Disk Imaging Survey of Chemistry with SMA: II. Southern Sky Protoplanetary Disk Data and Full Sample Statistics

This is the second in a series of papers based on data from DISCS, a Submillimeter Array observing program aimed at spatially and spectrally resolving the chemical composition of 12 protoplanetary disks. We present data on six Southern sky sources - IM Lup, SAO 206462 (HD 135344b), HD 142527, AS 209, AS 205 and V4046 Sgr - which complement the six sources in the Taurus star forming region reported previously. CO 2-1 and HCO+ 3-2 emission are detected and resolved in all disks and show velocity patterns consistent with Keplerian rotation. Where detected, the emission from DCO+ 3-2, N2H+ 3-2, H2CO 3-2 and 4-3,HCN 3-2 and CN 2-1 are also generally spatially resolved. The detection rates are highest toward the M and K stars, while the F star SAO 206462 has only weak CN and HCN emission, and H2CO alone is detected toward HD 142527. These findings together with the statistics from the previous Taurus disks, support the hypothesis that high detection rates of many small molecules depend on the presence of a cold and protected disk midplane, which is less common around F and A stars compared to M and K stars. Disk-averaged variations in the proposed radiation tracer CN/HCN are found to be small, despite two orders of magnitude range of spectral types and accretion rates. In contrast, the resolved images suggest that the CN/HCN emission ratio varies with disk radius in at least two of the systems. There are no clear observational differences in the disk chemistry between the classical/full T Tauri disks and transitional disks. Furthermore, the observed line emission does not depend on measured accretion luminosities or the number of infrared lines detected, which suggests that the chemistry outside of 100 AU is not coupled to the physical processes that drive the chemistry in the innermost few AU.Comment: accepted for publication in ApJ, 41 pages including 7 figure

Gene Expression Programs of Human Smooth Muscle Cells: Tissue-Specific Differentiation and Prognostic Significance in Breast Cancers

Smooth muscle is present in a wide variety of anatomical locations, such as blood vessels, various visceral organs, and hair follicles. Contraction of smooth muscle is central to functions as diverse as peristalsis, urination, respiration, and the maintenance of vascular tone. Despite the varied physiological roles of smooth muscle cells (SMCs), we possess only a limited knowledge of the heterogeneity underlying their functional and anatomic specializations. As a step toward understanding the intrinsic differences between SMCs from different anatomical locations, we used DNA microarrays to profile global gene expression patterns in 36 SMC samples from various tissues after propagation under defined conditions in cell culture. Significant variations were found between the cells isolated from blood vessels, bronchi, and visceral organs. Furthermore, pervasive differences were noted within the visceral organ subgroups that appear to reflect the distinct molecular pathways essential for organogenesis as well as those involved in organ-specific contractile and physiological properties. Finally, we sought to understand how this diversity may contribute to SMC-involving pathology. We found that a gene expression signature of the responses of vascular SMCs to serum exposure is associated with a significantly poorer prognosis in human cancers, potentially linking vascular injury response to tumor progression

Hubble Space Telescope NICMOS Polarization Measurements of OMC-1

We present 2micron polarization measurements of positions in the BN region of the Orion Molecular Cloud (OMC-1) made with NICMOS Camera 2 (0.2'' resolution) on HST. Our results are as follows: BN is sim 29% polarized by dichroic absorption and appears to be the illuminating source for most of the nebulosity to its north and up to sim 5'' to its south. Although the stars are probably all polarized by dichroic absorption, there are a number of compact, but non-point-source, objects that could be polarized by a combination of both dichroic absorption and local scattering of star light. We identify several candidate YSOs, including an approximately edge-on bipolar YSO 8.7'' east of BN, and a deeply-embedded variable star. Additional strongly polarized sources are IRc2-B, IRc2-D, and IRc7, all of which are obviously self-luminous at mid-infrared wavelengths and may be YSOs. None of these is a reflection nebula illuminated by a star located near radio source I, as was previously suggested. Other IRc sources are clearly reflection nebulae: IRc3 appears to be illuminated by IRc2-B or a combination of the IRc2 sources, and IRc4 and IRc5 appear to be illuminated by an unseen star in the vicinity of radio source I, or by Star n or IRc2-A. Trends in the magnetic field direction are inferred from the polarization of the 26 stars that are bright enough to be seen as NICMOS point sources. The most polarized star has a polarization position angle different from its neighbors by sim 40^o, but in agreement with the grain alignment inferred from millimeter polarization measurements of the cold dust cloud in the southern part of OMC-1.Comment: 41 pages, 8 figures, 4 tables, to appear in The Astrophysical Journa

Substituting abacavir for hyperlipidemia-associated protease inhibitors in HAART regimens improves fasting lipid profiles, maintains virologic suppression, and simplifies treatment

BACKGROUND: Hyperlipidemia secondary to protease inhibitors (PI) may abate by switching to anti-HIV medications without lipid effects. METHOD: An open-label, randomized pilot study compared changes in fasting lipids and HIV-1 RNA in 104 HIV-infected adults with PI-associated hyperlipidemia (fasting serum total cholesterol >200 mg/dL) who were randomized either to a regimen in which their PI was replaced by abacavir 300 mg twice daily (n = 52) or a regimen in which their PI was continued (n = 52) for 28 weeks. All patients had undetectable viral loads (HIV-1 RNA <50 copies/mL) at baseline and were naïve to abacavir and non-nucleoside reverse transcriptase inhibitors. RESULTS: At baseline, the mean total cholesterol was 243 mg/dL, low density lipoprotein (LDL)-cholesterol 149 mg/dL, high density lipoprotein (HDL)-cholesterol 41 mg/dL, and triglycerides 310 mg/dL. Mean CD4+ cell counts were 551 and 531 cells/mm(3 )in the abacavir-switch and PI-continuation arms, respectively. At week 28, the abacavir-switch arm had significantly greater least square mean reduction from baseline in total cholesterol (-42 vs -10 mg/dL, P < 0.001), LDL-cholesterol (-14 vs +5 mg/dL, P = 0.016), and triglycerides (-134 vs -36 mg/dL, P = 0.019) than the PI-continuation arm, with no differences in HDL-cholesterol (+0.2 vs +1.3 mg/dL, P = 0.583). A higher proportion of patients in the abacavir-switch arm had decreases in protocol-defined total cholesterol and triglyceride toxicity grades, whereas a smaller proportion had increases in these toxicity grades. At week 28, an intent-to treat: missing = failure analysis showed that the abacavir-switch and PI-continuation arms did not differ significantly with respect to proportion of patients maintaining HIV-1 RNA <400 or <50 copies/mL or adjusted mean change from baseline in CD4+ cell count. Two possible abacavir-related hypersensitivity reactions were reported. No significant changes in glucose, insulin, insulin resistance, C-peptide, or waist-to-hip ratios were observed in either treatment arm, nor were differences in these parameters noted between treatments. CONCLUSION: In hyperlipidemic, antiretroviral-experienced patients with HIV-1 RNA levels <50 copies/mL and CD4+ cell counts >500 cells/mm(3), substituting abacavir for hyperlipidemia-associated PIs in combination antiretroviral regimens improves lipid profiles and maintains virologic suppression over a 28-week period, and it simplifies treatment

Patients with an unexplained microsatellite instable tumour have a low risk of familial cancer

The cancer risk is unknown for those families in which a microsatellite instable tumour is neither explained by MLH1 promoter methylation nor by a germline mutation in a mismatch repair (MMR) gene. Such information is essential for genetic counselling. Families suspected of Lynch syndrome (n=614) were analysed for microsatellite instability, MLH1 promoter methylation and/or germline mutations in MLH1, MSH2, MSH6, and PMS2. Characteristics of the 76 families with a germline mutation (24 MLH1, 2 PMS2, 32 MSH2, and 18 MSH6) were compared with those of 18 families with an unexplained microsatellite instable tumour. The mean age at diagnosis of the index patients in both groups was comparable at 44 years. Immunohistochemistry confirmed the loss of an MMR protein. Together this suggests germline inactivation of a known gene. The Amsterdam II criteria were fulfilled in 50/75 families (66%) that carried a germline mutation in an MMR gene and in only 2/18 families (11%) with an unexplained microsatellite instable tumour (P<0.0001). Current diagnostic strategies can detect almost all highly penetrant MMR gene mutations. Patients with an as yet unexplained microsatellite instable tumour likely carry a different type of mutation that confers a lower risk of cancer for relatives

Cepred: Predicting the Co-Expression Patterns of the Human Intronic microRNAs with Their Host Genes

Identifying the tissues in which a microRNA is expressed could enhance the understanding of the functions, the biological processes, and the diseases associated with that microRNA. However, the mechanisms of microRNA biogenesis and expression remain largely unclear and the identification of the tissues in which a microRNA is expressed is limited. Here, we present a machine learning based approach to predict whether an intronic microRNA show high co-expression with its host gene, by doing so, we could infer the tissues in which a microRNA is high expressed through the expression profile of its host gene. Our approach is able to achieve an accuracy of 79% in the leave-one-out cross validation and 95% on an independent testing dataset. We further estimated our method through comparing the predicted tissue specific microRNAs and the tissue specific microRNAs identified by biological experiments. This study presented a valuable tool to predict the co-expression patterns between human intronic microRNAs and their host genes, which would also help to understand the microRNA expression and regulation mechanisms. Finally, this framework can be easily extended to other species

Cancer risk in MLH1, MSH2 and MSH6 mutation carriers; different risk profiles may influence clinical management

Background: Lynch syndrome (LS) is associated with a high risk for colorectal cancer (CRC) and extracolonic malignancies, such as endometrial carcinoma (EC). The risk is dependent of the affected mismatch repair gene. The aim of the present study was to calculate the cumulative risk of LS related cancers in proven MLH1, MSH2 and MSH6 mutation carriers.Methods: The studypopulation consisted out of 67 proven LS families. Clinical information including mutation status and tumour diagnosis was collected. Cumulative risks were calculated and compared using Kaplan Meier survival analysis.Results: MSH6 mutation carriers, both males and females had the lowest risk for developing CRC at age 70 years, 54% and 30% respectively and the age of onset was delayed by 3-5 years in males. With respect to endometrial carcinoma, female MSH6 mutation carriers had the highest risk at age 70 years (61%) compared to MLH1 (25%) and MSH2 (49%). Also, the age of EC onset was delayed by 5-10 years in comparison with MLH1 and MSH2.Conclusions: Although the cumulative lifetime risk of LS related cancer is similar, MLH1, MSH2 and MSH6 mutations seem to cause distinguishable cancer risk profiles. Female MSH6 mutation carriers have a lower CRC risk and a higher risk for developing endometrial carcinoma. As a consequence, surveillance colonoscopy starting at age 30 years instead of 20-25 years is more suitable. Also, prophylactic hysterectomy may be more indicated in female MSH6 mutation carriers compared to MLH1 and MSH2 mutation carriers

Identification and Characterization of RcMADS1, an AGL24 Ortholog from the Holoparasitic Plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae)

10.1371/journal.pone.0067243PLoS ONE86-POLN

Outcomes of antiretroviral treatment program in Ethiopia: Retention of patients in care is a major challenge and varies across health facilities

BACKGROUND: Many resource-limited countries are scaling up antiretroviral treatment (ART) towards universal access. However, there are few studies which evaluated outcomes of ART programs in these countries. In addition, these studies generally include a limited number of facilities and patients creating a clear need for studies with a wide range of facilities and large numbers of patients. In this study, we intended to evaluate the outcomes of the ART services in 55 health facilities in Ethiopia. METHODS: A retrospective longitudinal study was conducted to determine levels of patient retention in care, CD4 count and shift to second-line ART regimen in 30 hospitals and 25 health centers selected as sentinel sites for monitoring the outcomes of ART program in the country. The outcomes were determined at baseline, after 6, 12 and 24 months on ART. Data was collected from routine patient registers and charts, and entered and analyzed using EPI-Info statistical software. RESULTS: Health facilities were able to retain 29,893 (80%), 20,079 (74%) and 5,069 (68%) of their patients after 6, 12 and 24 months on ART, respectively. Retention rates vary across health facilities, ranging from 51% to 85% after 24 months on ART. Mortality was 5%, 6% and 8% after 6, 12 and 24 months on ART. More than 79% of patients with available CD4-cell counts had a baseline CD4-cell counts less than 200 cells per micro-liter of blood. The median CD4-cell counts (based on patients who were retained after 24 months on ART) increased from 125 (inter-quartile (IQ), 68-189) at baseline to 242 (IQ, 161-343), 269 (IQ, 185-380) and 316 (IQ, 226-445) cells per micro-liter after 6, 12, and 24 months on ART, respectively. The transition to second-line ART remained very low, 0.33%, 0.58% and 2.13% after 6, 12 and 24 months on ART. Discussion and conclusion: The outcomes of the ART services in the 55 health facilities in Ethiopia are similar to those in other countries. Retention of patients in care is a major challenge and varies across health facilities with high, medium and low retention rates. We therefore recommend further studies to understand the organization of care in health facilities with high, medium and low retention rates. It is also imperative that early initiation of patients on ART is taken seriously as more than 79% of the patients had baseline CD4-cell counts less than 200 cells per micro-liter of blood. Finally, we recommend that the shift to second-line ART might be too low and warrants close monitoring

Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers

BACKGROUND: Inadequate oxygen (hypoxia) triggers a multifaceted cellular response that has important roles in normal physiology and in many human diseases. A transcription factor, hypoxia-inducible factor (HIF), plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1α protein. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia among different cell types or how this variation might relate to tissue- and cell-specific diseases. METHODS AND FINDINGS: We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells, breast epithelial cells, smooth muscle cells, and endothelial cells with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This heightened response was associated with a uniquely high level of HIF-1α RNA in renal cells, and it could be diminished by reducing HIF-1α expression via RNA interference. A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in breast and ovarian cancers. In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use. CONCLUSIONS: The transcriptional response to hypoxia varies among human cells. Some of this variation is traceable to variation in expression of the HIF1A gene. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis in breast and ovarian cancer