BOLDMirror: a global mirror system of DNA barcode data

DNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well-organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open-sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding.

Investigation on maternal physiological and psychological factors of cheilopalatognathus

OBJECTIVE

Case-control study on mothers of cheilopalatognathus children was conducted, to investigate the maternal physiological and psychological factors for occurrence of cheilopalatognathus.

MATERIALS AND METHODS

One hundred ten mothers of cheilopalatognathus children who were scheduled for one-stage surgery were selected as a research group, and 110 mothers of normal children served as a normal control group at the same time. Trait Anxiety Inventory (T-AI), Life Events Scale (LES), Trait Coping Style Questionnaire (TCSQ), Type C Behavior Scale (CBS), adult Eysenck Personality Questionnaire (EPQ), and homemade general questionnaire survey were employed for the investigation.

RESULTS

Compared with the control group, the scores for negative event tension value, anxiety, and depressive factors were higher in the study group (p < 0.05); while the scores for positive event tension value, intellect, optimism, and social support factors were lower (p < 0.05). Regression analysis found that physiological factors included were five: education, changes in body weight during pregnancy, the intake amount of milk and beans, and intake of healthcare products, and supplementary folic acid taken or not, while the psychological factors included were four: positive event stimulation, negative event stimulation, the amount of social support, as well as introvert and extrovert personalities.

CONCLUSION

The study results suggest that pregnant women's physiological and psychological factors can cause changes in cheilopalatognathus incidence, which is expected to be guidance for healthcare during pregnancy, to prevent the occurrence of cheilopalatognathus.

HMGB1 promotes the differentiation of Th17 via up-regulating TLR2 and IL-23 of CD14+ monocytes from patients with rheumatoid arthritis

High-mobility group box 1 (HMGB1) is a non-histone nuclear protein that is released extracellulary and has been implicated in autoimmune disease. Toll-like receptor 2 (TLR2) signalling is thought to be essential for the inflammatory response and for immune disorders. In recent studies, enhanced HMGB1 and TLR2 expressions have been found in rheumatoid arthritis (RA), respectively. The aim of this study is to explore whether HMGB1 stimulation can up-regulate the expression of TLR2 on CD14(+) monocytes from patients with RA and to clarify the subsequent events involving Th17 cells and Th17 cell-associated cytokine changes. Our results showed that the frequency of CD14(+) cells in peripheral blood mononuclear cell (PBMC) was obviously increased, and enhanced expression of TLR2 on CD14(+) monocytes was also found in patients with RA, compared with healthy controls with statistical significance (P < 0.001). In addition, the levels of IL-17, IL-23 and IL-6 in supernatants from cultured monocytes from patients and in patient's plasma were increased, and NF-κB, the downstream target of TLR2, also showed a marked elevation after monocytes were stimulated by HMGB1. This implies that the enhanced TLR2 pathway and Th17 cell polarization may be due to HMGB1 stimulation in rheumatoid arthritis.

Abstract P4-02-08: Quantitative Characterization of 3D Vasculature Spatial Patterns Within Tumor Microenvironment of Breast Cancer Stem Cells

The sustainment characters of cancer stem cells (CSCs) such as self-renew and differentiation to other tumor cells greatly depend on the tumor microenvironment, which is composed of many components, e.g. vasculature, extracellular matrix, epithelial cells, stromal cells, as well as nutrients and oxygen. As vasculature is an important factor for the CSC and tumor development, the understanding of their spatial patterns is essential for calibrating the CSC-microenvironment interactions in mathematical modeling. In this study, we acquired the vasculature in side tumors and normal breast tissues by using two-photon fluorescence microscopy, which enables 3D in vivo imaging. We developed an advanced vasculature segmentation approach for an objective and accurate quantification of the vasculature in 3D image volumes. The approach integrates supervoxel analysis and the orientation guided hidden Markov random field (ori-HMRF) modeling together to compensate for low quality images, e.g., low signal-to-noise ratio (SNR) and uneven background. By constructing a new feature space that combines the CIELAB color space and the coordinates space, the supervoxel analysis divides an image volume into subregions with local similar intensity and restricted regular shape, boundaries of which can delineate the vasculature boundaries accurately even in low intensity contrast regions. We further designed a set of features for the separation of blood vessel regions from the background. To make use of the context information, i.e. the continuity of vasculature, the ori-HMRF model is used to incorporate the consistency of vasculatures' orientation in order to reduce the false positives and negatives. Experimental results on image volumes from both breast cancer and normal breast tissues show that the proposed method can effectively reconstruct the vasculature structure with the CSC embedded tumor microenvironment.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-02-08.

Living Liquid: Design and Evaluation of an Exploratory Visualization Tool for Museum Visitors

Interactive visualizations can allow science museum visitors to explore new worlds by seeing and interacting with scientific data. However, designing interactive visualizations for informal learning environments, such as museums, presents several challenges. First, visualizations must engage visitors on a personal level. Second, visitors often lack the background to interpret visualizations of scientific data. Third, visitors have very limited time at individual exhibits in museums. This paper examines these design considerations through the iterative development and evaluation of an interactive exhibit as a visualization tool that gives museumgoers access to scientific data generated and used by researchers. The exhibit prototype, Living Liquid, encourages visitors to ask and answer their own questions while exploring the time-varying global distribution of simulated marine microbes using a touchscreen interface. Iterative development proceeded through three rounds of formative evaluations using think-aloud protocols and interviews, each round informing a key visualization design decision: (1) what to visualize to initiate inquiry, (2) how to link data at the microscopic scale to global patterns, and (3) how to include additional data that allows visitors to pursue their own questions. Data from visitor evaluations suggests that, when designing visualizations for public audiences, one should (1) avoid distracting visitors from data that they should explore, (2) incorporate background information into the visualization, (3) favor understandability over scientific accuracy, and (4) layer data accessibility to structure inquiry. Lessons learned from this case study add to our growing understanding of how to use visualizations to actively engage learners with scientific data.

Icariin stimulates the proliferation of rat Sertoli cells in an ERK1/2-dependent manner in vitro

Icariin (ICA), a major constituent of flavonoids from the Chinese medical herb Epimedium brevicornum Maxim, is found to be protective for male reproductive ability, with the underlying mechanism largely unknown. Our study here investigated the effects of ICA on Sertoli cells, which act as nurse cells for the germ cells developing. Icariin was found to stimulate Sertoli cell proliferation in a dose-dependent manner. Further study revealed that Icariin induced an obvious phosphorylation of ERK in Sertoli cells. Inhibition of activation of ERK by the ERK inhibitor U0126 nearly blocked the Icariin-induced proliferation of Sertoli cells. Taken together, our results suggest that Icariin promotes the proliferation of Sertoli cells in vitro by activating the ERK1/2 signal pathway, which might at least partially, explain the protective role of Icariin on male reproductive ability.

The percutaneous compression plate versus the dynamic hip screw for treatment of intertrochanteric hip fractures: a systematic review and meta-analysis of comparative studies

BACKGROUND

The use of a percutaneous compression plate (PCCP) provides a minimally invasive technique for the fixation of stable intertrochanteric femoral fractures. It has several theoretically potential advantages over the dynamic hip screw (DHS) such as shorten incision and lower incidence of wound infection.

HYPOTHESIS

PCCP have several advantages than DHS, such as reduced blood loss, transfusion, mortality, shorter operative time, and lower incidence of complications. This systematic review and meta-analysis was performed to identify the clinical outcomes and safety of patients with stable intertrochanteric hip fractures operated on using PCCP compared with DHS.

MATERIALS AND METHODS

A systematic search of all studies published through April 2012 was conducted using the Medline, Embase, Sciencedirect, OVID and the Cochrane Central database. The randomized controlled trials (RCTs) and quasi-randomised control trials (qRCTs) that compared PCCP with DHS in treating adult patients with stable intertrochanteric hip fractures and provided data on safety and clinical effects were identified. Demographic characteristics, adverse events and clinical outcomes were manually extracted from all of the selected studies.

RESULTS

Nine studies encompassing 914 patients met the inclusion criteria. Overall, the result of meta-analysis indicated that over DHS, PCCP allowed significantly shorter operative time, reduced blood loss as well as transfusion, diminished incidence of cardiovascular events. However, there were no significant differences in length of hospitalization, rate of walking without help, early mortality and other complications.

DISCUSSION

Significant differences favoring PCCP were found with regard to operative time, blood loss, transfusion and lower incidence of cardiovascular events. However, owing to the limitations of this systematic review, future RCTs are still needed to confirm this data and the clinical efficiency of PCCP.

LEVEL OF EVIDENCE

Level II: low-powered prospective randomized trial.

High expression of CD98 alters epithelial barrier functions to promote induction of airway allergy

BACKGROUND

Epithelial barrier dysfunction is critical in the induction of allergy; the aetiology is to be further understood. A recent report indicates that CD98 plays a role in the intestinal epithelial barrier dysfunction.

OBJECTIVES

This study aimed to investigate the role of overexpression of CD98 in the induction of nasal allergy.

METHODS

The nasal epithelium samples were collected from 30 patients with allergic rhinitis and 30 healthy subjects. The contents of CD98 and Staphylococcal enterotoxin B (SEB) in the nasal epithelium samples were evaluated by using Western blotting. The effect of SEB of inducing the expression of CD98 was evaluated with an airway epithelial cell line, the 16HBE14o cells. The epithelial barrier function was assessed with the indicators of transepithelial resistance (TER) and permeability to horseradish peroxidase (HRP). A mouse model was employed to evaluate the role of CD98 in the induction of nasal allergy.

RESULTS

High levels of CD98 and SEB were detected in the nasal epithelium of patients with allergic rhinitis. A positive correlation was identified between CD98 and SEB in nasal epithelium samples. Exposure to SEB could induce the overexpression of CD98 in RPMI 2650 and 16HBE14o cells. The overexpression of CD98 down-regulated TER and increased the permeability to HRP in 16HBE14o monolayers. Concurrent exposure to SEB and OVA induced nasal allergies in a mouse model that could be blocked by pre-treatment with anti-CD98 antibody.

CONCLUSIONS AND CLINICAL RELEVANCE

CD98 plays a critical role in compromising the airway epithelial barrier function that contributes to the induction of airway allergy.

Expression of human beta 1,4-galactosyltransferase in gynecological cancer cell lines

We examined the expression of beta 1,4-GT gene products in 11 gynecological cancer cell lines. A 4.7 kb mRNA and protein (54,000 Da and 57,000 Da) were detected by Northern blot and Western blot. Immunocytochemical staining revealed that beta 1,4-GT was localized in the Golgi or ER of tumor cells. An intense beta 1,4-GT mRNA signal was detected in ovarian and cervical cancer cells, whereas the level of beta 1,4-GT mRNA was very low in uterine endometrial cancer cells. We also confirmed that expression of beta 1,4-GT mRNA corresponded to expression of beta 1,4-GT protein. These results suggest that expression of the beta 1,4-GT gene products is higher in human cervical and ovarian cancer cells than in uterine endometrial cancer cells.

Platelet-activating factor and distinct chemokines are elevated in mucosal biopsies of erosive compared with non-erosive reflux disease patients and controls

BACKGROUND

A distinction between symptomatic non-erosive reflux disease (NERD) and erosive esophagitis (EE) patients is supported by the presence of inflammatory response in the mucosa of EE patients, leading to a damage of mucosal integrity. To explore the underlying mechanism of this difference, we assessed inflammatory mediators in mucosal biopsies from EE and NERD patients and compared them with controls.

METHODS

Nineteen NERD patients, 15 EE patients, and 16 healthy subjects underwent endoscopy after a 3-week washout from PPI or H(2) antagonists. Biopsies obtained from the distal esophagus were examined by quantitative real-time polymerase chain reaction (qPCR) and multiplex enzyme-linked immunosorbent assay for selected chemokines and lyso-PAF acetyltransferase (LysoPAF-AT), the enzyme responsible for production of platelet-activating factor (PAF).

KEY RESULTS

Expression of LysoPAF-AT and multiple chemokines was significantly increased in mucosal biopsies derived from EE patients, when compared with NERD patients and healthy controls. Upregulated chemokines included interleukin 8, eotaxin-1, -2, and -3, macrophage inflammatory protein-1α (MIP-1α), and monocyte chemoattractant protein-1 (MCP-1). LysoPAF-AT and the chemokine profile in NERD patients were comparable with healthy controls.

CONCLUSIONS & INFERENCES

Levels of selected cytokines and Lyso-PAF AT were significantly higher in the esophageal mucosa of EE patients compared with NERD and control patients. This difference may explain the distinct inflammatory response occurring in EE patients' mucosa. In contrast, as no significant differences existed between the levels of all mediators in NERD and control subjects, an inflammatory response does not appear to play a major role in the pathogenesis of the abnormalities found in NERD patients.

Platelet-activating factor and distinct chemokines are elevated in mucosal biopsies of erosive compared with non-erosive reflux disease patients and controls

BACKGROUND

A distinction between symptomatic non-erosive reflux disease (NERD) and erosive esophagitis (EE) patients is supported by the presence of inflammatory response in the mucosa of EE patients, leading to a damage of mucosal integrity. To explore the underlying mechanism of this difference, we assessed inflammatory mediators in mucosal biopsies from EE and NERD patients and compared them with controls.

METHODS

Nineteen NERD patients, 15 EE patients, and 16 healthy subjects underwent endoscopy after a 3-week washout from PPI or H(2) antagonists. Biopsies obtained from the distal esophagus were examined by quantitative real-time polymerase chain reaction (qPCR) and multiplex enzyme-linked immunosorbent assay for selected chemokines and lyso-PAF acetyltransferase (LysoPAF-AT), the enzyme responsible for production of platelet-activating factor (PAF).

KEY RESULTS

Expression of LysoPAF-AT and multiple chemokines was significantly increased in mucosal biopsies derived from EE patients, when compared with NERD patients and healthy controls. Upregulated chemokines included interleukin 8, eotaxin-1, -2, and -3, macrophage inflammatory protein-1α (MIP-1α), and monocyte chemoattractant protein-1 (MCP-1). LysoPAF-AT and the chemokine profile in NERD patients were comparable with healthy controls.

CONCLUSIONS & INFERENCES

Levels of selected cytokines and Lyso-PAF AT were significantly higher in the esophageal mucosa of EE patients compared with NERD and control patients. This difference may explain the distinct inflammatory response occurring in EE patients' mucosa. In contrast, as no significant differences existed between the levels of all mediators in NERD and control subjects, an inflammatory response does not appear to play a major role in the pathogenesis of the abnormalities found in NERD patients.

Comparison of the antiviral effects of entecavir and adefovir dipivoxil in chronic HBV infection: a randomized control trial

AIMS

The purpose of this study is to compare the antiviral efficacy of entecavir (ETV) and adefovir dipivoxil (ADV) at various time points during the treatment.

METHODS

A randomized, controlled, open-label study was designed to analyze the kinetics of HBeAg seroconversion, HBV DNA level, and liver and renal functions in 72 ETV-treated chronic hepatitis B (CHB) patients and 66 ADV-treated CHB patients. The data was collected every 12 weeks up to 96 weeks after drug administration.

RESULTS

The negative rate of HBeAg seroconversion was significantly increased at 24 weeks in ETV-treated patients, whereas in ADV-treated patients, these changes were not significant. The serum HBV DNA levels were significantly decreased from 24 weeks in both ETV- and ADV-treated patients. Other than ETV showing significantly decreased levels of HBV DNA at 24 weeks when compared with ADV, there was no difference in virological response between two treatments at any other time points. The serum alanine aminotransferase (ALT) and total bilirubin (TBIL) levels were significantly decreased 12 weeks after either ETV- or ADV-treated patients without differences between two treatments. The urea nitrogen levels were in normal range and there was no difference between two groups.

CONCLUSIONS

Our study suggested that both ETV and ADV could be used as monotherapy for nucleotide-naive patients, but ETV has displayed potential efficacy in HBeAg seroconversion.

Differential expression of two antifreeze proteins in the desert beetle Anatolica polita (Coleoptera: Tenebriondae): seasonal variation and environmental effects

Antifreeze proteins (AFPs) can inhibit and modify the growth of ice crystals. Two antifreeze protein genes, Apafp752 and Apafp914, were cloned from the desert beetle Anatolica polita (Coleoptera: Tenebriondae), and they shared 61.3 percent similarity at the amino acid level. Apafp752 also contained one variation in the most conserved TCT motif of beetle AFPs. Apafp752 and Apafp914 mRNAs had similar seasonal expression pattern. Both were stimulated by cold stress, but they expressed slightly differentially with Apafp752 being more sensitive to cold stress than Apafp914, and no more sensitive to desiccation stress than Apafp914. The thermal hysteresis activity (THA) in the beetle's hemolymph followed approximately the patterns of mRNA seasonal expression and expression upon environmental stress, with a time lag. Summer adults of the desert beetle also express mRNA of Apafp752 and Apafp914, and exhibit some hemolymph THA, suggesting other likely function of these proteins beyond antifreeze.