Modelling forced vital capacity in idiopathic pulmonary fibrosis: optimising trial design.

INTRODUCTION: Forced vital capacity is the only registrational endpoint in idiopathic pulmonary fibrosis clinical trials. As most new treatments will be administered on top of standard of care, estimating treatment response will become more challenging. We developed a simulation model to quantify variability associated with forced vital capacity decline. METHODS: The model is based on publicly available clinical trial summary and home spirometry data. A single, illustrative trial setting is reported. Model assumptions are 400 subjects randomised 1:1 to investigational drug or placebo over 52 weeks, 50% of each group receiving standard of care (all-comer population), and a 90-mL treatment difference in annual forced vital capacity decline. Longitudinal profiles were simulated and the impact of varying clinical scenarios evaluated. RESULTS: Power to detect a significant treatment difference was 87-97%, depending on the analysis method. Repeated measures analysis generally outperformed analysis of covariance and mixed linear models, particularly with missing data (as simulated data were non-linear). A 15% yearly random dropout rate led to 0.6-5% power loss. Forced vital capacity decline-related dropout introduced greater power loss (up to 12%), as did subjects starting/stopping standard of care or investigational drug. Power was substantially lower for a 26-week trial due to the smaller assumed treatment effect at week 26 (sample size would need doubling to reach a power similar to that of a 52-week trial). CONCLUSIONS: Our model quantifies forced vital capacity decline and associated variability, with all the caveats of background therapy, permitting robust power calculations to inform future idiopathic pulmonary fibrosis clinical trial design. FUNDING: Galapagos NV (Mechelen, Belgium)

DAZL Relieves miRNA-Mediated Repression of Germline mRNAs by Controlling Poly(A) Tail Length in Zebrafish

BACKGROUND:During zebrafish embryogenesis, microRNA (miRNA) miR-430 contributes to restrict Nanos1 and TDRD7 to primordial germ cells (PGCs) by inducing mRNA deadenylation, mRNA degradation, and translational repression of nanos1 and tdrd7 mRNAs in somatic cells. The nanos1 and tdrd7 3'UTRs include cis-acting elements that allow activity in PGCs even in the presence of miRNA-mediated repression. METHODOLOGY/PRINCIPAL FINDINGS:Using a GFP reporter mRNA that was fused with tdrd7 3'UTR, we show that a germline-specific RNA-binding protein DAZ-like (DAZL) can relieve the miR-430-mediated repression of tdrd7 mRNA by inducing poly(A) tail elongation (polyadenylation) in zebrafish. We also show that DAZL enhances protein synthesis via the 3'UTR of dazl mRNA, another germline mRNA targeted by miR-430. CONCLUSIONS/SIGNIFICANCE:Our present study indicated that DAZL acts as an "anti-miRNA factor" during vertebrate germ cell development. Our data also suggested that miRNA-mediated regulation can be modulated on specific target mRNAs through the poly(A) tail control

Long-term effects of tongue piercing — a case control study

The aim of this study was to evaluate tooth and periodontal damage in subjects wearing a tongue piercing (TP) in comparison to matched control subjects without tongue piercing. Members of the German Federal Armed Forces who had TP (group TP) and a matched control group (group C) volunteered to take part in the study. The time in situ, localization and material of TP were documented. Dental examinations included DMF-T, oral hygiene, enamel fissures (EF), enamel cracks (EC) and recessions. Statistical analysis was determined by χ2 test and the t test. Both groups had 46 male subjects (mean age 22.1 years). The piercings had been in situ for 3.8 ± 3.1 years. Subjects in the TP group had a total of 1,260 teeth. Twenty-nine subjects had 115 teeth (9.1%) with EF (67% lingual). In group C (1,243 teeth), 30 subjects had 60 teeth with EF (4.8%, 78% vestibular) (p < 0.01). Thirty-eight subjects belonging to group TP had EC in 186 teeth (15%). In group C, 26 subjects with 56 teeth (4.5%) were affected by EC (p < 0.001). Twenty-seven subjects in group TP had 97 teeth (7.7%) with recessions. Lingual surfaces of anterior teeth in the lower jaw were affected most frequently (74%). In group C, 8 subjects had 19 teeth (1.5%) with recessions (65% vestibular). Differences between the two groups were statistically significant (p < 0.001). Tongue piercing is correlated with an increased occurrence of enamel fissures, enamel cracks and lingual recessions. Patients need better information on the potential complications associated with tongue piercing

A new classification of the long-horned caddisflies (Trichoptera: Leptoceridae) based on molecular data

Background: Leptoceridae are among the three largest families of Trichoptera (caddisflies). The current classification is founded on a phylogenetic work from the 1980's, based on morphological characters from adult males, i.e. wing venation, tibial spur formula and genital morphology. In order to get a new opinion about the relationships within the family, we undertook a molecular study of the family based on sequences from five genes, mitochondrial COI and the four nuclear genes CAD, EF-1 alpha, IDH and POL. Results: The resulting phylogenetic hypotheses are more or less congruent with the morphologically based classification, with most genera and tribes recovered as monophyletic, but with some major differences. For monophyly of the two subfamilies Triplectidinae and Leptocerinae, one tribe of each was removed and elevated to subfamily status; however monophyly of some genera and tribes is in question. All clades except Leptocerinae, were stable across different analysis methods. Conclusions: We elevate the tribes Grumichellini and Leptorussini to subfamily status, Grumichellinae and Leptorussinae, respectively. We also propose the synonymies of Ptochoecetis with Oecetis and Condocerus with Hudsonema.authorCount :

Is there an orthographic boost for ambiguous words during their processing?

The present study explores the issue of why ambiguous words are recognized faster than unambiguous ones during word recognition. To this end we contrasted two different hypotheses: the semantic feedback hypothesis (Hino and Lupker in J Exp Psychol Hum Percept Perform 22:1331-1356, 1996. https://doi.org/10.1037/0096-1523.22.6.1331 ), and the hypothesis proposed by Borowsky and Masson (J Exp Psychol Learn Mem Cognit 22:63-85, 1996. https://doi.org/10.1037/0278-7393.22.1.63 ). Although both hypotheses agree that ambiguous words benefit during recognition in that they engage more semantic activation, they disagree as to whether or not this greater semantic activation feeds back to the orthographic level, hence speeding up the orthographic coding of ambiguous words. Participants were presented with ambiguous and unambiguous words in two tasks, a lexical decision task (LDT) and a two-alternative forced-choice task (2AFC). We found differences between ambiguous and unambiguous words in both the LDT and the 2AFC tasks. These results suggest that the orthographic coding of ambiguous words is boosted during word processing. This finding lends support to the semantic feedback hypothesis.This research was funded by the Spanish Ministry of Economy and Competitiveness (PSI2015-63525-P) and by the Research Promotion Program of the Universitat Rovira i Virgili (2016PFR-URV-B2-37). This has also been partially supported by the FCT (Foundation for Science and Technology) through the state budget with Reference IF/00784/2013/CP1158/CT0013. The first author also holds a grant from the Universitat Rovira i Virgili (2015PMF-PIPF-16)

Candidate gene prioritization by network analysis of differential expression using machine learning approaches

<p>Abstract</p> <p>Background</p> <p>Discovering novel disease genes is still challenging for diseases for which no prior knowledge - such as known disease genes or disease-related pathways - is available. Performing genetic studies frequently results in large lists of candidate genes of which only few can be followed up for further investigation. We have recently developed a computational method for constitutional genetic disorders that identifies the most promising candidate genes by replacing prior knowledge by experimental data of differential gene expression between affected and healthy individuals.</p> <p>To improve the performance of our prioritization strategy, we have extended our previous work by applying different machine learning approaches that identify promising candidate genes by determining whether a gene is surrounded by highly differentially expressed genes in a functional association or protein-protein interaction network.</p> <p>Results</p> <p>We have proposed three strategies scoring disease candidate genes relying on network-based machine learning approaches, such as kernel ridge regression, heat kernel, and Arnoldi kernel approximation. For comparison purposes, a local measure based on the expression of the direct neighbors is also computed. We have benchmarked these strategies on 40 publicly available knockout experiments in mice, and performance was assessed against results obtained using a standard procedure in genetics that ranks candidate genes based solely on their differential expression levels (<it>Simple Expression Ranking</it>). Our results showed that our four strategies could outperform this standard procedure and that the best results were obtained using the <it>Heat Kernel Diffusion Ranking </it>leading to an average ranking position of 8 out of 100 genes, an AUC value of 92.3% and an error reduction of 52.8% relative to the standard procedure approach which ranked the knockout gene on average at position 17 with an AUC value of 83.7%.</p> <p>Conclusion</p> <p>In this study we could identify promising candidate genes using network based machine learning approaches even if no knowledge is available about the disease or phenotype.</p

Prevalence of apical periodontitis and endodontic treatment in a Kosovar adult population

<p>Abstract</p> <p>Background</p> <p>Despite numerous studies on the prevalence of apical periodontitis (AP) and endodontic treatment in diverse geographical populations, there are currently no data on the prevalence of these conditions in populations of adults native to Kosovo. Therefore, little is known about how widespread these conditions are, and whether there is any correlation between root canal treatment and AP. The purpose of our research was to address this anomaly by investigating AP and endodontic treatment in an adult Kosovar population based on radiographic examination.</p> <p>Methods</p> <p>The sample used for this study consisted of randomly selected individuals referred to the University Dentistry Clinical Center of Kosovo in the years 2006-2007. Orthopantomographs of 193 patients were evaluated. The periapical status of all teeth (with the exception of third molars) was examined according to Ørstavik's Periapical Index. The quality of the root canal filling was rated as 'adequate' or 'inadequate' based on whether all canals were filled, the depth of fill relative to the radiographic apex and the quality of compaction (absence/presence of voids). Data were analyzed statistically using the Chi-square test and calculation of odds ratios.</p> <p>Results</p> <p>Out of 4131 examined teeth, the prevalence of apical periodontitis (AP) and endodontic treatment was 12.3% and 2.3%, respectively. Of 95 endodontically-treated teeth, 46.3% were associated with AP. The prevalence of AP increased with age. The prevalence in subjects aged over 60 years old (20.2%) was higher than in other age groups. A statistically significant difference was found for the frequency of endodontically-treated teeth associated with AP in the 40-49 year age group (P < 0.001). Of some concern was the discovery that only 30.5% of the endodontically-treated teeth examined met the criteria of an acceptable root canal filling. Inadequately root-filled teeth were associated with an increased AP risk.</p> <p>Conclusions</p> <p>The prevalence of AP and the frequency of endodontically-treated teeth with AP in this Kosovar population are higher than those found in other countries. Inadequate root canal fillings were associated with an increased prevalence of AP.</p

Common SNPs explain some of the variation in the personality dimensions of neuroticism and extraversion

The personality traits of neuroticism and extraversion are predictive of a number of social and behavioural outcomes and psychiatric disorders. Twin and family studies have reported moderate heritability estimates for both traits. Few associations have been reported between genetic variants and neuroticism/extraversion, but hardly any have been replicated. Moreover, the ones that have been replicated explain only a small proportion of the heritability (<∼2%). Using genome-wide single-nucleotide polymorphism (SNP) data from ∼12 000 unrelated individuals we estimated the proportion of phenotypic variance explained by variants in linkage disequilibrium with common SNPs as 0.06 (s.e.=0.03) for neuroticism and 0.12 (s.e.=0.03) for extraversion. In an additional series of analyses in a family-based sample, we show that while for both traits ∼45% of the phenotypic variance can be explained by pedigree data (that is, expected genetic similarity) one third of this can be explained by SNP data (that is, realized genetic similarity). A part of the so-called ‘missing heritability' has now been accounted for, but some of the reported heritability is still unexplained. Possible explanations for the remaining missing heritability are that: (i) rare variants that are not captured by common SNPs on current genotype platforms make a major contribution; and/ or (ii) the estimates of narrow sense heritability from twin and family studies are biased upwards, for example, by not properly accounting for nonadditive genetic factors and/or (common) environmental factors

Hydrothermal alteration of andesitic lava domes can lead to explosive volcanic behaviour

Dome-forming volcanoes are among the most hazardous volcanoes on Earth. Magmatic outgassing can be hindered if the permeability of a lava dome is reduced, promoting pore pressure augmentation and explosive behaviour. Laboratory data show that acid-sulphate alteration, common to volcanoes worldwide, can reduce the permeability on the sample lengthscale by up to four orders of magnitude and is the result of pore- and microfracture-filling mineral precipitation. Calculations using these data demonstrate that intense alteration can reduce the equivalent permeability of a dome by two orders of magnitude, which we show using numerical modelling to be sufficient to increase pore pressure. The fragmentation criterion shows that the predicted pore pressure increase is capable of fragmenting the majority of dome-forming materials, thus promoting explosive volcanism. It is crucial that hydrothermal alteration, which develops over months to years, is monitored at dome-forming volcanoes and is incorporated into real-time hazard assessments