Reveals new lung adenocarcinoma cancer genes based on gene expression

BACKGROUND

Lung adenocarcinoma (LAC) is the most common type of lung cancer, accounting for 30-35% of all cases.

AIM

In this study we aim to predict potential genes and confirm pathways which are associated with LAC.

MATERIALS AND METHODS

By using the meta-analysis method, GSE10072 and GSE 2514 datasets were merged to find potential genes and pathways which are associated with LAC.

RESULTS

Our analysis indicated identified differentially expressed genes enriched in multicellular organismal metabolic process, gland development, and urogenital system development. Further, we predicted genes including EGF-like domain might be the potential target genes for further study, such as NGX6, MUC17, and Nel. In addition, a number of genes that associated with axon guidance, focal adhesion, and complement and coagulation cascades pathway might be also involved in LAC in a direct or indirectly manner.

CONCLUSIONS

Our analysis indicated identified differentially expressed genes enriched in multicellular organismal metabolic process, gland development, and urogenital system development We anticipate numerous advances in LAC research in the coming years based on our meta-analysis.

Bioequivalence evaluation of cefdinir in healthy fasting subjects

A simple and sensitive HPLC method was developed to determine cefdinir (CAS 91832-40-5) in human plasma. The method was validated by investigating the accuracy and precision for intra- and inter-day runs in a linear concentration from 0.05-2.0 µg/ml. The object of this study was to compare the bioavailability of cefdinir capsule (reference) and cefdinir granule (test) containing 100 mg of cefdinir. A randomized, open-label, single-dose, 2-way crossover bioequivalence study in 20 healthy, Chinese, male subjects was conducted. A 1-week wash-out period was applied. Blood samples were collected before and with 10 h after drug administration. The formulations were compared using the following pharmacokinetic parameters: AUC0-t, AUC0-∞ and C max. The 90% confidence interval (CI) of the ratios of log-transformed AUC0-t and AUC0-∞ were used to assess bioequivalence between the 2 formulations using the equivalence interval of 80 and 125%. The results showed that the 90% CI of the ratios of AUC0-t, AUC0-∞ and C max were 102.5% (94.7-111.0%), 103.4% (94.8-112.7%) and 106.4% (97.0-116.7%), respectively, which indicated 2 formulations of cefidinir are bioequivalent. Both treatments showed similar tolerability and safety.

Detecting abnormalities of corpus callosum connectivity in autism using magnetic resonance imaging and diffusion tensor tractography

The corpus callosum (CC) has emerged as one of the primary targets of autism research. To detect aberrant CC interhemispheric connectivity in autism, we performed T1-weighted magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI)-based tractography in 18 children with high functioning autism (HFA) and 16 well-matched typically developing (TD) children. We compared global and regional T1 measures (CC volume, and CC density), and the DTI measures [fractional anisotropy (FA), apparent diffusion coefficient (ADC), average fiber length (AFL), and fiber number (FN)] of transcallosal fibers, between the two groups. We also evaluated the relationships between scores on the Childhood Autism Rating Scale (CARS) and CC T1 or DTI measurements. Significantly less white matter density in the anterior third of the CC, and higher ADC and lower FN values of the anterior third transcallosal fiber tracts were found in HFA patients compared to TD children. These results suggested that the anterior third CC density and transcallosal fiber connectivity were affected in HFA children.

Microbial strategies to control aflatoxins in food and feed

Aflatoxins are a group of toxic and carcinogenic fungal metabolites. They are commonly found in cereals, nuts and animal feeds and create a significant threat to the food industry and animal production. Several strategies have been developed to avoid or reduce harmful effects of aflatoxins since the 1960s. However, prevention of aflatoxin contamination pre/post harvest or during storage has not been satisfactory and control strategies such as physical removing and chemical inactivating used in food commodities have their deficiencies, which limit their large scale application. It is expected that progress in the control of aflatoxin contamination will depend on the introduction of technologies for specific, efficient and environmentally sound detoxification. The utilisation of biological detoxification agents, such as microorganisms and/or their enzymatic products to detoxify aflatoxins in contaminated food and feed can be a choice of such technology. To date, many of the microbial strategies have only showed reduced concentration of aflatoxins and the structure and toxicity of the detoxified products are unclear. More attention should be paid to the detoxification reactions, the structure of biotransformed products and the enzymes responsible for the detoxification. In this article, microbial strategies for aflatoxin control such as microbial binding and microbial biotransformation are reviewed.

A rare case of circumferential intramural dissection of the thoracic esophagus

Esophageal intramural dissection is a rare disease, and whole thoracic esophageal intramural dissection is extremely rare. We report a case of circumferential intramural dissection of the thoracic esophagus, which occurred between the submucosal layer and the muscularis propria layer, with inflammation in the false lumen mimicking esophageal mediastinal fistula in the endoscopic view. The diagnosis was finally confirmed at operation and cured by thoracic esophagectomy.

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model

Motivation: Digital reconstruction of 3D neuron structures is an important step toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns.

Results: We developed a graph-augmented deformable model (GD) to reconstruct (trace) the 3D structure of a neuron when it has a broken structure and/or fuzzy boundary. We formulated a variational problem using the geodesic shortest path, which is defined as a combination of Euclidean distance, exponent of inverse intensity of pixels along the path and closeness to local centers of image intensity distribution. We solved it in two steps. We first used a shortest path graph algorithm to guarantee that we find the global optimal solution of this step. Then we optimized a discrete deformable curve model to achieve visually more satisfactory reconstructions. Within our framework, it is also easy to define an optional prior curve that reflects the domain knowledge of a user. We investigated the performance of our method using a number of challenging 3D neuronal image datasets of different model organisms including fruit fly, Caenorhabditis elegans, and mouse. In our experiments, the GD method outperformed several comparison methods in reconstruction accuracy, consistency, robustness and speed. We further used GD in two real applications, namely cataloging neurite morphology of fruit fly to build a 3D ‘standard’ digital neurite atlas, and estimating the synaptic bouton density along the axons for a mouse brain.

Availability: The software is provided as part of the V3D-Neuron 1.0 package freely available at http://penglab.janelia.org/proj/v3d

Contact:pengh@janelia.hhmi.org

Pulmonary sequestration: angioarchitecture evaluated by three-dimensional computed tomography angiography

Pulmonary sequestration represents an anomaly of nonfunctioning tracheobronchial branching with retention of the embryonic systemic arterial supply. We report a case of intralobar pulmonary sequestration, in which the abnormal supplying artery and especially the abnormal draining vein were demonstrated by three-dimensional computed tomography angiography and were confirmed and treated using a video-assisted thoracoscopic procedure.

Central role of nitric oxide synthase in AICAR and caffeine-induced mitochondrial biogenesis in L6 myocytes

5-Aminoimidazole-4-carboxamide-ribonucleoside (AICAR) and caffeine, which activate AMP-activated protein kinase (AMPK) and cause sarcoplasmic reticulum calcium release, respectively, have been shown to increase mitochondrial biogenesis in L6 myotubes. Nitric oxide (NO) donors also increase mitochondrial biogenesis. Since neuronal and endothelial NO synthase (NOS) are calcium dependent and are also phosphorylated by AMPK, we hypothesized that NOS inhibition would attenuate the activation of mitochondrial biogenesis in response to AICAR and caffeine. L6 myotubes either were not treated (control) or were exposed acutely or for 5 h/day over 5 days to 100 microM of N(G)-nitro-L-arginine methyl ester (L-NAME, NOS inhibitor), 100 microM S-nitroso-N-acetyl-penicillamine (SNAP) (NO donor) +/- 100 microM L-NAME, 2 mM AICAR +/- 100 microM L-NAME, or 5 mM caffeine +/- 100 microM L-NAME (n = 12/treatment). Acute AICAR administration increased (P < 0.05) phospho- (P-)AMPK, but also increased P-CaMK, with resultant chronic increases in peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1 alpha), cytochrome-c oxidase (COX)-1, and COX-4 protein expression compared with control cells. NOS inhibition, which had no effect on AICAR-stimulated P-AMPK, surprisingly increased P-CaMK and attenuated the AICAR-induced increases in COX-1 and COX-4 protein. Caffeine administration, which increased P-CaMK without affecting P-AMPK, increased COX-1, COX-4, PGC-1 alpha, and citrate synthase activity. NOS inhibition, surprisingly, greatly attenuated the effect of caffeine on P-CaMK and attenuated the increases in COX-1 and COX-4 protein. SNAP increased all markers of mitochondrial biogenesis, and it also increased P-AMPK and P-CaMK. In conclusion, AICAR and caffeine increase mitochondrial biogenesis in L6 myotubes, at least in part, via interactions with NOS.

Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains

Automatic alignment (registration) of 3D images of adult fruit fly brains is often influenced by the significant displacement of the relative locations of the two optic lobes (OLs) and the center brain (CB). In one of our ongoing efforts to produce a better image alignment pipeline of adult fruit fly brains, we consider separating CB and OLs and align them independently. This paper reports our automatic method to segregate CB and OLs, in particular under conditions where the signal to noise ratio (SNR) is low, the variation of the image intensity is big, and the relative displacement of OLs and CB is substantial. We design an algorithm to find a minimum-cost 3D surface in a 3D image stack to best separate an OL (of one side, either left or right) from CB. This surface is defined as an aggregation of the respective minimum-cost curves detected in each individual 2D image slice. Each curve is defined by a list of control points that best segregate OL and CB. To obtain the locations of these control points, we derive an energy function that includes an image energy term defined by local pixel intensities and two internal energy terms that constrain the curve's smoothness and length. Gradient descent method is used to optimize this energy function. To improve both the speed and robustness of the method, for each stack, the locations of optimized control points in a slice are taken as the initialization prior for the next slice. We have tested this approach on simulated and real 3D fly brain image stacks and demonstrated that this method can reasonably segregate OLs from CBs despite the aforementioned difficulties.

Multicontext wavelet-based thresholding segmentation of brain tissues in magnetic resonance images

A novel segmentation method based on wavelet transform is presented for gray matter, white matter and cerebrospinal fluid in thin-sliced single-channel brain magnetic resonance (MR) scans. On the basis of the local image model, multicontext wavelet-based thresholding segmentation (MCWT) is proposed to classify 2D MR data into tissues automatically. In MCWT, the wavelet multiscale transform of local image gray histogram is done, and the gray threshold is gradually revealed from large-scale to small-scale coefficients. Image segmentation is independently performed in each local image to calculate the degree of membership of a pixel to each tissue class. Finally, a strategy is adopted to integrate the intersected outcomes from different local images. The result of the experiment indicates that MCWT outperforms other traditional segmentation methods in classifying brain MR images.

Gender difference in hemodynamic responses of prefrontal area to emotional stress by near-infrared spectroscopy

Presentation of negative pictures was used as emotional stress to assess gender differences in prefrontal area activation in a functional near-infrared spectroscopy (NIRS) study. Compared with neutral condition, the response of oxy-HB for men yielded no significant difference during stress period, but the response induced by stress pictures for women showed significant enhancement. It was indicated that it is crucial to take gender difference into account when negative stimuli are used in functional brain imaging.

RP-HPLC analysis of flucloxacillin in human plasma: validation and application to a bioequivalence study

A RP-HPLC method with rapid sample processing was developed for quantitation of flucloxacillin in human plasma using dicloxacillin as the internal standard. The plasma sample (100 microL) was acidified with glacial acetic acid, and deproteinized by precipitation with acetonitrile. The supernatant was directly injected into the HPLC system. Separation was achieved on an Alltima C18 column (250 mmx4.6 mm I.D., 5 microm), with a mixture of 10 mmol x L(-1) KH2PO4-acetonitrile (64.5:35.5, v/v) as mobile phase. The assay was successfully applied to a randomized, two-period cross-over bioequivalence study in 20 healthy Chinese volunteers following a single oral dose of 250 mg flucloxacillin capsules. A non-compartmental method was used for pharmacokinetic analysis. Compared with data in the literature, flucloxacillin was eliminated more slowly in Chinese than in Caucasians. Cmax, AUC(0-t) and AUC(0-infinity) were tested for bioequivalence after log-transformation of data. No significant difference was found. Tmax was analyzed by Wilcoxon's test and no significant difference was obtained (P > 0.05). Based on these statistical inferences, the two formulations were judged to be bioequivalent and, thus, can be prescribed interchangeably.

Expression of the novel co-stimulatory molecule B7-H4 by renal tubular epithelial cells

Crosstalk between T cells and renal tubular epithelial cells (TECs) in the pathogenesis of tubular lesions, the most important sign of progressive renal diseases, has not been clarified. Previous work has shown that TECs harbor co-stimulatory signals that promote T-cell activation, which induces tubular lesions. Nevertheless, the expression and functional role of B7-H4, a recently identified co-stimulatory ligand of the B7 superfamily, in pathologic human kidneys is unclear. We investigated the expression of B7-H4 on cryostat renal biopsies from patients with idiopathic membranous nephropathy (n=20), immunoglobulin A nephropathy (n=19), lupus nephritis (n=16), and acute renal allograft rejection (n=15) using immunohistochemistry. In addition, we also analyzed TEC-associated B7-H4 in the regulation of T-cell activation. Immunohistological staining revealed that B7-H4 antigen is restricted to tubular epithelium and that the protein is prominent in sections with severe tubular lesions, although no correlation was observed between tubular B7-H4 expression and levels of serum creatinine, serum urea nitrogen concentration, and 24-h proteinuria in each type of nephropathy. In vitro, mixed lymphocyte reactions revealed that TEC-related B7-H4 promotes cytokine (interleukin-2 and interferon-gamma) production and proliferation of co-cultured T cells. Interestingly, the secretion of interleukin-2 by C10 T cell hybridomas also increased when C10 cells were co-cultured with the B7-H4-transgenic murine TEC line, 3M-1-secreting tubular epithelial cells (MCT) in the presence of the antigen hen egg lysozyme. Our results clearly show that TEC-associated B7-H4 induces T-cell activation and we propose that B7-H4 is a potential activator that promotes tubular lesion.