A robust approach for analyzing and mapping hierarchical brain connectome towards laminar-specific neural networks.

Probing neuronal activity and functional connectivity at cortical layer and sub-cortical nucleus level provides opportunities for mapping local and remote neural circuits and resting-state networks (RSN) critical for understanding cognition and behaviors. However, conventional resting-state fMRI (rs-fMRI) has been applied predominantly at relatively low spatial resolution and macroscopic level, unable to obtain laminar-specific information and neural circuits across the cortex at mesoscopic level. In addition, it is lack of sophisticated processing pipeline to deal with small laminar structures in rodent brains.

Quantitative mapping of key glucose metabolic rates in the human brain using dynamic deuterium magnetic resonance spectroscopic imaging.

Deuterium (H) magnetic resonance spectroscopic imaging (DMRSI) is a newly developed technology for assessing glucose metabolism by simultaneously measuring deuterium-labeled glucose and its downstream metabolites (1) and has a potential to provide a powerful neurometabolic imaging tool for quantitative studies of cerebral glucose metabolism involving multiple metabolic pathways in the human brain. In this work, we developed a dynamic DMRSI method that combines advanced radiofrequency coil and postprocessing techniques to substantially improve the imaging signal-to-noise ratio for detecting deuterated metabolites and enable robust dynamic DMRSI of the human brain at 7 T with very high resolution (HR; 0.7 cc nominal voxel and 2.

Simultaneous assessment of cerebral glucose and oxygen metabolism and perfusion in rats using interleaved deuterium (H) and oxygen-17 (O) MRS.

Cerebral glucose and oxygen metabolism and blood perfusion play key roles in neuroenergetics and oxidative phosphorylation to produce adenosine triphosphate (ATP) energy molecules in supporting cellular activity and brain function. Their impairments have been linked to numerous brain disorders. This study aimed to develop an in vivo magnetic resonance spectroscopy (MRS) method capable of simultaneously assessing and quantifying the major cerebral metabolic rates of glucose (CMR) and oxygen (CMRO) consumption, lactate formation (CMR), and tricarboxylic acid (TCA) cycle (V); cerebral blood flow (CBF); and oxygen extraction fraction (OEF) via a single dynamic MRS measurement using an interleaved deuterium (H) and oxygen-17 (O) MRS approach.

Dual-frequency resonant coil design for low-γ X-nuclear and proton magnetic resonance imaging at ultrahigh fields.

Low-γ X-nuclear MRS and imaging have played a key role in studying metabolism and physiopathology, especially at ultrahigh fields. We design and demonstrate a novel and simple dual-frequency RF resonant coil that can operate at both low-γ X-nuclear and proton frequencies. The dual-frequency resonant coil comprises an LC coil loop and a tuning-matching circuit bridged by two short wires of the desired length to generate two resonant modes: one for proton MRI and the other for low-γ X-nuclear MRS imaging with a large difference in their Larmor frequencies at ultrahigh fields.

Identification, Molecular Characterization, and Tissue Expression Profiles of Three Genes from Water Buffalo ().

Smads are involved in a variety of biological activities by mediating bone morphogenetic protein (BMP) signals. The full-length coding sequences (CDSs) of buffalo , , and were isolated and identified through RT-PCR in this study. Their lengths are 1398 bp, 1662 bp, and 1398 bp, respectively.

Elongase of very long chain fatty acids 6 (ELOVL6) promotes lipid synthesis in buffalo mammary epithelial cells.

Recent studies have shown elongase of very-long-chain fatty acids 6 (ELOVL6) is a vital protein for endogenous synthesis of saturated and monounsaturated long-chain fatty acids in some mammals. Nevertheless, its role in lipid synthesis in buffalo mammary gland is still unclear. In this work, the full-length coding sequence (CDS) of ELOVL6 was cloned and identified from buffalo mammary gland.

QCL-Based Dual-Comb Spectrometer for Multi-Species Measurements at High Temperatures and High Pressures.

Rapid multi-species sensing is an overarching goal in time-resolved studies of chemical kinetics. Most current laser sources cannot achieve this goal due to their narrow spectral coverage and/or slow wavelength scanning. In this work, a novel mid-IR dual-comb spectrometer is utilized for chemical kinetic investigations.

SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species.

Motivation: DNA N4-methylcytosine (4mC) modification is an important epigenetic modification in prokaryotic DNA due to its role in regulating DNA replication and protecting the host DNA against degradation. An efficient algorithm to identify 4mC sites is needed for downstream analyses.

Results: In this study, we propose a new prediction method named SOMM4mC based on a second-order Markov model, which makes use of the transition probability between adjacent nucleotides to identify 4mC sites.

Discovering Cancer-Related miRNAs from miRNA-Target Interactions by Support Vector Machines.

MicroRNAs (miRNAs) have been shown to be closely related to cancer progression. Traditional methods for discovering cancer-related miRNAs mostly require significant marginal differential expression, but some cancer-related miRNAs may be non-differentially or only weakly differentially expressed. Such miRNAs are called dark matters miRNAs (DM-miRNAs) and are targeted through the Pearson correlation change on miRNA-target interactions (MTIs), but the efficiency of their method heavily relies on restrictive assumptions.

Large-scale femtosecond holography for near simultaneous optogenetic neural modulation.

For better understanding of brain functions, optogenetic neural modulation has been widely employed in neural science research. For deep tissue in vivo applications, large-scale two-photon based near simultaneous 3D laser excitation is needed. Although 3D holographic laser excitation is nowadays common practice, the inherent short coherence length of the commonly used femtosecond pulses fundamentally restricts the achievable field-of-view.

MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model.

Motivation: Recent studies have shown that DNA N6-methyladenine (6mA) plays an important role in epigenetic modification of eukaryotic organisms. It has been found that 6mA is closely related to embryonic development, stress response and so on. Developing a new algorithm to quickly and accurately identify 6mA sites in genomes is important for explore their biological functions.

miR+Pathway: the integration and visualization of miRNA and KEGG pathways.

miRNAs represent a type of noncoding small molecule RNA. Many studies have shown that miRNAs are widely involved in the regulation of various pathways. The key to fully understanding the regulatory function of miRNAs is the determination of the pathways in which the miRNAs participate.

Discovering the 'Dark matters' in expression data of miRNA based on the miRNA-mRNA and miRNA-lncRNA networks.

Background: Since miRNAs can play important roles in different cancer types, how to discover cancer related miRNAs is an important issue. In general, the miRNAs with differential expression is the focus of attention. However, some important cancer related miRNAs are not excavated by differential expression analysis.

LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs.

Long non-coding RNAs (lncRNAs) are endogenous molecules longer than 200 nucleotides, and lack coding potential. LncRNAs that interact with microRNAs (miRNAs) are known as a competing endogenous RNAs (ceRNAs) and have the ability to regulate the expression of target genes. The ceRNAs play an important role in the initiation and progression of various cancers.

Identification of cancer-related miRNA-lncRNA biomarkers using a basic miRNA-lncRNA network.

LncRNAs are regulatory noncoding RNAs that play crucial roles in many biological processes. The dysregulation of lncRNA is thought to be involved in many complex diseases; lncRNAs are often the targets of miRNAs in the indirect regulation of gene expression. Numerous studies have indicated that miRNA-lncRNA interactions are closely related to the occurrence and development of cancers.

Knockdown of XBP1 by RNAi in Mouse Granulosa Cells Promotes Apoptosis, Inhibits Cell Cycle, and Decreases Estradiol Synthesis.

Granulosa cells are crucial for follicular growth, development, and follicular atresia. X-box binding protein 1 (XBP1), a basic region-leucine zipper protein, is widely involved in cell differentiation, proliferation, apoptosis, cellular stress response, and other signaling pathways. In this study, RNA interference, flow cytometry, western blot, real-time PCR, Cell Counting Kit (CCK8), and ELISA were used to investigate the effect of XBP1 on steroidogenesis, apoptosis, cell cycle, and proliferation of mouse granulosa cells.

Study on the Method of Voigt Profiles Two Wings Fitting Non-Uniform Flow Field Absorbance.

In the field of the absorption spectrum, especially for direct tunable diode laser absorption spectroscopy (dTDLAS) technology, the integrated area of the absorption spectrum is needed to be measured accurately for calculating the temperature and the component concentration of the flow field. Doing single optical path absorption spectroscopic measurement in the non-uniform flow field, spectral lineshape broadening is varied with the flow changes, in previous research reports, researchers mainly use single Voigt or Lorentz profile to fit absorbance curve or use directly integral to obtain the integrated area of the absorption spectrum. There are some shortcomings in these methods, resulting in certain error between the fitting result and the actual area, which is not conducive to the accurate measurement of flow field parameters.

V-ELMpiRNAPred: Identification of human piRNAs by the voting-based extreme learning machine (V-ELM) with a new hybrid feature.

Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work.

LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature.

As a novel class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been verified to be associated with various diseases. As large scale transcripts are generated every year, it is significant to accurately and quickly identify lncRNAs from thousands of assembled transcripts. To accurately discover new lncRNAs, we develop a classification tool of random forest (RF) named LncRNApred based on a new hybrid feature.

[Reconstruction Research for Gas Concentration and Temperature of Flame Based on Algebraic Reconstruction Technique].

We specify water vapor among combustion products as the target gas based on tunable diode absorption spectroscopy in this paper. The direct absorption signals of water vapor after being processed can be used to calculate the gas concentration distributions and temperature distributions of the combustion region of methane and air flat flame furnace via algebraic reconstruction technique (ART). In the numerical simulation, reconstruction region is a grid of five by five, we assume a temperature and water vapor concentration distribution of 25 grid, then simulate different direction laser rays which cross the combustion region, generating projection of each ray, by ART reconstruction algorithm, it turns out that the temperature and water vapor distribution reconstruction error is less than 1%.

[Study of high temperature water vapor concentration measurement method based on absorption spectroscopy].

Tunable diode laser absorption spectroscopy (TDLAS) has been developed to realize the real-time and dynamic measurement of the combustion temperature, gas component concentration, velocity and other flow parameters, owing to its high sensitivity, fast time response, non-invasive character and robust nature. In order to obtain accurate water vapor concentration at high temperature, several absorption spectra of water vapor near 1.39 μm from 773 to 1273 K under ordinary pressure were recorded in a high temperature experiment setup using a narrow band diode laser.