Characteristics of brain connectivity during verbal fluency test: Convolutional neural network for functional near-infrared spectroscopy analysis

Human connectome describes the complicated connection matrix of nervous system among human brain. It also possesses high potential of assisting doctors to monitor the brain injuries and recoveries in patients. In order to unravel the enigma of neuron connections and functions, previous research has strived to dig out the relations between neurons and brain regions. Verbal fluency test (VFT) is a general neuropsychological test, which has been used in functional connectivity investigations. In this study, we employed convolutional neural network (CNN) on a brain hemoglobin concentration changes (ΔHB) map obtained during VFT to investigate the connections of activated brain areas and different mental status. Our results show that feature of functional connectivity can be identified accurately with the employment of CNN on ΔHB mapping, which is beneficial to improve the understanding of brain functional connections.     

Quantitative analysis of hemoglobin oxygenation state of rat brain in situ by near-infrared spectrophotometry

The light in the near-infrared region (700-900 nm) was illuminated on the rat head, and absorption spectra were measured with the transmitted light under various conditions. The absorbance changes less than 780 nm were attributable to hemoglobin in the brain tissue, whereas those greater than 780 nm were associated with both hemoglobin and cytochrome oxidase. The changes of oxy- and total (oxy- plus deoxy-) hemoglobin content in the rat head could be monitored quantitatively by expressions of delta A700--1.20 delta A730 and delta A700--1.52 delta A730, respectively. The oxyhemoglobin content in the tissue was decreased as the O2 tension in inspired gas was lowered. At 10% O2 approximately 50% of hemoglobin was deoxygenated. The total hemoglobin content was increased under anoxic conditions. Inhalation of 5% CO2 and intravenous injection of a Ca2+ blocker nicardipine increased the O2 saturation of hemoglobin in the brain. These conclusions were confirmed by measuring the difference absorption spectra in the near-infrared region.     

Labview在动物脑电信号采集分析中的应用

分析动物行为活动中的脑电特征是脑机接口(Brain-computer interface,BCI)研究中的一个重要内容.本文利用最新测控软件-虚拟仪器技术(LabVIEW)进行脑电信号采集与处理,实现了信号实时显示、中值滤波、小渡消噪的设计.实验结果显示提取出了与特定行为(抓食)相关的脑电活动特征信号,为研究大脑如何控制行为提供了一个有效的方法.     

Shh signal and its functional roles in normal and diseased brain

The identification of a Sonic Hedgehog (Shh) signaling pathway in the adult vertebrate central nervous system has paved the way to the characterization of the functional roles of Shh signals in normal and diseased brain. This morphogen is proposed to play a key role in the establishment and maintenance of adult neurogenic niches and to modulate the proliferation of neuronal or glial precursors. Consistent with its role during embryogenesis, alteration of Shh signaling is associated with tumorigenesis while its recruitment in damaged neural tissue might be part of the regenerating process. We will discuss the most recent data of the Hedgehog pathway in the adult brain and its relevance as a novel therapeutic approach for brain diseases including brain tumors.     

功能性脑成像的多维模式分析方法

利用非侵入式的功能性脑成像记录大脑活动极大地提升了我们对人类认知功能的理解.与此同时,分析成像数据的手段也逐渐从传统的一元方式向更加有效的多元分析转变.在本综述中,特别针对在认知神经科学领域占主导地位的功能性磁共振成像技术,介绍其多元数据分析方法的发展以及这种分析方法的生理学基础和未来发展方向.     

A dual functional signal mediator showing RhoGAP and phospholipase C-delta stimulating activities.

We have cloned a novel regulator protein, p122, in the PLC-delta signalling pathway by screening a rat brain expression library with antiserum raised against purified phospholipase C-delta 1 (PLC-delta 1). This novel p122-RhoGAP binds to PLC-delta 1 and activates the phosphatidylinositol 4,5-bisphosphate (PIP2) hydrolyzing activity of PLC-delta 1. As suggested by the deduced amino acid sequence, this regulator protein shows a similarity to the GTPase activating protein (GAP) homology region of Bcr and possesses GAP activity for RhoA, but not for Rac1; no guanine nucleotide exchange activity for RhoA and Rac1 was detected. These findings suggest that this novel RhoGAP is involved in the Rho signalling pathway, probably downstream of Rho activation, and mediates the stimulation of PLC-delta, which leads to actin-related cytoskeletal changes through the hydrolysis of PIP2, which binds to actin binding proteins such as gelsolin and profilin.     

Phosphoproteomics strategies for the functional analysis of signal transduction

Protein phosphorylation is a key regulatory mechanism of cellular signalling processes. The analysis of phosphorylated proteins and the characterisation of phosphorylation sites under different biological conditions are some of the most challenging tasks in current proteomics research. Reduction of the sample complexity is one major step for the analysis of low-abundance kinase substrates, which can be achieved by various subcellular fractionation techniques. One strategy is the enrichment of phosphorylated proteins or peptides by immunoprecipitation or chromatography, e.g. immobilised metal affinity chromatography, prior to analysis. 2-DE gels are powerful tools for the analysis of phosphoproteins when combined with new multiplexing techniques like DIGE, phosphospecific stains, autoradiography or immunoblotting. In addition, several gel-free methods combining chromatography with highly sensitive MS have been successfully applied for the analysis of complex phosphoproteomes. Recently developed approaches like KESTREL or 'chemical genetics' and also protein microarrays offer new possibilities for the identification of specific kinase targets. This review summarises various strategies for the analyses of phosphoproteins with a special focus on the identification of novel kinase substrates.     

Mitochondrial signal transduction in accelerated wound and retinal healing by near-infrared light therapy

Photobiomodulation by light in the red to near infrared range (630-1000 nm) using low energy lasers or light-emitting diode (LED) arrays has been shown to accelerate wound healing, improve recovery from ischemic injury in the heart and attenuate degeneration in the injured optic nerve. Recent evidence indicates that the therapeutic effects of red to near infrared light result, in part, from intracellular signaling mechanisms triggered by the interaction of NIR light with the mitochondrial photoacceptor molecule cytochrome c oxidase. We have demonstrated that NIR-LED photo-irradiation increases the production of cytochrome oxidase in cultured primary neurons and reverses the reduction of cytochrome oxidase activity produced by metabolic inhibitors. We have also shown that NIR-LED treatment prevents the development of oral mucositis in pediatric bone marrow transplant patients. Photobiomodulation improves wound healing in genetically diabetic mice by upregulating genes important in the promotion of wound healing. More recent studies have provided evidence for the therapeutic benefit of NIR-LED treatment in the survival and functional recovery of the retina and optic nerve in vivo after acute injury by the mitochondrial toxin, formic acid generated in the course of methanol intoxication. Gene discovery studies conducted using microarray technology documented a significant upregulation of gene expression in pathways involved in mitochondrial energy production and antioxidant cellular protection. These findings provide a link between the actions of red to near infrared light on mitochondrial oxidative metabolism in vitro and cell injury in vivo. Based on these findings and the strong evidence that mitochondrial dysfunction is involved in the pathogenesis of numerous diseases processes, we propose that NIR-LED photobiomodulation represents an innovative and non-invasive therapeutic approach for the treatment of tissue injury and disease processes in which mitochondrial dysfunction is postulated to play a role including diabetic retinopathy, age-related macular degeneration, Leber's hereditary optic neuropathy and Parkinson's disease.     

Classifying mild traumatic brain injuries with functional network analysis

Background

Traumatic brain injury (TBI) represents a critical health problem of which timely diagnosis and treatment remain challenging. TBI is a result of an external force damaging brain tissue, accompanied by delayed pathogenic events which aggravate the injury. Molecular responses to different mild TBI subtypes have not been well characterized. TBI subtype classification is an important step towards the development and application of novel treatments. The computational systems biology approach is proved to be a promising tool in biomarker discovery for central nervous system injury.

Results

In this study, we have performed a network-based analysis on gene expression profiles to identify functional gene subnetworks. The gene expression profiles were obtained from two experimental models of injury in rats: the controlled cortical impact and the fluid percussion injury. Our method integrates protein interaction information with gene expression profiles to identify subnetworks of genes as biomarkers. We have demonstrated that the selected gene subnetworks are more accurate to classify the heterogeneous responses to different injury models, compared to conventional analysis using individual marker genes selected without network information.

Conclusions

The systems approach can lead to a better understanding of the underlying complexities of the molecular responses after TBI and the identified subnetworks will have important prognostic functions for patients who sustain mild TBIs.

     

Redox behavior of cytochrome oxidase in the rat brain measured by near-infrared spectroscopy

Hoshi, Yoko, Osamu Hazeki, Yasuyuki Kakihana, and MamoruTamura. Redox behavior of cytochrome oxidase in the rat brain measured by near-infrared spectroscopy. J. Appl.Physiol. 83(6): 1842-1848, 1997.Usingnear-infrared spectroscopy, we developed a new approach for measuringthe redox state of cytochrome oxidase in the brain under normalblood-circulation conditions. Our algorithm does not require theabsorption coefficient of cytochrome oxidase, which differs from studyto study. We employed this method for evaluation of effects of changesin oxygen delivery on cerebral oxygenation in rats. When fractionalinspired oxygen was decreased in a stepwise manner from100 to <10%, at which point the concentration of oxygenatedhemoglobin([HbO₂])decreased by ~60%, cytochrome oxidase started to be reduced.Increases in arterial PO₂ underhyperoxic conditions caused an increase in[HbO₂], whereas further oxidation of cytochrome oxidase was not observed. The dissociation of the responses of hemogloblin and cytochrome oxidase wasalso clearly observed after the injection of epinephrine under severelyhypoxic conditions; that is, cytochrome oxidase was reoxidized withincreasing blood pressure, whereas hemoglobin oxygenation was notchanged. These data indicated that oxygen-dependent redox changes incytochrome oxidase occur only when oxygen delivery is extremelyimpaired. This is consistent with the in vitro data of our previousstudy.

     

Determination of figures of merit for near-infrared and raman spectrometry by net analyte signal analysis for a 4-component solid dosage system

Process analytical technology has elevated the role of sensors in pharmaceutical manufacturing. Often the ideal technology must be selected from many suitable candidates based on limited data. Net analyte signal (NAS) theory provides an effective platform for method characterization based on multivariate figures of merit (FOM). The objective of this work was to demonstrate that these tools can be used to characterize the performance of 2 dissimilar analyzers based on different underlying spectroscopic principles for the analysis of pharmaceutical compacts. A fully balanced, 4-constituent mixture design composed of anhydrous theophylline, lactose monohydrate, microcrystalline cellulose, and starch was generated; it consisted of 29 design points. Six 13-mm tablets were produced from each mixture at 5 compaction levels and were analyzed by near-infrared and Raman spectroscopy. Partial least squares regression and NAS analyses were performed for each component, which allowed for the computation of FOM. Based on the calibration error statistics, both instruments were capable of accurately modeling all constituents. The results of this work indicate that these statistical tools are a suitable platform for comparing dissimilar analyzers and illustrate the complexity of technology selection.     

Kalman estimator- and general linear model-based on-line brain activation mapping by near-infrared spectroscopy

Background

Methods of manual cell localization and outlining are so onerous that automated tracking methods would seem mandatory for handling huge image sequences, nevertheless manual tracking is, astonishingly, still widely practiced in areas such as cell biology which are outside the influence of most image processing research. The goal of our research is to address this gap by developing automated methods of cell tracking, localization, and segmentation. Since even an optimal frame-to-frame association method cannot compensate and recover from poor detection, it is clear that the quality of cell tracking depends on the quality of cell detection within each frame.

Methods

Cell detection performs poorly where the background is not uniform and includes temporal illumination variations, spatial non-uniformities, and stationary objects such as well boundaries (which confine the cells under study). To improve cell detection, the signal to noise ratio of the input image can be increased via accurate background estimation. In this paper we investigate background estimation, for the purpose of cell detection. We propose a cell model and a method for background estimation, driven by the proposed cell model, such that well structure can be identified, and explicitly rejected, when estimating the background.

Results

The resulting background-removed images have fewer artifacts and allow cells to be localized and detected more reliably. The experimental results generated by applying the proposed method to different Hematopoietic Stem Cell (HSC) image sequences are quite promising.

Conclusion

The understanding of cell behavior relies on precise information about the temporal dynamics and spatial distribution of cells. Such information may play a key role in disease research and regenerative medicine, so automated methods for observation and measurement of cells from microscopic images are in high demand. The proposed method in this paper is capable of localizing single cells in microwells and can be adapted for the other cell types that may not have circular shape. This method can be potentially used for single cell analysis to study the temporal dynamics of cells.     

Postnatal changes in functional activities of the pig's brain: a combined functional magnetic resonance imaging and immunohistochemical study

Developmental changes in brain activation after pain stimulation and after passive movement of the hind paw were assessed by functional magnetic resonance imaging (fMRI) in pigs of postnatal ages 2, 4 and 6 months. Response patterns were correlated with histological maturation parameters. At 2 months, fMRI failed to detect brain activation after pain stimulation and revealed weak, but widespread activation after passive movement. At 4 months, strong reaction of numerous cortical areas on the contralateral side was seen after pain stimulation. Following passive movement, activation was weaker but more widespread, and the brainstem was also involved. By 6 months, cortical activation became more restricted to the contralateral sensory cortex and brainstem after pain stimulation and to the contralateral sensory and ipsilateral premotor and motor cortices after passive movement. Neocortical synaptophysin immunoreaction increased significantly between 2 and 4 months and slightly decreased by 6 months. The density of GABA-immunoreactive neurons and fibers significantly increased, reaching a maximum at 6 months. Our studies indicate that remodeling of synapses and development of inhibitory GABA neurons last until 6 months postnatally, when the fMRI response of the pig's brain also attains its mature adult pattern.     

Induction of non-bilayer lipid structures by functional signal peptides.

Using 31P NMR and freeze-fracture electron microscopy we investigated the effect of several synthetic signal peptides on lipid structure in model membranes mimicking the lipid composition of the Escherichia coli inner membrane. It is demonstrated that the signal peptide of the E. coli outer membrane protein PhoE, as well as that of the M13 phage coat protein, strongly promote the formation of non-bilayer lipid structures. This effect appears to be correlated to in vivo translocation efficiency, since a less functional analogue of the PhoE signal peptide was found to be less active in destabilizing the bilayer. It is proposed that signal sequences can induce local changes in lipid structure that are involved in protein translocation across the membrane.     

A functional decaisoleucine-containing signal sequence. Construction by cassette mutagenesis

An alkaline phosphatase signal sequence optimized for formation of a hydrophobic alpha-helix functions very efficiently in the transport process. This mutant contained a core region comprised of 9 consecutive leucine residues (Kendall, D. A., Bock, S. C., and Kaiser, E. T. (1986) Nature 321, 706-708). We have now constructed a second mutant containing a decaisoleucine core region. Isoleucine was chosen because it is an isomer of leucine with comparable hydrophobicity but in synthetic peptides isoleucine favors beta-sheet formation. Surprisingly, this mutant precursor was also processed efficiently, and mature alkaline phosphatase was correctly targeted to the Escherichia coli periplasm. Since the effective length of a beta-strand is extended relative to an alpha-helix, conformational differences should be mirrored by the relative effectiveness of shortened polyisoleucine and polyleucine core regions. However, analysis of two additional mutants containing truncated segments of either polyleucine or polyisoleucine did not reveal any differences and both accumulate as precursors. We conclude that these mutants do not adopt critically different structures. This comparative analysis was facilitated by construction of a new plasmid, CASS3. This plasmid contains unique restriction sites flanking the DNA region coding for the signal sequence hydrophobic core segment. Consequently, the wild type core-encoding region can be readily replaced with synthetic oligonucleotides coding for new structural units and multiple amino acid substitutions can be made without the need for step-wise mutagenesis.     

Network analysis of intrinsic functional brain connectivity in Alzheimer's disease

Functional brain networks detected in task-free (“resting-state”) functional magnetic resonance imaging (fMRI) have a small-world architecture that reflects a robust functional organization of the brain. Here, we examined whether this functional organization is disrupted in Alzheimer's disease (AD). Task-free fMRI data from 21 AD subjects and 18 age-matched controls were obtained. Wavelet analysis was applied to the fMRI data to compute frequency-dependent correlation matrices. Correlation matrices were thresholded to create 90-node undirected-graphs of functional brain networks. Small-world metrics (characteristic path length and clustering coefficient) were computed using graph analytical methods. In the low frequency interval 0.01 to 0.05 Hz, functional brain networks in controls showed small-world organization of brain activity, characterized by a high clustering coefficient and a low characteristic path length. In contrast, functional brain networks in AD showed loss of small-world properties, characterized by a significantly lower clustering coefficient (p<0.01), indicative of disrupted local connectivity. Clustering coefficients for the left and right hippocampus were significantly lower (p<0.01) in the AD group compared to the control group. Furthermore, the clustering coefficient distinguished AD participants from the controls with a sensitivity of 72% and specificity of 78%. Our study provides new evidence that there is disrupted organization of functional brain networks in AD. Small-world metrics can characterize the functional organization of the brain in AD, and our findings further suggest that these network measures may be useful as an imaging-based biomarker to distinguish AD from healthy aging.     

Resting-state brain organization revealed by functional covariance networks

Background

Brain network studies using techniques of intrinsic connectivity network based on fMRI time series (TS-ICN) and structural covariance network (SCN) have mapped out functional and structural organization of human brain at respective time scales. However, there lacks a meso-time-scale network to bridge the ICN and SCN and get insights of brain functional organization.

Methodology and Principal Findings

We proposed a functional covariance network (FCN) method by measuring the covariance of amplitude of low-frequency fluctuations (ALFF) in BOLD signals across subjects, and compared the patterns of ALFF-FCNs with the TS-ICNs and SCNs by mapping the brain networks of default network, task-positive network and sensory networks. We demonstrated large overlap among FCNs, ICNs and SCNs and modular nature in FCNs and ICNs by using conjunctional analysis. Most interestingly, FCN analysis showed a network dichotomy consisting of anti-correlated high-level cognitive system and low-level perceptive system, which is a novel finding different from the ICN dichotomy consisting of the default-mode network and the task-positive network.

Conclusion

The current study proposed an ALFF-FCN approach to measure the interregional correlation of brain activity responding to short periods of state, and revealed novel organization patterns of resting-state brain activity from an intermediate time scale.     

Quantification of enzyme activities in brain sections by microphotometry

1. Catalytic enzyme histochemistry offers the possibility to demonstrate enzyme activities quantitatively (microphotometry) in brain sections of those sites where they are localized. 2. A prerequisite for quantification are appropriate histochemical procedures for the demonstration of enzymes, which are shortly discussed. 3. For the microphotometric determination of enzymes in brain sections the scanning microphotometry is at present the technique of choice. 4. This is described in the example of an image plane scanning system. 5. Using this technique two measuring procedures can be applied for the quantification of enzyme activities, i.e. kinetic and end-point measurements. 6. Methods for the microphotometric determination of certain important oxido-reductases and further enzymes are presented. 7. It is concluded that quantitative catalytic enzyme histochemistry could be a source of results complementary to those provided by conventional biochemistry.