Variable-Selection Emerges on Top in Empirical Comparison of Whole-Genome Complex-Trait Prediction Methods

Accurate prediction of complex traits based on whole-genome data is a computational problem of paramount importance, particularly to plant and animal breeders. However, the number of genetic markers is typically orders of magnitude larger than the number of samples (p >> n), amongst other challenges. We assessed the effectiveness of a diverse set of state-of-the-art methods on publicly accessible real data. The most surprising finding was that approaches with feature selection performed better than others on average, in contrast to the expectation in the community that variable selection is mostly ineffective, i.e. that it does not improve accuracy of prediction, in spite of p >> n. We observed superior performance despite a somewhat simplistic approach to variable selection, possibly suggesting an inherent robustness. This bodes well in general since the variable selection methods usually improve interpretability without loss of prediction power. Apart from identifying a set of benchmark data sets (including one simulated data), we also discuss the performance analysis for each data set in terms of the input characteristics.     

On the Subjective Acceptance during Cardiovascular Magnetic Resonance Imaging at 7.0 Tesla

Purpose

This study examines the subjective acceptance during UHF-CMR in a cohort of healthy volunteers who underwent a cardiac MR examination at 7.0T.

Methods

Within a period of two-and-a-half years (January 2012 to June 2014) a total of 165 healthy volunteers (41 female, 124 male) without any known history of cardiac disease underwent UHF-CMR. For the assessment of the subjective acceptance a questionnaire was used to examine the participants experience prior, during and after the UHF-CMR examination. For this purpose, subjects were asked to respond to the questionnaire in an exit interview held immediately after the completion of the UHF-CMR examination under supervision of a study nurse to ensure accurate understanding of the questions. All questions were answered with “yes” or “no” including space for additional comments.

Results

Transient muscular contraction was documented in 12.7% of the questionnaires. Muscular contraction was reported to occur only during periods of scanning with the magnetic field gradients being rapidly switched. Dizziness during the study was reported by 12.7% of the subjects. Taste of metal was reported by 10.1% of the study population. Light flashes were reported by 3.6% of the entire cohort. 13% of the subjects reported side effects/observations which were not explicitly listed in the questionnaire but covered by the question about other side effects. No severe side effects as vomiting or syncope after scanning occurred. No increase in heart rate was observed during the UHF-CMR exam versus the baseline clinical examination.

Conclusions

This study adds to the literature by detailing the subjective acceptance of cardiovascular magnetic resonance imaging examinations at a magnetic field strength of 7.0T. Cardiac MR examinations at 7.0T are well tolerated by healthy subjects. Broader observational and multi-center studies including patient cohorts with cardiac diseases are required to gain further insights into the subjective acceptance of UHF-CMR examinations.     

Explosive evolution of an ancient group of Cyphophthalmi (Arachnida: Opiliones) in the Balkan Peninsula

Aim  To investigate the phylogeny of the genus Cyphophthalmus in the Balkan Peninsula and to test the current recognition of 'phyletic lines' and phylogenetic groups proposed in previous studies in order to elucidate the biogeographical history of the region.
Location  Europe, Balkan Peninsula, Adria microplate.
Methods  Two mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and two nuclear (28S rRNA and 18S rRNA) markers were used to infer the phylogenetic history of the group. Molecular dating with relaxed molecular clocks was used to elucidate the relative time of diversification within the genus Cyphophthalmus and its constituent lineages.
Results  Our analyses confirm the monophyly of the genus Cyphophthalmus , and that of the Aegean and gjorgjevici lineages, whereas the 'Dinaric lineage' appears paraphyletic.
Main conclusions  We show that the genus Cyphophthalmus is an old endemic from the Balkan biogeographical region, which gave origin to at least three main lineages. Those lineages have diversified within overlapping ranges. According to our molecular dating, they have also diversified within the same timeframe. The Dinaric Alps, although presenting a large number of species, cannot be inferred as the centre of origin of the group. Instead, the biogeographical evolution of the genus could be related to the palaeogeographic history of the Adria microplate.     

Extracellular matrix remodelling in rat endometrium during early pregnancy: The role of fibronectin and laminin

The endometrial extracellular matrix (ECM) remodelling has a crucial role in the establishment of a successful pregnancy. In addition to its basic function such as regulation of cell function, differentiation, migration, proliferation, the substantial alterations in the endometrial ECM may play a specific role in the trophoblast invasion, placentation, cell death and formation of the proper and functional implantation chamber around the embryo. In the present study, immunolocalizations of fibronectin and laminin were determined using avidin-biotin complex-peroxidase in rat implantation sites during 7-10 days of pregnancy. Both proteins were present in the basal membrane of blood vessels and in decidual matrix whereas they were absent or had very weak reactivity in the primary decidual zone on day 7. When placentation has begun, the immunoreactivity of both proteins was increased in the placental bed and in the basal membrane of blood vessels of the mesometrial region. The immunolocalization of both proteins seemed to be decreased in the antimesometrial decidua, however, it was increased in the mesometrial decidual matrix on days 9 and 10. Therefore, it could be suggested laminin and fibronectin demonstrating dynamic expressions in relation with the morphological differentiation of endometrial stroma may play crucial roles in the control of trophoblast adhesion and invasion, in placentation and angiogenesis, in the determination of cell shape and fate thus contributing the endometrial receptivity and a successful pregnancy.     

Astragalus trifoliastrum (Fabaceae), a revived species for the flora of Turkey

As the result of surveying the relevant type specimens, together with macro‐ and micro‐morphological studies, chromosome counting and ITS sequencing, Astragalus trifoliastrum was found to be a species independent of A. laguriformis (with which it has peviously been synonymized). In contrast, A. wanensis, assumed to be a synonym of A. trifoliastrum, indeed appears to be identical with A. trifoliastrum. The diploid chromosome number of 2n = 16 is reported for the first time for A. trifoliastrum.     

Chemosystematics in the Opiliones (Arachnida): a comment on the evolutionary history of alkylphenols and benzoquinones in the scent gland secretions of Laniatores

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best‐studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best‐fitting explanation of the distribution of scent‐gland secretion compounds across extant laniatorean taxa, and hence represent a key toward a well‐founded opilionid chemosystematics.     

Modification of the erythrocyte membrane lipids in rats under conditions of alimentary stress

Erythrocyte phospholipids and lipid fatty acid composition was investigated at different stages of exposure to high-caloric diet in male Wistar rats. The revealed modification of erythrocyte lipids shows specific features of membrane response to stress factors of alimentary nature, in particular, cell protection compensatory mechanism initiation on the 90th day and their depletion by the 180th day of high-caloric diet.     

A rare case of monosomy 18p: translocation between chromosomes 18 and 21

A rare case of monosomy 18p with molecular cytogenetic characterization of 18;21 whole arm translocation is presented. An 8-year-old gril with mental deficiency and growth deficiency was the child of a 45-year-old healthy mother and 50-year-old nonconsanguineous father with unremarkable prenatal history. She had a round face, flat nasal bridge, micrognathia and hypotonia. Cytogenetic studies revealed de novo 45,XX,del(18)t(18;21) karyotype, which was confirmed by fluorescence in situ hybridization (FISH).     

Klippel-Feil syndrome and Dandy-Walker malformation

The Klippel-Feil deformity is a complex of osseous and visceral anomalies, which include low hairline, platybasia, fused cervical vertebrae with a short neck, and deafness. Associated central nervous system abnormalities include occipital cephalocele, Chiari I malformation, syrinx, microcephaly, and hydrocephalus. Herein, we report a case with Klippel-Feil syndrome and Dandy-Walker malformation.     

Effectiveness of latanoprost (Xalatan) monotherapy in newly discovered and previously medicamentously treated primary open angle glaucoma patients

We evaluated the effectiveness of latanoprost (Xalatan) monotherapy in primary open angle glaucoma (POAG). Latanoprost is a prostaglandin analogue, the pure 15(R) epimer of 13,14-dihydro-17-phenyl-18,19,20-trinor-PGF2alpha-isopropyl ester. As a prodrug it is being activated by enzymatic hydrolysis in the cornea after which it becomes active acid of latanoprost. Latanoprost is lowering the intraocular pressure (IOP) by increasing the uveoscleral outflow. In this study, latanoprost was used once daily as monotherapy what offers much better compliance for the patients than other combinations of drugs, preserving good IOP control. Based on the significant reduction of the IOP, measured on the day 60 of the trial (mean change in IOP was -5.1 mmHg, with 95% confidence interval in range from -5.6 to -4.5), it is concluded that use of latanoprost is advisable when calculating better IOP control, few side-effects and reductions in costs of potential surgical procedures.