates per 100,000 population were 103.83 (95% UI, 87.93-118.87) and 23.32 (95% UI, 5.66-61.31), respectively, for dementia in 2019. From 1990 to 2019, a significant average annual percentage change (AAPC) in the age-standardized incidence rate was observed in both males [0.49% (95% CI, 0.43-0.55%)] and females [0.31% (95% CI, 0.24-0.38%)], and the age-standardized mortality rate significantly increased in males [0.42% (95% CI, 0.31-0.53%)]. The population aged 55-59 years had the highest AAPC in the incidence of dementia [0.87% (95% CI, 0.81-0.93%)]. The age effect showed that the relative risks (RRs) of incident dementia and dementia-associated mortality increased with age among males and females, and individuals aged 60 years and older had significantly higher RRs. The RR of incident dementia increased with time, and the RR started to substantially increase in 2009. The cohort effect showed that the incidence decreased in successive birth cohorts.
Alzheimer's disease and other forms of dementia continue to become more common among males and females in China, and the associated mortality rate in males significantly increased from 1990 to 2019. Early interventions should be implemented to reduce the burden of dementia on individuals at high risk in China.
Journal Article
Resurrected memories: Sleep-dependent memory consolidation saves memories from competition induced by retrieval practice
Retrieval practice improves retention of tested information, and it can either impair or facilitate retention of untested information. Here, we investigated how semantic relatedness, episodic context, and sleep-dependent memory consolidation determine the effects of retrieval practice on retention of untested items. Participants studied lists of scene-word associations. Each scene was associated with two different words (“pairmates”) that were either semantically related or unrelated and either in the same (temporally close) or different lists (temporally far). In three experiments, retrieval practice of scene-word associations facilitated retention of unpracticed, temporally close pairmates and impaired retention of temporally far, semantically unrelated pairmates. Critically, retrieval practice impaired retention of temporally far, semantically related pairmates if participants were unable to sleep during the retention interval, but it facilitated retention of these items if participants were able to sleep. Our findings suggest that sleep extends the benefits of testing to related information learned in temporally separate episodes.
Journal Article
Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production
Plant natural products (PNPs) are widely used as pharmaceuticals, nutraceuticals, seasonings, pigments, etc., with a huge commercial value on the global market. However, most of these PNPs are still being extracted from plants. A resource-conserving and environment-friendly synthesis route for PNPs that utilizes microbial cell factories has attracted increasing attention since the 1940s. However, at the present only a handful of PNPs are being produced by microbial cell factories at an industrial scale, and there are still many challenges in their large-scale application. One of the challenges is that most biosynthetic pathways of PNPs are still unknown, which largely limits the number of candidate PNPs for heterologous microbial production. Another challenge is that the metabolic fluxes toward the target products in microbial hosts are often hindered by poor precursor supply, low catalytic activity of enzymes and obstructed product transport. Consequently, despite intensive studies on the metabolic engineering of microbial hosts, the fermentation costs of most heterologously produced PNPs are still too high for industrial-scale production. In this paper, we review several aspects of PNP production in microbial cell factories, including important design principles and recent progress in pathway mining and metabolic engineering. In addition, implemented cases of industrial-scale production of PNPs in microbial cell factories are also highlighted.
Journal Article
Combined proximity labeling and affinity purification−mass spectrometry workflow for mapping and visualizing protein interaction networks
Affinity purification coupled with mass spectrometry (AP–MS) and proximity-dependent biotinylation identification (BioID) methods have made substantial contributions to interaction proteomics studies. Whereas AP−MS results in the identification of proteins that are in a stable complex, BioID labels and identifies proteins that are in close proximity to the bait, resulting in overlapping yet distinct protein identifications. Integration of AP–MS and BioID data has been shown to comprehensively characterize a protein’s molecular context, but interactome analysis using both methods in parallel is still labor and resource intense with respect to cell line generation and protein purification. Therefore, we developed the Multiple Approaches Combined (MAC)-tag workflow, which allows for both AP–MS and BioID analysis with a single construct and with almost identical protein purification and mass spectrometry (MS) identification procedures. We have applied the MAC-tag workflow to a selection of subcellular markers to provide a global view of the cellular protein interactome landscape. This localization database is accessible via our online platform (
http://proteomics.fi
) to predict the cellular localization of a protein of interest (POI) depending on its identified interactors. In this protocol, we present the detailed three-stage procedure for the MAC-tag workflow: (1) cell line generation for the MAC-tagged POI; (2) parallel AP–MS and BioID protein purification followed by MS analysis; and (3) protein interaction data analysis, data filtration and visualization with our localization visualization platform. The entire procedure can be completed within 25 d.
This protocol describes the MAC-tag approach, which combines affinity purification and biotinylation identification proximity labeling in a single tag. Binding proteins are identified by liquid chromatography–mass spectrometry, followed by visualization of protein localization using an online platform.
Journal Article
Arabidopsis class I formins control membrane-originated actin polymerization at pollen tube tips
A population of dynamic apical actin filaments is required for rapid polarized pollen tube growth. However, the cellular mechanisms driving their assembly remain incompletely understood. It was postulated that formin is a major player in nucleating apical actin assembly, but direct genetic and cytological evidence remains to be firmly established. Here we found that both Arabidopsis formin 3 (AtFH3) and formin 5 (AtFH5) are involved in the regulation of apical actin polymerization and actin array construction in pollen tubes, with AtFH3 playing a more dominant role. We found that both formins have plasma membrane (PM) localization signals but exhibit distinct PM localization patterns in the pollen tube, and loss of their function reduces the amount of apical actin filaments. Live-cell imaging revealed that the reduction in filamentous actin is very likely due to the decrease in filament elongation. Furthermore, we found that the rate of tip-directed vesicle transport is reduced and the pattern of apical vesicle accumulation is altered in formin loss-of-function mutant pollen tubes, which explains to some extent the reduction in pollen tube elongation. Thus, we provide direct genetic and cytological evidence showing that formin is an important player in nucleating actin assembly from the PM at pollen tube tips.
Journal Article
Correcting the hebbian mistake: Toward a fully error-driven hippocampus
The hippocampus plays a critical role in the rapid learning of new episodic memories. Many computational models propose that the hippocampus is an autoassociator that relies on Hebbian learning (i.e., “cells that fire together, wire together”). However, Hebbian learning is computationally suboptimal as it does not learn in a way that is driven toward, and limited by, the objective of achieving effective retrieval. Thus, Hebbian learning results in more interference and a lower overall capacity. Our previous computational models have utilized a powerful, biologically plausible form of error-driven learning in hippocampal CA1 and entorhinal cortex (EC) (functioning as a sparse autoencoder) by contrasting local activity states at different phases in the theta cycle. Based on specific neural data and a recent abstract computational model, we propose a new model called Theremin (Total Hippocampal ERror MINimization) that extends error-driven learning to area CA3—the mnemonic heart of the hippocampal system. In the model, CA3 responds to the EC monosynaptic input prior to the EC disynaptic input through dentate gyrus (DG), giving rise to a temporal difference between these two activation states, which drives error-driven learning in the EC→CA3 and CA3↔CA3 projections. In effect, DG serves as a teacher to CA3, correcting its patterns into more pattern-separated ones, thereby reducing interference. Results showed that Theremin, compared with our original Hebbian-based model, has significantly increased capacity and learning speed. The model makes several novel predictions that can be tested in future studies.
Journal Article
TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs
Background
In plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed.
Results
Here, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at
http://www.biosequencing.cn/TarDB
.
Conclusions
In summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.
Journal Article
Human transcription factor protein interaction networks
Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription.
Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here the authors identify 6703 and 1536 protein–protein interactions for 109 different human TFs through BioID and AP-MS analyses, respectively.
Journal Article