Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera

The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloës (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also polyphyletic. Thysanorea is introduced to accommodate Periconiella papuana (Herpotrichiellaceae), which is unrelated to the type species, P. velutina (Mycosphaerellaceae)

From fuzzy to annotated semantic web languages

The aim of this chapter is to present a detailed, selfcontained and comprehensive account of the state of the art in representing and reasoning with fuzzy knowledge in Semantic Web Languages such as triple languages RDF/RDFS, conceptual languages of the OWL 2 family and rule languages. We further show how one may generalise them to so-called annotation domains, that cover also e.g. temporal and provenance extensions

The LOFAR Two-Metre Sky Survey (LoTSS): VI. Optical identifications for the second data release

The second data release of the LOFAR Two-Metre Sky Survey (LoTSS) covers 27% of the northern sky, with a total area of $\sim 5,700$ deg$^2$. The high angular resolution of LOFAR with Dutch baselines (6 arcsec) allows us to carry out optical identifications of a large fraction of the detected radio sources without further radio followup; however, the process is made more challenging by the many extended radio sources found in LOFAR images as a result of its excellent sensitivity to extended structure. In this paper we present source associations and identifications for sources in the second data release based on optical and near-infrared data, using a combination of a likelihood-ratio cross-match method developed for our first data release, our citizen science project Radio Galaxy Zoo: LOFAR, and new approaches to algorithmic optical identification, together with extensive visual inspection by astronomers. We also present spectroscopic or photometric redshifts for a large fraction of the optical identifications. In total 4,116,934 radio sources lie in the area with good optical data, of which 85% have an optical or infrared identification and 58% have a good redshift estimate. We demonstrate the quality of the dataset by comparing it with earlier optically identified radio surveys. This is by far the largest ever optically identified radio catalogue, and will permit robust statistical studies of star-forming and radio-loud active galaxies.Comment: 29 pages. Accepted by A&A; data products available at https://lofar-surveys.org/dr2_release.htm

DNA methylation profiles delineate epigenetic heterogeneity in seminoma and non-seminoma

Background: It remains important to understand the biology and identify biomarkers for less studied cancers like testicular cancer. The purpose of this study was to determine the methylation frequency of several cancer-related genes in different histological types of testicular cancer and normal testis tissues (NT). Methods: DNA was isolated from 43 seminomas (SEs), 14 non-SEs (NSEs) and 23 NT, and was assayed for promoter methylation status of 15 genes by quantitative methylation-specific PCR. The methylation status was evaluated for an association with cancer, and between SEs and NSEs. Results: We found differential methylation pattern in SEs and NSEs. MGMT, VGF, ER-Β and FKBP4 were predominately methylated in NSEs compared with SEs. APC and hMLH1 are shown to be significantly more methylated in both subtypes in comparison with NT. When combining APC, hMLH1, ER-Β and FKBP4, it is possible to identify 86% of the NSEs, whereas only 7% of the SEs. Conclusions: Our results indicate that the methylation profile of cancer-associated genes in testicular cancer correlates with histological types and show cancer-specific pattern for certain genes. Further methylation analysis, in a larger cohort is needed to elucidate their role in testicular cancer development and potential for therapy, early detection and disease monitoring

Neural correlates of evidence accumulation during value-based decisions revealed via simultaneous EEG-fMRI

Current computational accounts posit that, in simple binary choices, humans accumulate evidence in favour of the different alternatives before committing to a decision. Neural correlates of this accumulating activity have been found during perceptual decisions in parietal and prefrontal cortex; however the source of such activity in value-based choices remains unknown. Here we use simultaneous EEG–fMRI and computational modelling to identify EEG signals reflecting an accumulation process and demonstrate that the within- and across-trial variability in these signals explains fMRI responses in posterior-medial frontal cortex. Consistent with its role in integrating the evidence prior to reaching a decision, this region also exhibits task-dependent coupling with the ventromedial prefrontal cortex and the striatum, brain areas known to encode the subjective value of the decision alternatives. These results further endorse the proposition of an evidence accumulation process during value-based decisions in humans and implicate the posterior-medial frontal cortex in this process

The unfolded protein response and its relevance to connective tissue diseases

The unfolded protein response (UPR) has evolved to counter the stresses that occur in the endoplasmic reticulum (ER) as a result of misfolded proteins. This sophisticated quality control system attempts to restore homeostasis through the action of a number of different pathways that are coordinated in the first instance by the ER stress-senor proteins IRE1, ATF6 and PERK. However, prolonged ER-stress-related UPR can have detrimental effects on cell function and, in the longer term, may induce apoptosis. Connective tissue cells such as fibroblasts, osteoblasts and chondrocytes synthesise and secrete large quantities of proteins and mutations in many of these gene products give rise to heritable disorders of connective tissues. Until recently, these mutant gene products were thought to exert their effect through the assembly of a defective extracellular matrix that ultimately disrupted tissue structure and function. However, it is now becoming clear that ER stress and UPR, because of the expression of a mutant gene product, is not only a feature of, but may be a key mediator in the initiation and progression of a whole range of different connective tissue diseases. This review focuses on ER stress and the UPR that characterises an increasing number of connective tissue diseases and highlights novel therapeutic opportunities that may arise

Minimal residual disease and circulating tumor cells in breast cancer

Tumor cell dissemination in bone marrow or other organs is thought to represent an important step in the metastatic process. The detection of bone marrow disseminated tumor cells is associated with worse outcome in early breast cancer. Moreover, the detection of peripheral blood circulating tumor cells is an adverse prognostic factor in metastatic breast cancer, and emerging data suggest that this is also true for early disease. Beyond enumeration, the characterization of these cells has the potential to improve risk assessment, treatment selection and monitoring, and the development of novel therapeutic agents, and to advance our understanding of the biology of metastasis

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)