Using Artificial Neural Networks to Determine Ontologies Most Relevant to Scientific Texts

This paper provides an insight into the possibility of how to find ontologies most relevant to scientific texts using artificial neural networks. The basic idea of the presented approach is to select a representative paragraph from a source text file, embed it to a vector space by a pre-trained fine-tuned transformer, and classify the embedded vector according to its relevance to a target ontology. We have considered different classifiers to categorize the output from the transformer, in particular random forest, support vector machine, multilayer perceptron, k-nearest neighbors, and Gaussian process classifiers. Their suitability has been evaluated in a use case with ontologies and scientific texts concerning catalysis research. From results we can say the worst results have random forest. The best results in this task brought support vector machine classifier

Oligonucleotide microarray for identification of Enterococcus species

For detection of most members of the Enterococcaceae, the specificity of a novel oligonucleotide microarray (ECC-PhyloChip) consisting of 41 hierarchically nested 16S or 23S rRNA gene-targeted probes was evaluated with 23 pure cultures (including 19 Enterococcus species). Target nucleic acids were prepared by PCR amplification of a 4.5-kb DNA fragment containing large parts of the 16S and 23S rRNA genes and were subsequently labeled fluorescently by random priming. Each tested member of the Enterococcaceae was correctly identified on the basis of its unique microarray hybridization pattern. The evaluated ECC-PhyloChip was successfully applied for identification of Enterococcus faecium and Enterococcus faecalis in artificially contaminated milk samples demonstrating the utility of the ECC-PhyloChip for parallel identification and differentiation of Enterococcus species in food sample

A Homogenous Set of Globular Cluster Relative Distances and Reddenings

We present distance modulus and reddening determinations for 72 Galactic globular clusters from the homogeneous photometric database of Piotto et al. (2002), calibrated to the HST flight F439W and F555W bands. The distances have been determined by comparison with theoretical absolute magnitudes of the ZAHB. For low and intermediate metallicity clusters, we have estimated the apparent Zero Age Horizontal Branch (ZAHB) magnitude from the RR Lyrae level. For metal rich clusters, the ZAHB magnitude was obtained from the fainter envelope of the red HB. Reddenings have been estimated by comparison of the HST colour-magnitude diagrams (CMD) with ground CMDs of low reddening template clusters. The homogeneity of both the photometric data and the adopted methodological approach allowed us to obtain highly accurate relative cluster distances and reddenings. Our results are also compared with recent compilations in the literature.Comment: 12 pages, 6 figures, accepted for publication in Astronomy & Astrophysic

Clinical Impact of Physical Activity and Cough on Disease Progression in Fibrotic Interstitial Lung Disease

Physical activity limitations and cough are common in patients with interstitial lung disease (ILD), potentially leading to reduced health-related quality of life. We aimed to compare physical activity and cough between patients with subjective, progressive idiopathic pulmonary fibrosis (IPF) and fibrotic non-IPF ILD. In this prospective observational study, wrist accelerometers were worn for seven consecutive days to track steps per day (SPD). Cough was evaluated using a visual analog scale (VAScough) at baseline and weekly for six months. We included 35 patients (IPF: n = 13; non-IPF: n = 22; mean ± SD age 61.8 ± 10.8 years; FVC 65.3 ± 21.7% predicted). Baseline mean ± SD SPD was 5008 ± 4234, with no differences between IPF and non-IPF ILD. At baseline, cough was reported by 94.3% patients (mean ± SD VAScough 3.3 ± 2.6). Compared to non-IPF ILD, patients with IPF had significantly higher burden of cough (p = 0.020), and experienced a greater increase in cough over six months (p = 0.009). Patients who died or underwent lung transplantation (n = 5), had significantly lower SPD (p = 0.007) and higher VAScough (p = 0.047). Long-term follow up identified VAScough (HR: 1.387; 95%-CI 1.081–1.781; p = 0.010) and SPD (per 1000 SPD: HR 0.606; 95%-CI: 0.412–0.892; p = 0.011) as significant predictors for transplant-free survival. In conclusion, although activity didn’t differ between IPF and non-IPF ILD, cough burden was significantly greater in IPF. SPD and VAScough differed significantly in patients who subsequently experienced disease progression and were associated with long-term transplant-free survival, calling for better acknowledgement of both parameters in disease management

Variability of forced vital capacity in progressive interstitial lung disease: a prospective observational study

BACKGROUND Fibrotic interstitial lung disease (ILD) is often associated with poor outcomes, but has few predictors of progression. Daily home spirometry has been proposed to provide important information about the clinical course of idiopathic pulmonary disease (IPF). However, experience is limited, and home spirometry is not a routine component of patient care in ILD. Using home spirometry, we aimed to investigate the predictive potential of daily measurements of forced vital capacity (FVC) in fibrotic ILD. METHODS In this prospective observational study, patients with fibrotic ILD and clinical progression were provided with home spirometers for daily measurements over 6~months. Hospital based spirometry was performed after three and 6~months. Disease progression, defined as death, lung transplantation, acute exacerbation or FVC decline \textgreater 10% relative was assessed in the cohort. RESULTS From May 2017 until August 2018, we included 47 patients (IPF n = 20; non-IPF n = 27). Sufficient daily measurements were performed by 85.1% of the study cohort. Among these 40 patients (IPF n = 17; non-IPF n = 23), who had a mean ± SD age of 60.7 ± 11.3 years and FVC 64.7 ± 21.7% predicted (2.4 ± 0.8 L), 12 patients experienced disease progression (death: n =~2; lung transplantation: n = 3; acute exacerbation: n = 1; FVC decline \textgreater 10%: n = 6). Within the first 28 days, a group of patients had high daily variability in FVC, with 60.0% having a variation \geq5%. Patients with disease progression had significantly higher FVC variability than those in the stable group (median variability 8.6% vs. 4.8%; p = 0.002). Cox regression identified FVC variability as independently associated with disease progression when controlling for multiple confounding variables (hazard ratio: 1.203; 95% CI:1.050-1.378; p = 0.0076). CONCLUSIONS Daily home spirometry is feasible in IPF and non-IPF ILD and facilitates the identification of FVC variability, which was associated with disease progression

Prognostic value of immune cell infiltration, tertiary lymphoid structures and PD-L1 expression in Merkel cell carcinomas

Merkel cell carcinoma (MCC) is an aggressive, virus-associated, neuroendocrine tumor of the skin mainly affecting immunocompromised patients. Higher intratumoral infiltration with CD3 and CD8 positive T-cells is associated with a better prognosis, highlighting the relevance of the immune system for MCC development and progression. In this study 21 primary MCCs were stained with immune cell markers including CD3, CD4, CD8, CD68, CD20, and S100. Furthermore, tumor-infiltrating neutrophils, tertiary lymphoid structures and PD-L1 expression were analyzed and correlated with overall and recurrence free survival. All MCCs were Merkel Cell Polyomavirus positive. Overall and recurrence-free survival did not correlate with intra-and peritumoral CD3 and CD8 T-cell infiltration. In addition, no significant association regarding prognosis was found for tumor-associated neutrophils, tumor-associated macrophages or PD-L1 positivity in MCCs. Interestingly, the presence of tertiary lymphoid structures (TLS) in the tumor microenvironment significantly correlated with recurrence-free survival (P=0.025). In addition, TLS were significantly associated with a higher CD8/CD4 ratio in the tumor periphery (P=0.032), but not in the center of the tumor (P > 0.999). These results demonstrate for the first time that TLS, easily assessed in paraffin-embedded tissue in the tumor periphery of MCCs, may be a valuable prognostic factor indicating prolonged recurrence free survival

The MUSCLES Extension for Atmospheric and Transmission Spectroscopy: UV and X-ray Host-star Observations for JWST ERS & GTO Targets

X-ray through infrared spectral energy distributions (SEDs) are essential for understanding a star's effect on exoplanet atmospheric composition and evolution. We present a catalog of panchromatic SEDs, hosted on the Barbara A. Mikulski Archive for Space Telescopes (MAST), for 11 exoplanet hosting stars which have guaranteed JWST observation time as part of the ERS or GTO programs but have no previous UV characterization. The stars in this survey range from spectral type F4-M6 (0.14-1.57 M$_\odot$), rotation periods of ~4-132 days, and ages of approximately 0.5-11.4 Gyr. The SEDs are composite spectra using data from the Chandra X-ray Observatory and XMM-Newton, the Hubble Space Telescope, BT-Settl stellar atmosphere models, and scaled spectra of proxy stars of similar spectral type and activity. From our observations, we have measured a set of UV and X-ray fluxes as indicators of stellar activity level. We compare the chromospheric and coronal activity indicators of our exoplanet-hosting stars to the broader population of field stars and find that a majority of our targets have activity levels lower than the average population of cool stars in the solar neighborhood. This suggests that using SEDs of stars selected from exoplanet surveys to compute generic exoplanet atmosphere models may underestimate the typical host star's UV flux by an order of magnitude or more, and consequently, that the observed population of exoplanetary atmospheres receive lower high-energy flux levels than the typical planet in the solar neighborhood.Comment: 28 pages, 10 figures, 7 tables, accepted for publication in A

Long-term effects of intravenous iloprost in patients with idiopathic pulmonary arterial hypertension deteriorating on non-parenteral therapy

Background: The majority of patients with idiopathic pulmonary arterial hypertension (IPAH) in functional classes II and III are currently being treated with non-parenteral therapies, including endothelin receptor antagonists (ERA), phosphodiesterase (PDE)-5 inhibitors, inhaled iloprost or combinations of these substances. If these treatments fail, current guidelines recommend the addition of parenteral prostanoid therapy. There is, however, limited evidence for the efficacy of parenteral prostanoids when added to combinations of non-parenteral therapies. Methods: In this retrospective, multicentre study we collected data from consecutive IPAH patients receiving intravenous iloprost in addition to optimized non-parenteral therapy between Jan 2002 and Dec 2009. Analyses included 6 min walk distance (6MWD), functional class, need for transplantation, and survival. Results: During the observation period, 50 patients were treated with intravenous iloprost in addition to non-parenteral therapy; 44% of the patients were on dual combination therapy and 52% on triple combination. Three months after initiation of iloprost, functional class had improved in 24% of the patients and the median 6MWD had increased from 289 m to 298 m (n.s.). During the observation period, 22 patients (44%) died and 14 (28%) underwent lung transplantation. The probabilities of LuTx-free survival at 1, 3 and 5 years following iloprost initiation were 38%, 17% and 17%, respectively. A 6MWD < 300 m and persistent functional class IV at 3 months after initiation of intravenous iloprost were predictors of an adverse outcome. Conclusion: In essence, late initiation of intravenous iloprost in IPAH patients who previously failed to respond to non-parenteral therapies appears to be of limited efficacy in the majority patients. Alternative therapeutic options are currently not available, underlying the need for the development of new drugs