Random-Forest-Algorithm-Based Applications of the Basic Characteristics and Serum and Imaging Biomarkers to Diagnose Mild Cognitive Impairment.

Background: Mild cognitive impairment (MCI) is considered the early stage of Alzheimer's Disease (AD). The purpose of our study was to analyze the basic characteristics and serum and imaging biomarkers for the diagnosis of MCI patients as a more objective and accurate approach.

Methods: The Montreal Cognitive Test was used to test 119 patients aged ≥65.

The Construction Model of the TCM Clinical Knowledge Coding Database Based on Knowledge Organization.

Based on the knowledge organization method, this paper explores the construction method of the traditional Chinese medicine (TCM) clinical knowledge coding model by taking TCM clinical electronic medical record data as the research object. Firstly, extracting technology is used to obtain the required data in the electronic medical record. Then, by constructing the clinical knowledge coding model, the tacit knowledge is made explicit, establishing the clinical knowledge base and exploring the connotation of TCM clinical knowledge.

Soil NO emission in Cinnamomum camphora plantations along an urbanization gradient altered by changes in litter input and microbial community composition.

Urbanization alters land use, increasing the rate of greenhouse gas (GHG) emissions and hence atmospheric compositions. Nitrous oxide (NO) is a major GHG that contributes substantially to global warming. NO emissions are sensitive to changes in substrate availabilities, such as litter and N input, as well as micro-environmental factors caused by land-use change upon urbanization.

Biochar derived from spent mushroom substrate reduced NO emissions with lower water content but increased CH emissions under flooded condition from fertilized soils in Camellia oleifera plantations.

Agricultural soils are major sources of greenhouse gases (GHGs) that related with intensive fertilizer input. Biochar is widely used to mitigate GHGs, which may interact with soil water content impacting GHG emissions. Camellia oleifera fruit shell (FS) and spent mushroom substrate (MS) are ideal biochar feedstocks.

[Long-term water use characteristics and patterns of typical tree species in seasonal drought regions].

In the areas with seasonal drought, water is the key factor affecting plant growth and development. Based on long-term continuous observation data, it is of great significance to explore plant water use patterns for vegetation construction in areas with seasonal drought. Taking in Beijing mountainous area as the research object, stable hydrogen and oxygen isotope technique was applied to measure the isotopic composition of water from the soil, plant branches, and precipitation from 2012 to 2017.

HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression.

Gene expression data features high dimensionality, multicollinearity, and non-Gaussian distribution noise, posing hurdles for identification of true regulatory genes controlling a biological process or pathway. In this study, we integrated the Huber loss function and the Berhu penalty (HB) into partial least squares (PLS) framework to deal with the high dimension and multicollinearity property of gene expression data, and developed a new method called HB-PLS regression to model the relationships between regulatory genes and pathway genes. To solve the Huber-Berhu optimization problem, an accelerated proximal gradient descent algorithm with at least 10 times faster than the general convex optimization solver (CVX), was developed.

Soil C-N-P pools and stoichiometry as affected by intensive management of camellia oleifera plantations.

Intensive management of C. oleifera has produced many pure C. oleifera plantations.

JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions.

Motivation: Joint reconstruction of multiple gene regulatory networks (GRNs) using gene expression data from multiple tissues/conditions is very important for understanding common and tissue/condition-specific regulation. However, there are currently no computational models and methods available for directly constructing such multiple GRNs that not only share some common hub genes but also possess tissue/condition-specific regulatory edges.

Results: In this paper, we proposed a new graphic Gaussian model for joint reconstruction of multiple gene regulatory networks (JRmGRN), which highlighted hub genes, using gene expression data from several tissues/conditions.

TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction.

Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene mutual interaction (TGMI) for identifying these regulators using high-throughput gene expression data.

SSGA and MSGA: two seed-growing algorithms for constructing collaborative subnetworks.

The establishment of a collaborative network of transcription factors (TFs) followed by decomposition and then construction of subnetworks is an effective way to obtain sets of collaborative TFs; each set controls a biological process or a complex trait. We previously developed eight gene association methods for genome-wide coexpression analysis between each TF and all other genomic genes and then constructing collaborative networks of TFs but only one algorithm, called Triple-Link Algorithm, for building collaborative subnetworks. In this study, we developed two more algorithms, Single Seed-Growing Algorithm (SSGA) and Multi-Seed Growing Algorithm (MSGA), for building collaborative subnetworks of TFs by identifying the fully-linked triple-node seeds from a decomposed collaborative network and then growing them into subnetworks with two different strategies.

Recursive random forest algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways.

Background: Present knowledge indicates a multilayered hierarchical gene regulatory network (ML-hGRN) often operates above a biological pathway. Although the ML-hGRN is very important for understanding how a pathway is regulated, there is almost no computational algorithm for directly constructing ML-hGRNs.

Results: A backward elimination random forest (BWERF) algorithm was developed for constructing the ML-hGRN operating above a biological pathway.

Using carbon nanotubes-gold nanocomposites to quench energy from pinnate titanium dioxide nanorods array for signal-on photoelectrochemical aptasensing.

On the basis of the absorption and emission spectra overlap, an enhanced resonance energy transfer caused by excition-plasmon resonance between carbon nanotubes-gold nanoparticles (CNTs-Au) and pinnate titanium dioxide nanorods array (P-TiO2 NA) was obtained. Three-dimensional single crystalline P-TiO2 were prepared successfully on fluorine-doped tin oxide conducting glass (FTO glass), and its optical absorption properties and photoelectrochemical (PEC) properties were investigated. With the synergy of CNTs-Au as energy acceptor, it resulted in the enhancement of energy transfer between excited P-TiO2 NA and CNTs-Au.

Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes.

Background: Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways.

Results: A bottom-up graphic Gaussian model (GGM) algorithm was developed for constructing ML-hGRN operating above a biological pathway using small- to medium-sized microarray or RNA-seq data sets.

An aldehyde group-based P-acid probe for selective fluorescence turn-on sensing of cysteine and homocysteine.

A highly sensitive and selective turn on fluorescent probe P-acid-aldehyde (P-CHO) is developed for the determination of cysteine (Cys) and homocysteine (Hcy). The probe is designed and synthesized by incorporating the specific functional group aldehyde group for thiols into a stable π-conjugated material 4,4'-(2,5-dimethoxy-1,4-phenylene) bis(ethyne-2,1-diyl) dibenzoic acid (P-acid). The probe fluorescence is quenched through donor photoinduced electron transfer (d-PET) between the fluorophore (P-acid) and the recognition group (aldehyde group).

Application of ZnO quantum dots dotted carbon nanotube for sensitive electrochemiluminescence immunoassay based on simply electrochemical reduced Pt/Au alloy and a disposable device.

We report on a disposable microdevice suitable for sandwich-type electrochemiluminescence (ECL) detection of prostate specific antigen (PSA). The method is making use of ZnO quantum dots dotted carbon nanotube (ZnO@CNT) and simply electrochemical reduced Pt/Au alloy. The latter was selected as immunosensing probe to modify screen-printed carbon electrode, due to its excellent electrical property.

A dual amplification strategy for ultrasensitive electrochemiluminescence immunoassay based on a Pt nanoparticles dotted graphene-carbon nanotubes composite and carbon dots functionalized mesoporous Pt/Fe.

A facile and sensitive electrochemiluminescence (ECL) immunosensor for the detection of human carcinoembryonic antigen (CEA) was designed. The immunosensor used Pt nanoparticles dotted graphene-carbon nanotubes composites (Pt/Gr-CNTs) as a platform and carbon dots functionalized Pt/Fe nanoparticles (Pt/Fe@CDs) as bionanolabels. The Pt/Gr-CNTs was first synthesized using a facile ultrasonic method to modify the working electrode, which increases the surface area to capture a large amount of primary anti-CEA antibodies as well as improving the electronic transmission rate.

A highly sensitive electrically driven electrochemiluminescent assay for quantification of bile acids in human serum.

A capillary electrically driven assay with electrochemiluminescent (ECL) detection for total bile acids in human serum was developed and fully validated. Quantification was performed by multiple reactions. First, the bile acids react with nicotinamide adenine dinucleotide (NAD(+)) under catalysis of 3α-hydroxysteroid dehydrogenase (3α-HSD), which is converted to 3-ketosteroid and concomitantly NAD(+) turns into reduced nicotinamide adenine dinucleotide (NADH).

Primary bile acids as potential biomarkers for the clinical grading of intrahepatic cholestasis of pregnancy.

Objective: To identify possible biomarkers for the clinical grading of intrahepatic cholestasis of pregnancy (ICP) through serum bile acid (SBA) profiling in women with ICP.

Methods: Serum samples were collected in the last trimester of pregnancy from 33 women with severe ICP, 28 women with mild ICP, and 35 women with a normal pregnancy. The SBA levels were determined by high-performance liquid chromatography-tandem mass spectrometry.

CO2 in solid para-hydrogen: spectral splitting and the CO2···(o-H2)n clusters.

Complicated high-resolution spectral structures are often observed for molecules doped in solid molecular hydrogen. The structures can result from miscellaneous effects and are often interpreted differently in references. The spectrum of the ν(3) band of CO(2) in solid para-H(2) presents a model system which exhibits rich spectral structures.

Analysis of tryptophan catabolism in HBV patients by HPLC with programmed wavelength ultraviolet detection.

Background: In order to understand the tryptophan catabolism in acute and chronic hepatitis B patients, we quantitatively analyzed plasma kynurenine and tryptophan simultaneously by high performance liquid chromatography with programmed wavelength ultraviolet detection.

Methods: A new and specific high performance liquid chromatography method to simultaneously measure plasma kynurenine and tryptophan with programmed wavelength ultraviolet detection using 3-nitro-tyrosine as internal standard was elaborated. Thirty patients were recruited (10 patients with acute HBV, 10 with chronic HBV and 10 healthy subjects).

A frequency-stabilized difference frequency generation laser spectrometer for precise line profile studies in the midinfrared.

A midinfrared laser spectrometer is built up based on the difference frequency generation (DFG) of a Nd:YAG (yttrium aluminum garnet) laser and a tunable Ti:sapphire (Ti:Sa) laser. Tuning the Ti:Sa laser and operating properly with the periodically poled lithium niobate crystal, the DFG emission is tunable in the spectral range of 2.3-5.