Function Clustering Self-Organization Maps (FCSOMs) for mining differentially expressed genes in Drosophila and its correlation with the growth medium

The central task of this study was to mine the gene-to-medium relationship. Adequate knowledge of this relationship could potentially improve the accuracy of differentially expressed gene mining. One of the approaches to differentially expressed gene mining uses conventional clustering algorithms to identify the gene-to-medium relationship. Compared to conventional clustering algorithms, self-organization maps (SOMs) identify the nonlinear aspects of the gene-to-medium relationships by mapping the input space into another higher dimensional feature space. However, SOMs are not suitable for huge datasets consisting of millions of samples. Therefore, a new computational model, the Function Clustering Self-Organization Maps (FCSOMs), was developed. FCSOMs take advantage of the theory of granular computing as well as advanced statistical learning methodologies, and are built specifically for each information granule (a function cluster of genes), which are intelligently partitioned by the clustering algorithm provided by the DAVID_6.7 software platform. However, only the gene functions, and not their expression values, are considered in the fuzzy clustering algorithm of DAVID. Compared to the clustering algorithm of DAVID, these experimental results show a marked improvement in the accuracy of classification with the application of FCSOMs. FCSOMs can handle huge datasets and their complex classification problems, as each FCSOM (modeled for each function cluster) can be easily parallelized.

Yes-associated protein (YAP) expression is involved in epithelial-mesenchymal transition in hepatocellular carcinoma

PURPOSE

To investigate biological impact of the downregulation of yes-associated protein (YAP) through RNA interference in the process of epithelial-mesenchymal transition in MHCC97H and MHCC97L.

METHODS

MHCC97H and MHCC97L cells were transiently transfected by YAP-siRNA. Furthermore, protein expressions and mRNA levels of characteristic markers of epithelial-mesenchymal transition (E-cadherin, N-cadherin) were examined by Western blotting and real-time polymerase chain reaction, and transwell invasion assay was used to detect changes of invasiveness of MHCC97H and MHCC97L cells.

RESULTS

The transfected group with YAP-siRNA in MHCC97H after 72 h by Western blotting showed obviously higher expression of E-cadherin compared with the control group (P < 0.05), and lower expression of N-cadherin (P < 0.05). In MHCC97L cells, the expression of E-cadherin was also significantly increased (P < 0.05); however, N-cadherin expression did not significantly change (P > 0.05). Moreover, compared with the control group, Transwell invasion assay showed that the number of the transfected groups was significantly decreased in MHCC97H and MHCC97L cell lines (both P < 0.05). The result of real-time polymerase chain reaction indicated that mRNA levels of E-cadherin increased (P < 0.05), but the mRNA levels of N-cadherin did not significantly change (P > 0.05) in these two cell lines, indicating some effects of post-transcriptional regulation mechanism after silencing YAP.

CONCLUSIONS

YAP expression in human hepatocellular carcinoma cell lines MHCC97H and MHCC97L is closely related with the characteristic markers of epithelial-mesenchymal transition, N-cadherin and E-cadherin expression.

Online monitoring of oil film using electrical capacitance tomography and level set method

In the application of oil-air lubrication system, electrical capacitance tomography (ECT) provides a promising way for monitoring oil film in the pipelines by reconstructing cross sectional oil distributions in real time. While in the case of small diameter pipe and thin oil film, the thickness of the oil film is hard to be observed visually since the interface of oil and air is not obvious in the reconstructed images. And the existence of artifacts in the reconstructions has seriously influenced the effectiveness of image segmentation techniques such as level set method. Besides, level set method is also unavailable for online monitoring due to its low computation speed. To address these problems, a modified level set method is developed: a distance regularized level set evolution formulation is extended to image two-phase flow online using an ECT system, a narrowband image filter is defined to eliminate the influence of artifacts, and considering the continuity of the oil distribution variation, the detected oil-air interface of a former image can be used as the initial contour for the detection of the subsequent frame; thus, the propagation from the initial contour to the boundary can be greatly accelerated, making it possible for real time tracking. To testify the feasibility of the proposed method, an oil-air lubrication facility with 4 mm inner diameter pipe is measured in normal operation using an 8-electrode ECT system. Both simulation and experiment results indicate that the modified level set method is capable of visualizing the oil-air interface accurately online.

Treatment and mechanism of BMMSCs on deep II degree scald of hamster skin

In this study, we examined the treatment and mechanism of BMMSC on a deep II degree scald of the hamster skin. A deep II degree scald model on the skin of 40 hamsters was duplicated and divided randomly into a stem cell plantation group (group A) and model control group (group B). Skin cells were cultured in vitro until the allogeneic BMMSCs of the 5th generation formed with a cell count of 1 x 10(7)/mL. Local injection plus liquid supernatant smearing was used to plant the cells into the position of the scald in the stem cell plantation group. The control group was given an equivalent amount of normal saline to observe the healing action, and 5 samples were taken in each group after 1, 3, 7, and 14 days for hematoxylin and eosin staining for physiological observation. Polymerase chain reaction was used to detect the amount of chymotrypsin in mast cells. The speed of healing in the stem cell transplantation group was greater than that in the control group; staining results showed that the quality of healing in the transplantation group was better than that in the control group. Chymotrypsin expression was detected in both groups, reaching a peak on day 3. BMMSCs can accelerate wound healing, and chymotrypsin in mast cells may participate in the wound healing process.

Prone positioning decreases cardiac output and increases systemic vascular resistance in neonates

OBJECTIVE

To evaluate the cardiovascular response to short-term prone positioning in neonates.

STUDY DESIGN

In this prospective study, we continuously monitored heart rate (HR), stroke volume (SV) and cardiac output (CO) by electrical velocimetry in hemodynamically stable neonates in each of the following positions for 10 min: supine, prone and back-to-supine position. Skin blood flow (SBF) was also continuously assessed on the forehead or foot using Laser Doppler technology. Systemic vascular resistance (SVR) index was calculated as mean blood pressure (BP)/CO. Data were analyzed using repeated measures analysis of variance.

RESULTS

Thirty neonates (gestational age: 35±4 weeks; postmenstrual age: 36±3 weeks) were enrolled. HR did not change in response to positioning. However, in prone position, SV, CO and SBF decreased and SVR index increased from 1.5±0.3 to 1.3±0.3 ml kg(-1) (mean ±s.d., P<0.01), 206±44 to 180±41 ml kg(-1) min(-1) (P<0.01), 0.54±0.30 to 0.44±0.29 perfusion units (P<0.01) and 0.25±0.06 to 0.30±0.07 mm Hg ml(-1) kg(-1) min(-1) (P<0.01), respectively. After placing the infants back-to-supine position, SV, CO, SBF and SVR index returned to baseline. The above pattern of cardiovascular changes was consistent in vast majority of the studied neonates.

CONCLUSIONS

Short-term prone positioning is associated with decreased SV, CO and SBF and increased calculated SVR index.

The timecourse of apoptotic cell death during postnatal remodeling of the mouse cochlea and its premature onset by triiodothyronine (T3)

Apoptosis underlies various forms of tissue remodeling during development. Prior to the onset of hearing, thyroid hormone (T3) promotes cochlear remodeling, which involves regression of the greater epithelial ridge (GER), a transient structure of columnar cells adjacent to the mechanosensory hair cells. We investigated the timecourse of apoptosis in the GER and the influence of ectopic T3 on apoptosis. In saline-treated mice, activated caspase 3-positive cells were detected in the GER between postnatal days 7 and 13 and appeared progressively along the cochlear duct from base to apex over developmental time. T3 given on P0 and P1 advanced the overall program of apoptosis and remodeling by ~4 days. Thyroid hormone receptor β was required for these actions, suggesting a receptor-mediated process of initiation of apoptosis. Finally, T3 given only at P0 or P1 resulted in deafness in adult mice, thus revealing a transient period of susceptibility to long-term damage in the neonatal auditory system.

Household transmissibility of avian influenza A (H7N9) virus, China, February to May 2013 and October 2013 to March 2014

To study human-to-human transmissibility of the avian influenza A (H7N9) virus in China, household contact information was collected for 125 index cases during the spring wave (February to May 2013), and for 187 index cases during the winter wave (October 2013 to March 2014). Using a statistical model, we found evidence for human-to-human transmission, but such transmission is not sustainable. Under plausible assumptions about the natural history of disease and the relative transmission frequencies in settings other than household, we estimate the household secondary attack rate (SAR) among humans to be 1.4% (95% CI: 0.8 to 2.3), and the basic reproductive number R0 to be 0.08 (95% CI: 0.05 to 0.13). The estimates range from 1.3% to 2.2% for SAR and from 0.07 to 0.12 for R0 with reasonable changes in the assumptions. There was no significant change in the human-to-human transmissibility of the virus between the two waves, although a minor increase was observed in the winter wave. No sex or age difference in the risk of infection from a human source was found. Human-to-human transmissibility of H7N9 continues to be limited, but it needs to be closely monitored for potential increase via genetic reassortment or mutation.

LincRNA-ROR induces epithelial-to-mesenchymal transition and contributes to breast cancer tumorigenesis and metastasis

LncRNAs have critical roles in various biological processes ranging from embryonic development to human diseases, including cancer progression, although their detailed mechanistic functions remain illusive. The lncRNA linc-ROR has been shown to contribute to the maintenance of induced pluripotent stem cells and embryonic stem cells. In this study, we discovered that linc-ROR was upregulated in breast tumor samples, and ectopic overexpression of linc-ROR in immortalized human mammary epithelial cells induced an epithelial-to-mesenchymal transition (EMT) program. Moreover, we showed that linc-ROR enhanced breast cancer cell migration and invasion, which was accompanied by generation of stem cell properties. Contrarily, silencing of linc-ROR repressed breast tumor growth and lung metastasis in vivo. Mechanistically, our data revealed that linc-ROR was associated with miRNPs and functioned as a competing endogenous RNA to mi-205. Specifically, linc-ROR prevented the degradation of mir-205 target genes, including the EMT inducer ZEB2. Thus our results indicate that linc-ROR functions as an important regulator of EMT and can promote breast cancer progression and metastasis through regulation of miRNAs. Potentially, the findings of this study implicate the relevance of linc-ROR as a possible therapeutic target for aggressive and metastatic breast cancers.

Inhibition enhancer of zeste homologue 2 promotes senescence and apoptosis induced by doxorubicin in p53 mutant gastric cancer cells

OBJECTIVES

Enhancer of zeste homologue 2 (EZH2) is crucially involved in epigenetic silencing by acting as a histone methyltransferase. Although EZH2 is overexpressed in many cancers and is involved in malignant cell proliferation and invasion, the role of EZH2 in senescence induced by DNA damage has up to now remained largely unknown. In this study, we sought to explore the outcome of EZH2 depletion along with exposure of doxorubicin (DOX), and related mechanisms, in gastric cancer cells.

MATERIALS AND METHODS

Here, senescence induced by DNA damage was achieved in gastric cancer cells by DOX treatment. EZH2 was downregulated by transfection with siRNA or treated with (-)-epigallocatechin-3-gallate, a targeted inhibitor. Senescence-associated β galactosidase (SA-β-gal) and formation of senescence-associated heterochromatin foci were used to identify cell senescence. To investigate effects of EZH2 depletion on the cell cycle, apoptosis and proliferation, flow cytometry and MTT analysis were employed. Changes in p53-p21 axis activation were detected by Western blotting.

RESULTS

We found that cell proliferative arrest caused by DOX could be promoted by EZH2 depletion. Mechanistically, EZH2 depletion not only worked in coordination with DNA damage during the progression of cell senescence but also promoted apoptosis in p53 mutant cells. However, it had no cooperative relationship with DOX in p53 wild-type cells.

CONCLUSIONS

These data help unravel a crucial role for EZH2 in senescence and apoptosis in gastric cancer cells and that p53 genomic status was associated with different cell responses to EZH2 silencing.

Mitochondrial bioenergetic deficits in the hippocampi of rats with chronic ischemia-induced vascular dementia

Vascular dementia (VD), defined as a loss of memory and cognitive function resulting from vascular lesions in the brain, is the second-most-common cause of dementia in the elderly, after Alzheimer's disease. In recent years, research has focused on the pathogenesis of VD, and mitochondrial bioenergetic deficits have been suggested to contribute to VD onset. To further investigate the role of mitochondria in VD, we used a rat model of VD, which involved permanent bilateral occlusion of the common carotid arteries (with a 1-week interval between artery occlusion to avoid an abrupt reduction in cerebral blood flow) leading to chronic cerebral hypoperfusion. Prior to occlusion, male Wistar rats underwent 7 days of Morris water maze training. Only animals that could swim and passed the Morris water maze test were chosen for the study. After 5 days of Morris water maze training, mitochondria from the hippocampi of rats, which were randomly selected from animals that could complete the Morris water maze test, were isolated for functional assessment. Mitochondria isolated from the hippocampi of rats from the ischemia group had decreased pyruvate dehydrogenase protein levels, and increased oxidative stress, as manifested by increased hydrogen peroxide production. The ischemia group mitochondria also exhibited decreased respiration coupled to decreased expression and activity of the electron transport chain complex IV (cytochrome c oxidase). These results indicate that the mitochondrial oxidative metabolism is inhibited in the hippocampi of rats following chronic ischemia-induced VD. As the mitochondrial oxidative metabolism deficits, namely mitochondrial bioenergetic deficits directly affect the functions of neurons, it may contribute to VD onset.

Apparent diffusion coefficients of normal uterus in premenopausal women with 3 T MRI

AIM

To investigate the apparent diffusion coefficient (ADC) values of the normal uterine cervical zonal structures (cervical epithelium, the junctional zone, and myometrium) during different phases of the menstrual cycle among premenopausal women in different age groups.

MATERIALS AND METHODS

Seventy healthy women, who were divided into three age groups (group A, 24 women in their twenties; group B, 23 women in their thirties; group C, 23 women in their forties), underwent 3 T magnetic resonance imaging (MRI) with T2-weighted and diffusion-weighted imaging (DWI) during the mid-proliferative and the mid-secretory phases.

RESULTS

The ADC values of each cervical zonal structure were significantly different from one another (p < 0.001). The ADC values of the epithelium and junctional zones were both lower during the mid-secretory phase than those during the mid-proliferative phase in each age group (p < 0.05). There were no significant differences in the ADC values of any of the cervical zones among the three age groups for a given phase (p > 0.05).

CONCLUSION

ADC values of normal cervical epithelium and the junctional zone change with different phases of the menstrual cycle, which should be taken into consideration when early cervical disease is detected, when monitoring treatment response, and differentiating early tumour recurrence.