Perfluorooctane sulfonate concentrations in amniotic fluid, biomarkers of fetal Leydig cell function, and cryptorchidism and hypospadias in Danish boys (1980–1996)

Background: Exposure to perfluorooctane sulfonate (PFOS) may potentially disturb fetal Leydig cell hormone production and male genital development. Objectives: We aimed to study the associations between levels of amniotic fluid PFOS, fetal steroid hormone, and insulin-like factor 3 (INSL3) and the prevalence of cryptorchidism and hypospadias. Methods: Using the Danish National Patient Registry, we selected 270 cryptorchidism cases,75 hypospadias cases, and 300 controls with stored maternal amniotic fluid samples available in a Danish pregnancy-screening biobank (1980–1996). We used mass spectrometry to measure PFOS in amniotic fluid from 645 persons and steroid hormones in samples from 545 persons. INSL3 was measured by immunoassay from 475 persons. Associations between PFOS concentration in amniotic fluid, hormone levels, and genital malformations were assessed by confounder-adjusted linear and logistic regression. Results: The highest tertile of PFOS exposure (> 1.4 ng/mL) in amniotic fluid was associated with a 40% (95% CI: –69, –11%) lower INSL3 level and an 18% (95% CI: 7, 29%) higher testosterone level compared with the lowest tertile (< 0.8 ng/mL). Amniotic fluid PFOS concentration was not associated with cryptorchidism or hypospadias. Conclusions: Environmental PFOS exposure was associated with steroid hormone and INSL3 concentrations in amniotic fluid, but was not associated with cryptorchidism or hypospadias in our study population. Additional studies are needed to determine whether associations with fetal hormone levels may have long-term implications for reproductive health

RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

The utility of B-type natriuretic peptide in the diagnosis of heart failure in the emergency department: a systematic review

<p>Abstract</p> <p>Background</p> <p>Dyspnea is a common chief complaint in the emergency department (ED); differentiating heart failure (HF) from other causes can be challenging. Brain Natriuretic Peptide (BNP) is a new diagnostic test for HF for use in dyspneic patients in the ED. The purpose of this study is to systematically review the accuracy of BNP in the emergency diagnosis of HF.</p> <p>Methods</p> <p>We searched MEDLINE (1975–2005) supplemented by reference tracking. We included studies that reported the sensitivity and specificity of BNP for diagnosing HF in ED patients with acute dyspnea. Two reviewers independently assessed study quality. We pooled sensitivities and specificities within five ranges of BNP cutoffs.</p> <p>Results</p> <p>Ten studies including 3,344 participants met inclusion criteria. Quality was variable; possible verification or selection bias was common. No studies eliminated patients with obvious medical causes of dyspnea. Most studies used the Triage BNP assay; all utilized a clinical reference standard. Pooled sensitivity and specificity at a BNP cutoff of 100–105 pg/ml were 90% and 74% with negative likelihood ratio (LR) of 0.14; pooled sensitivity was 81% with specificity of 90% at cutoffs between 300 and 400 pg/ml with positive LR of 7.6.</p> <p>Conclusion</p> <p>Our analysis suggests that BNP has moderate accuracy in detecting HF in the ED. Our results suggest utilizing a BNP of less than 100 pg/ml to rule out HF and a BNP of greater than 400 pg/ml to diagnose HF. Many studies were of marginal quality, and all included patients with varying degrees of diagnostic uncertainty. Further studies focusing on patients with diagnostic uncertainty will clarify the real-world utility of BNP in the emergency management of dyspnea.</p

Phthalates and Perfluorooctanesulfonic Acid in Human Amniotic Fluid: Temporal Trends and Timing of Amniocentesis in Pregnancy

Background: Measures of prenatal environmental exposures are important, and amniotic fluid levels may directly reflect fetal exposures during hypothesized windows of vulnerability

Prevalence and associated factors in burnout and psychological morbidity among substance misuse professionals

<p>Abstract</p> <p>Background</p> <p>Studies of psychological stress among substance misuse professionals rarely describe the nature of burnout and psychological morbidity. The main aim of this study was to determine the extent, pattern and predictors of psychological morbidity and burnout among substance misuse professionals.</p> <p>Methods</p> <p>This study was a cross-sectional mail survey of 194 clinical staff of substance misuse services in the former South Thames region of England, using the General Health Questionnaire (GHQ-12) the Maslach Burnout Inventory (MBI) as measures of psychological morbidity and burnout, respectively.</p> <p>Results</p> <p>Rates of psychological morbidity (82%: 95% CI = 76–87) and burnout (high emotional exhaustion – 33% [27–40]; high depersonalisation – 17% [12–23]; and diminished personal accomplishment – 36% [29–43]) were relatively high in the study sample. High levels of alienation and tension (job stressors) predicted emotional exhaustion and depersonalisation (burnout) but not psychological morbidity. Diminished personal accomplishment was associated with higher levels of psychological morbidity</p> <p>Conclusion</p> <p>In the sample of substance misuse professionals studied, rates of psychological morbidity and burnout were high, suggesting a higher level of vulnerability than in other health professionals. Furthermore, pathways to psychological morbidity and burnout are partially related. Therefore, targeted response is required to manage stress, burnout and psychological morbidity among substance misuse professionals. Such a response should be integral to workforce development.</p

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

<p>Abstract</p> <p>Background</p> <p>Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized.</p> <p>Results</p> <p>We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage.</p> <p>Conclusion</p> <p>The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.</p

Long-Term Health Outcomes in Children Born to Mothers with Diabetes: A Population-Based Cohort Study

BACKGROUND: To examine whether prenatal exposure to parental type 1 diabetes, type 2 diabetes, or gestational diabetes is associated with an increased risk of malignant neoplasm or diseases of the circulatory system in the offspring. METHODS/PRINCIPAL FINDINGS: We conducted a population-based cohort study of 1,781,576 singletons born in Denmark from 1977 to 2008. Children were followed for up to 30 years from the day of birth until the onset of the outcomes under study, death, emigration, or December 31, 2009, whichever came first. We used Cox proportional hazards model to estimate hazard ratios (HR) with 95% confidence intervals (95% CI) for the outcomes under study while adjusting for potential confounders. An increased risk of malignant neoplasm was found in children prenatally exposed to maternal type 2 diabetes (HR = 2.2, 95%CI: 1.5-3.2). An increased risk of diseases of the circulatory system was found in children exposed to maternal type 1 diabetes (HR = 2.2, 95%CI: 1.6-3.0), type 2 diabetes (HR = 1.4, 95%CI: 1.1-1.7), and gestational diabetes (HR = 1.3, 95%CI: 1.1-1.6), but results were attenuated after excluding children with congenital malformations. An increased risk of diseases of the circulatory system was also found in children exposed to paternal type 2 diabetes (HR = 1.5, 95%CI: 1.1-2.2) and the elevated risk remained after excluding children with congenital malformations. CONCLUSIONS: This study suggests that susceptibility to malignant neoplasm is modified partly by fetal programming. Diseases of the circulatory system may be modified by genetic factors, other time-stable family factors, or fetal programming

Directed acyclic graph kernels for structural RNA analysis

<p>Abstract</p> <p>Background</p> <p>Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the similarities between two RNA sequences from the viewpoint of secondary structures. However, applying stem kernels directly to large data sets of ncRNAs is impractical due to their computational complexity.</p> <p>Results</p> <p>We have developed a new technique based on directed acyclic graphs (DAGs) derived from base-pairing probability matrices of RNA sequences that significantly increases the computation speed of stem kernels. Furthermore, we propose profile-profile stem kernels for multiple alignments of RNA sequences which utilize base-pairing probability matrices for multiple alignments instead of those for individual sequences. Our kernels outperformed the existing methods with respect to the detection of known ncRNAs and kernel hierarchical clustering.</p> <p>Conclusion</p> <p>Stem kernels can be utilized as a reliable similarity measure of structural RNAs, and can be used in various kernel-based applications.</p