Properties of the Molecular Cores of Low Luminosity Objects

We present a survey toward 16 Low Luminosity Objects (LLOs with an internal luminosity, Lint, lower than 0.2 Lsun) with N2H+ (1-0), N2H+ (3-2), N2D+ (3-2), HCO+ (3-2) and HCN (3-2) using the Arizona Radio Observatory Kitt Peak 12m Telescope and Submillimeter Telescope. Our goal is to probe the nature of these faint protostars which are believed to be either very low mass or extremely young protostars. We find that the N2D+/N2H+ column density ratios of LLOs are similar to those of typical starless cores and Class 0 objects. The N2D+/N2H+ column density ratios are relatively high (> 0.05) for LLOs with kinetic temperatures less than 10 K in our sample. The distribution of N2H+ (1-0) line widths spreads between that of starless cores and young Class 0 objects. If we use the line width as a dynamic evolutionary indicator, LLOs are likely young Class 0 protostellar sources. We further use the optically thick tracers, HCO+ (3-2) and HCN (3-2), to probe the infall signatures of our targets. We derive the asymmetry parameters from both lines and estimate the infall velocities by fitting the HCO+ (3-2) spectra with two-layer models. As a result, we identify eight infall candidates based on the infall velocities and seven candidates have infall signatures supported by asymmetry parameters from at least one of HCO+ (3-2) and HCN (3-2).Comment: 15 pages, 8 figures, accepted to Ap

Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are short non-coding RNA molecules, which play an important role in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs) over the years. Recently, <it>ab initio </it>approaches have attracted more attention because they do not depend on homology information and provide broader applications than comparative approaches. Kernel based classifiers such as support vector machine (SVM) are extensively adopted in these <it>ab initio </it>approaches due to the prediction performance they achieved. On the other hand, logic based classifiers such as decision tree, of which the constructed model is interpretable, have attracted less attention.</p> <p>Results</p> <p>This article reports the design of a predictor of pre-miRNAs with a novel kernel based classifier named the generalized Gaussian density estimator (G²DE) based classifier. The G²DE is a kernel based algorithm designed to provide interpretability by utilizing a few but representative kernels for constructing the classification model. The performance of the proposed predictor has been evaluated with 692 human pre-miRNAs and has been compared with two kernel based and two logic based classifiers. The experimental results show that the proposed predictor is capable of achieving prediction performance comparable to those delivered by the prevailing kernel based classification algorithms, while providing the user with an overall picture of the distribution of the data set.</p> <p>Conclusion</p> <p>Software predictors that identify pre-miRNAs in genomic sequences have been exploited by biologists to facilitate molecular biology research in recent years. The G²DE employed in this study can deliver prediction accuracy comparable with the state-of-the-art kernel based machine learning algorithms. Furthermore, biologists can obtain valuable insights about the different characteristics of the sequences of pre-miRNAs with the models generated by the G²DE based predictor.</p

Effective gene expression in the rat dorsal root ganglia with a non-viral vector delivered via spinal nerve injection

Delivering gene constructs into the dorsal root ganglia (DRG) is a powerful but challenging therapeutic strategy for sensory disorders affecting the DRG and their peripheral processes. The current delivery methods of direct intra-DRG injection and intrathecal injection have several disadvantages, including potential injury to DRG neurons and low transfection efficiency, respectively. This study aimed to develop a spinal nerve injection strategy to deliver polyethylenimine mixed with plasmid (PEI/DNA polyplexes) containing green fluorescent protein (GFP). Using this spinal nerve injection approach, PEI/DNA polyplexes were delivered to DRG neurons without nerve injury. Within one week of the delivery, GFP expression was detected in 82.8% ± 1.70% of DRG neurons, comparable to the levels obtained by intra-DRG injection (81.3% ± 5.1%, p = 0.82) but much higher than those obtained by intrathecal injection. The degree of GFP expression by neurofilament(+) and peripherin(+) DRG neurons was similar. The safety of this approach was documented by the absence of injury marker expression, including activation transcription factor 3 and ionized calcium binding adaptor molecule 1 for neurons and glia, respectively, as well as the absence of behavioral changes. These results demonstrated the efficacy and safety of delivering PEI/DNA polyplexes to DRG neurons via spinal nerve injection.National Science Council of Taiwan (100-2321-B-002-007)National Science Council of Taiwan (100-2320-B-002-083-MY3)Taiwan. Ministry of Science and Technology (104-2300-B-002-019-MY3)National Taiwan University. College of Medicine (Translational Medicine Project)National Taiwan University Hospital (101C101-201

Functional interaction between Env oncogene from Jaagsiekte sheep retrovirus and tumor suppressor Sprouty2

<p>Abstract</p> <p>Background</p> <p>Jaagsiekte sheep retrovirus (JSRV) is a type D retrovirus capable of transforming target cells <it>in vitro </it>and <it>in vivo</it>. The Envelope <it>(Env) </it>gene from JSRV and from related retroviruses can induce oncogenic transformation, although the detailed mechanism is yet to be clearly understood. Host cell factors are envisaged to play a critical determining role in the regulation of <it>Env</it>-mediated cell transformation.</p> <p>Results</p> <p>JSRV <it>Env</it>-mediated transformation of a lung adenocarcinoma cell line induced rapid proliferation, anchorage-independent growth and tumor formation, but completely abrogated the migration ability. An analysis of the signaling scenario in the transformed cells suggested the involvement of the ERK pathway regulated by Sprouty2 in cell migration, and the PI3K-Akt and STAT3 pathways in proliferation and anchorage-independence. On the other hand, in a normal lung epithelial cell line, <it>Env</it>-mediated transformation only decreased the migration potential while the other functions remained unaltered. We observed that <it>Env </it>induced the expression of a tumor suppressor, Sprouty2, suggesting a correlation between <it>Env</it>-effect and Sprouty2 expression. Overexpression of Sprouty2 <it>per se </it>not only decreased the migratory potential and tumor formation potential of the target cells but also made them resistant to subsequent <it>Env</it>-mediated transformation. On the other hand, over expression of the functional mutants of Sprouty2 had no inhibitory effect, confirming the role of Sprouty2 as a tumor suppressor.</p> <p>Conclusions</p> <p>Our studies demonstrate that <it>Env </it>and Sprouty2 have a functional relationship, probably through shared signaling network. Sprouty2 functions as a tumor suppressor regulating oncogenic transformation of cells, and it therefore has the potential to be exploited as a therapeutic anti-cancer agent.</p

Multiplex PCR System for Rapid Detection of Pathogens in Patients with Presumed Sepsis – A Systemic Review and Meta-Analysis

Background: Blood culture is viewed as the golden standard for the diagnosis of sepsis but suffers from low sensitivity and long turnaround time. LightCycler SeptiFast (LC-SF) is a real-time multiplex polymerase chain reaction test able to detect 25 common pathogens responsible for bloodstream infections within hours. We aim to assess the accuracy of LC-SF by systematically reviewing the published studies. Method Related literature on Medline, Embase, and Cochrane databases was searched up to October 2012 for studies utilizing LC-SF to diagnose suspected sepsis and that provided sufficient data to construct two-by-two tables. Results: A total of 34 studies enrolling 6012 patients of suspected sepsis were included. The overall sensitivity and specificity for LC-SF to detect bacteremia or fungemia was 0·75 (95% CI: 0·65–0·83) and 0·92 (95%CI:0·90–0·95), respectively. LC-SF had a high positive likelihood ratio (10·10) and a moderate negative likelihood ratio (0·27). Specifically, LC-SF had a sensitivity of 0·80 (95%CI: 0·70–0·88) and a specificity of 0·95(95%CI: 0·93–0·97) for the bacteremia outcome, and a sensitivity of 0·61 (95%CI: 0·48–0·72) and a specificity of 0·99 (95%CI: 0·99–0·99) for the fungemia outcome. High heterogeneity was found in the bacteremia outcome subgroup but not in the fungemia outcome subgroup. Conclusion: LC-SF is of high rule-in value for early detection of septic patients. In a population with low pretest probability, LC-SF test can still provide valuable information for ruling out bacteremia or fungemia

Site classification and Vs30 estimation of free-field TSMIP stations using the logging data of EGDT

The Engineering Geological Database for TSMIP (EGDT), the Taiwan Strong Motion Instrumentation Program, has been under construction by the National Center for Research on Earthquake Engineering and the Central Weather Bureau in Taiwan since 2000. Site characterization, comprising surface investigations and logging measurements, was carried out throughout the project. We provide a set of specifications and a description to help users understand the subject matter of the database. EGDT contains 469 surveyed stations, 439 of which were drilled and the logging measurements completed. Of these, 385 had logging data reaching at least 30 m, and we used these to examine and determine the most accurate extrapolation of Vs30 (the average S-wave velocity of the top 30 m of strata) for the other 54 stations with velocity profiles less than 30 m. The chosen method assumed that the bottom velocity is identical from the actual depth of the hole to a distance of 30 m, that is, the Bottom Constant Velocity (BCV) method. In order to utilize other existing boreholes which have only N values but no velocities in the future, the empirical S-wave velocity equations for seven different regions and the whole of Taiwan were evaluated by a multivariable analysis. Henceforth, for those existing boreholes which have an N profile less than 30 m, the S-wave velocity profile can first be calculated by empirical S-wave velocity equations, and then Vs30 can be estimated by reliable extrapolation. Some other studies of site classifications of TSMIP stations were compared with our results to demonstrate the necessity of reclassification. Ultimately, the Vs30 values of the 439 drilled free-field TSMIP stations were derived and the new site classification was achieved according to the Vs30-based provisions of the National Earthquake Hazards Reduction Program

GT-repeat polymorphism in the heme oxygenase-1 gene promoter and the risk of carotid atherosclerosis related to arsenic exposure

<p>Abstract</p> <p>Background</p> <p>Arsenic is a strong stimulus of heme oxygenase (HO)-1 expression in experimental studies in response to oxidative stress caused by a stimulus. A functional GT-repeat polymorphism in the HO-1 gene promoter was inversely correlated to the development of coronary artery disease in diabetics and development of restenosis following angioplasty in patients. The role of this potential vascular protective factor in carotid atherosclerosis remains unclear. We previously reported a graded association of arsenic exposure in drinking water with an increased risk of carotid atherosclerosis. In this study, we investigated the relationship between HO-1 genetic polymorphism and the risk of atherosclerosis related to arsenic.</p> <p>Methods</p> <p>Three-hundred and sixty-seven participants with an indication of carotid atherosclerosis and an additional 420 participants without the indication, which served as the controls, from two arsenic exposure areas in Taiwan, a low arsenic-exposed Lanyang cohort and a high arsenic-exposed LMN cohort, were studied. Carotid atherosclerosis was evaluated using a duplex ultrasonographic assessment of the extracranial carotid arteries. Allelic variants of (GT)n repeats in the 5'-flanking region of the HO-1 gene were identified and grouped into a short (S) allele (< 27 repeats) and long (L) allele (≥ 27 repeats). The association of atherosclerosis and the HO-1 genetic variants was assessed by a logistic regression analysis, adjusted for cardiovascular risk factors.</p> <p>Results</p> <p>Analysis results showed that arsenic's effect on carotid atherosclerosis differed between carriers of the class S allele (OR 1.39; 95% CI 0.86-2.25; <it>p </it>= 0.181) and non-carriers (OR 2.65; 95% CI 1.03-6.82; <it>p </it>= 0.044) in the high-exposure LMN cohort. At arsenic exposure levels exceeding 750 μg/L, difference in OR estimates between class S allele carriers and non-carriers was borderline significant (<it>p </it>= 0.051). In contrast, no such results were found in the low-exposure Lanyang cohort.</p> <p>Conclusions</p> <p>This exploratory study suggests that at a relatively high level of arsenic exposure, carriers of the short (GT)n allele (< 27 repeats) in the HO-1 gene promoter had a lower probability of developing carotid atherosclerosis than non-carriers of the allele after long-term arsenic exposure via ground water. The short (GT)n repeat in the HO-1 gene promoter may provide protective effects against carotid atherosclerosis in individuals with a high level of arsenic exposure.</p

Proteomic profiling reveals α1-antitrypsin, α1-microglobulin, and clusterin as preeclampsia-related serum proteins in pregnant women

AbstractObjectivePreeclampsia is a major cause of mortality in pregnant women but the underlying mechanism remains unclear to date. In this study, we attempted to identify candidate proteins that might be associated with preeclampsia in pregnant women by means of proteomics tools.Materials and methodsDifferentially expressed proteins in serum samples obtained from pregnant women with severe preeclampsia (n = 8) and control participants (n = 8) were identified using two-dimensional gel electrophoresis (2-DE) followed by peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Additional serum samples from 50 normal and 41 pregnant women with severe preeclampsia were analyzed by immunoassay for validation.ResultsTen protein spots were found to be upregulated significantly in women with severe preeclampsia. These protein spots had the peptide mass fingerprints matched to α1-antitrypsin, α1-microglobulin, clusterin, and haptoglobin. Immunoassays in an independent series of serum samples showed that serum α1-antitrypsin, α1-microglobulin, and clusterin levels of severe preeclampsia patients (n = 41) were significantly higher than those in the normal participants (n = 50; α1-antitrypsin 295.95 ± 50.94 mg/dL vs. 259.31 ± 33.90 mg/dL, p = 0.02; α1-microglobulin 0.029 ± 0.004 mg/mL vs. 0.020 ± 0.004 mg/mL, p < 0.0001; clusterin 77.6 ± 16.15 μg/dL vs. 67.6 ± 15.87 μg/dL, p < 0.05).ConclusionIdentification of these proteins by proteomics analysis enables further understanding of the pathophysiology of preeclampsia. Further studies are warranted to investigate the role of these biomarkers in prediction of this disease