Miracle-dz/UniFAR-FTUs huggingface dataset:
Tunable thiol–epoxy shape memory polymer foams

Shape memory polymers (SMPs) are uniquely suited to a number of applications due to their shape storage and recovery abilities and the wide range of available chemistries. However, many of the desired performance properties are tied to the polymer chemistry which can make optimization difficult. The use of foaming techniques is one way to tune mechanical response of an SMP without changing the polymer chemistry. In this work, a novel thiol–epoxy SMP was foamed using glass microspheres (40 and 50% by volume Q-Cel 6019), using expandable polymer microspheres (1% 930 DU 120), and by a chemical blowing agent (1% XOP-341). Each approach created SMP foam with a differing density and microstructure from the others. Thermal and thermomechanical analysis was performed to observe the behavioral difference between the foaming techniques and to confirm that the glass transition (Tg) was relatively unchanged near 50 °C while the glassy modulus varied from 19.1 to 345 MPa and the rubbery modulus varied from 0.04 to 2.2 MPa. The compressive behavior of the foams was characterized through static compression testing at different temperatures, and cyclic compression testing at Tg. Constrained shape recovery testing showed a range of peak recovery stress from 5 MPa for the syntactic Q-Cel foams to ∼0.1 MPa for the chemically blown XOP-341 foam. These results showed that multiple foaming approaches can be used with a novel SMP to vary the mechanical response independent of Tg and polymer chemistry.
The ‘surprise’ question in advanced cancer patients: A prospective study among general practitioners

Background: Using the ‘surprise’ question ‘Would you be surprised if this patient died in the next year? ’ may improve physicians’ prognostic accuracy and identify people appropriate for palliative care. Aim: Determine the prognostic accuracy of general practitioners asking the ‘surprise’ question about their patients with advanced (stage IV) cancer. Design: Prospective cohort study. Setting/participants: Between December 2011 and February 2012, 42 of 50 randomly selected general practitioners (Bologna area, Italy) prospectively classified 231 patients diagnosed with advanced cancer according to the ‘surprise’ question and supplied the status of each patient 1 year later. Results: Of the 231 patients, general practitioners responded ‘No’ to the ‘surprise’ question for 126 (54.5%) and ‘Yes’ for 105 (45.5%). After 12 months, 104 (45.0%) patients had died; 87 (83.7%) were in the ‘No’ group. The sensitivity of the ‘surprise’ question was 69.3%; the specificity was 83.6%. Positive predictive value was 83.8%; negative predictive value was 69.0%. The answer to the ‘surprise’ question was significantly correlated with survival at 1 year. Patients in the ‘No’ group had an odds ratio of 11.55 (95% confidence interval: 5.83–23.28) and a hazard ratio of 6.99 (95% confidence interval: 3.75–13.03) of being dead in the next year compared to patients in the ‘Yes’ group (p = 0.000 for both odds ratio and hazard ratio). Conclusion: When general practitioners used the ‘surprise’ question for their patients with advanced cancer, the accuracy of survival prognosis was very high. This has clinical potential as a method to identify patients who might benefit from palliative care.
CQT-based Convolutional Neural Networks for Audio Scene Classification

In this paper, we propose a parallel Convolutional Neural Network architecture for the task of classifying acoustic scenes and urban sound scapes. A popular choice for input to a Convolutional Neural Network in audio classification problems are Mel-transformed spectrograms. We, however, show in this paper that a ConstantQ-transformed input improves results. Furthermore, we evaluated critical parameters such as the number of necessary bands and filter sizes in a Convolutional Neural Network. These are non-trivial in audio tasks due to the different semantics of the two axes of the input data: time vs. frequency. Finally, we propose a parallel (graphbased) neural network architecture which captures relevant audio characteristics both in time and in frequency. Our approach shows a 10.7 % relative improvement of the baseline system of the DCASE 2016 Acoustic Scenes Classification task [1].
Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer

Background Genetic intratumoral heterogeneity (ITH) hinders biomarker development in metastatic clear cell renal cancer (mccRCC). Epigenetic relative to genetic ITH or the presence of consistent epigenetic changes following targeted therapy in mccRCC have not been evaluated. The aim of this study was to determine methylome/genetic ITH and to evaluate specific epigenetic and genetic changes associated with sunitinib therapy. Patients and methods Multi-region DNA sampling performed on sequential frozen pairs of primary tumor tissue from 14 metastatic ccRCC patients, in the Upfront Sunitinib (SU011248) Therapy Followed by Surgery in Patients with Metastatic Renal Cancer: a Pilot Phase II Study (SuMR; ClinicalTrials.gov identifier: NCT01024205), at presentation (biopsy) and after 3-cycles of 50mg sunitinib (nephrectomy). Untreated biopsy and nephrectomy samples before and after renal artery ligation were controls. Ion Proton sequencing of 48 key ccRCC genes, and MethylCap-seq DNA methylation analysis was performed, data was analysed using the statistical computing environment R. Results Unsupervised hierarchical clustering revealed complete methylome clustering of biopsy and three nephrectomy samples for each patient (14/14 patients). For mutational status, untreated biopsy and all treated nephrectomy samples clustered together in 8/13 (61.5%) patients. The only methylation target significantly altered following sunitinib therapy was VHL promoter region 7896829 which was hypermethylated with treatment (FDR=0.077, P<0.001) and consistent for all patients (pre-treatment 50% patients had VHL mutations, 14% patients VHL hypermethylation). Renal artery ligation did not affect this result. No significant differences in driver or private mutation count was found with sunitinib treatment. Conclusions Demonstration of relative methylome homogeneity and consistent VHL hypermethylation, after sunitinib, may overcome the hurdle of ITH present at other molecular levels for biomarker research.
Almanac 2013: heart failure

The National Heart Failure Audit continues to be an invaluable resource for understanding how acute heart failure is managed in England and Wales. The most recent report1 describes just over 37 000 hospitalisations. As in previous publications, fewer than half the patients were managed in cardiology wards, yet those who were had a better outcome; half were referred at discharge to cardiologists for follow-up and they, too, had a better outcome. An innovation in the audit this time was the publication of hospital level analysis. It would be invidious to pick out names, but it is very striking how variable are the rates of such basic items as the use of echocardiography, availability of a cardiologist to manage the patients and the rate of prescription of different drugs. Studies show that, during long-term follow-up, patients managed by heart failure specialists including ‘heart failure nurses’ are more likely to be treated with the appropriate medication in the appropriate dose, have lower (re-)admission rates to hospital and a better prognosis.2 There is reasonable evidence that there are better outcomes if part of the multidisciplinary intervention is made in the home.3 There is strong evidence that specialist clinics reduce the risk of readmission with heart failure immediately after an index admission.4 Also available to the clinician are the heart failure guidelines from the National Institute for Health and Care Excellence (NICE)5 ,6 and the associated quality standards.7 The NICE standards make it clear what NHS services across England and Wales should be striving towards. Combined with the hospital level analysis from the audit, the quality standards should give clinical teams the ammunition they need when discussing their heart failure service with management teams in both primary and secondary care. However, it is becoming ever clearer that the …
The Impact of PNPLA3 rs738409 Genetic Polymorphism and Weight Gain ≥10 kg after Age 20 on Non-Alcoholic Fatty Liver Disease in Non-Obese Japanese Individuals

Non-alcoholic fatty liver disease (NAFLD) in non-obese individuals is inadequately elucidated. We aim to investigate the impact of known genetic polymorphisms on NAFLD and the interaction between genetic risks and weight gain on NAFLD in obese and non-obese Japanese individuals. A total of 1164 participants who received health checkups were included. Participants with excessive alcohol consumption, with viral hepatitis or other inappropriate cases were excluded. Fatty liver was diagnosed by ultrasonography. Participants with a body mass index (BMI) of <18.5 kg/m2, 18.5–22.9 kg/m2, 23.0–24.9 kg/m2 and ≥25 kg/m2 were classified underweight, normal weight, overweight and obese, respectively. Self-administered questionnaire for lifestyle was assessed and a total of 8 previously reported genetic polymorphisms were chosen and examined. In all, 824 subjects were enrolled. The overall prevalence of NAFLD was 33.0%: 0% in underweight, 15.3% in normal weight, 41.1% in overweight and 71.7% in obese individuals. The prevalence of NAFLD is more affected by the G allele of patatin-like phospholipase domain-containing protein 3 (PNPLA3) rs738409 in normal weight (odds ratio (OR) 3.52; 95%-CI: 1.42–8.71; P = 0.0063) and in overweight individuals (OR 2.60; 95%-CI: 1.14–5.91; P = 0.0225) than in obese individuals (not significant). Moreover, the G allele of PNPLA3 rs738409 and weight gain ≥10 kg after age 20 had a joint effect on the risk of NAFLD in the normal weight (OR 12.00; 95% CI: 3.71–38.79; P = 3.3×10−5) and the overweight individuals (OR 13.40; 95% CI: 2.92–61.36; P = 0.0008). The G allele of PNPLA3 rs738409 is a prominent risk factor for NAFLD and the interaction between the PNPLA3 rs738409 and weight gain ≥10 kg after age 20 plays a crucial role in the pathogenesis of NAFLD, especially in non-obese Japanese individuals.
Capacity maximizing MMSE-optimal pilots for wireless OFDM over frequency-selective block Rayleigh-fading channels

The location, number, and power of pilot symbols embedded in multicarrier block transmissions over rapidly fading channels, are important design parameters affecting not only channel estimation performance, but also channel capacity. Considering orthogonal frequency-division multiplexing (OFDM) systems with decoupled information-bearing symbols from pilot symbols transmitted over wireless frequency-selective Rayleigh-fading channels, we show that equispaced and equipowered pilot symbols are optimal in terms of minimizing the mean-square channel estimation error. We also design the number of pilots, and the power distributed between information bearing and pilot symbols, using as criterion a lower bound on the average capacity. Numerical results corroborate our theoretical findings.
Molecular hydrogen: a therapeutic antioxidant and beyond

Molecular hydrogen (H2 ) medicine research has flourished since a landmark publication in Nature Medicine that revealed the antioxidant and cytoprotective effects of hydrogen gas in a focal stroke model. Emerging evidence has consistently demonstrated that molecular hydrogen is a promising therapeutic option for a variety of diseases and the underlying comprehensive mechanisms is beyond pure hydroxyl radicals scavenging. The non-toxicity at high concentrations and rapid cellular diffusion features of molecular hydrogen ensure the feasibility and readiness of its clinical translation to human patients.
The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data

The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. We present an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon and exon–exon junction expression. In contrast to previous counting-based approaches, EQP takes into account only reads whose alignment pattern agrees with the splicing pattern of the features of interest. This leads to improved gene expression estimates as well as to the generation of exon counts that allow disambiguating reads between overlapping exons. Unlike other methods that quantify skipped introns, EQP offers a novel way to compute junction counts based on the agreement of the read alignments with the exons on both sides of the junction, thus providing a uniformly derived set of counts. We evaluated the performance of EQP on both simulated and real Illumina RNA-seq data and compared it with other quantification tools. Our results suggest that EQP provides superior gene expression estimates and we illustrate the advantages of EQP's exon and junction counts. The provision of uniformly derived high-quality counts makes EQP an ideal quantification tool for differential expression and differential splicing studies. EQP is freely available for download at https://github.com/Novartis/EQP-cluster.
Perception of Moving, Sounding Objects by Four-Month-Old Infants

Infants and adults were presented with two moving objects accompanied by a single percussive sound. In different experiments, the sound occurred when one object moved through a particular spatial position, when it abruptly changed its direction of movement, or when it made contact with a rigid surface. Infants responded to the sound—object relationship whenever the sound occurred as the object changed direction, irrespective of its impacts with the surface. Adults, in contrast, responded to the sound—object relationship most clearly when sounds were synchronized with impacts. In infancy, perception of auditory—visual relationships thus depends in part on detection of discontinuities in the movement of a visible object.
Phylogenetic congruence between subtropical trees and their associated fungi

Abstract Recent studies have detected phylogenetic signals in pathogen–host networks for both soil‐borne and leaf‐infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next‐generation high‐throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host–fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant–fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant–fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.
Decreased Anti-Inflammatory Responses to Vitamin D in Neonatal Neutrophils

Neutrophil activity is prolonged in newborns, suggesting decreased exposure and/or responses to immunosuppressive modulators, such as 1,25-hydroxyvitamin D3 (1,25-vit D3). We hypothesized that 1,25-vit D3 suppresses neutrophil activation and that this response is impaired in newborns. Consistent with this, 1,25-vit D3 decreased LPS-induced expression of macrophage inflammatory protein-1β and VEGF in adult, but not neonatal, neutrophils. Expression of vitamin D receptor (VDR) and 25-hydroxyvitamin D3-1α-hydroxylase was reduced in neonatal, relative to adult neutrophils. Moreover, 1,25-vit D3 induced VDR gene expression in activated adult, but not neonatal, neutrophils. 1,25-vit D3 also suppressed expression of cyclooxygenase-2 and induced expression of 5-lipoxygenase in LPS-exposed adult neutrophils, while neonatal cells were not affected. 1,25-vit D3 had no effect on respiratory burst in either adult or neonatal cells. Anti-inflammatory activity of vitamin D is impaired in neonatal neutrophils, and this may be due to decreased expression of VDR and 1α-hydroxylase. Insensitivity to 1,25-vit D3 may contribute to chronic inflammation in neonates.
Novel stability criterion for neural network swith time-varying delay via free-matrix-based integral inequality

This paper investigates the problem of stability analysis of neural networks with time-varying delay. Some augmented double integral term and triple integral terms are introduced to the Lyapunov-Krasovskii functional (LKF). And the derivative of the LKF is estimated by the free-matrix-based integral inequality. Then, a less conservative stability criterion is derived. Finally, a numerical example is provided to verify the effectiveness and benefit of the proposed stability criterion.
A Noninvasive Imaging Modality for Cardiac Arrhythmias

BackgroundThe last decade witnessed an explosion of information regarding the genetic, molecular, and mechanistic basis of heart disease. Translating this information into clinical practice requires the development of novel functional imaging modalities for diagnosis, localization, and guided intervention. A noninvasive modality for imaging cardiac arrhythmias is not yet available. Present electrocardiographic methods cannot precisely localize a ventricular tachycardia (VT) or its key reentrant circuit components. Recently, we developed a noninvasive electrocardiographic imaging modality (ECGI) that can reconstruct epicardial electrophysiological information from body surface potentials. Here, we extend its application to image reentrant arrhythmias. Methods and ResultsEpicardial potentials were recorded during VT with a 490 electrode sock during an open chest procedure in 2 dogs with 4-day-old myocardial infarctions. Body surface potentials were generated from these epicardial potentials in a human torso model. Realistic geometry errors and measurement noise were added to the torso data, which were then used to noninvasively reconstruct epicardial isochrones, electrograms, and potentials with excellent accuracy. ECGI reconstructed the reentry pathway and its key components, including (1) the central common pathway, (2) the VT exit site, (3) lines of block, and (4) regions of slow and fast conduction. This allowed for detailed characterization of the reentrant circuit morphology. ConclusionsECGI can noninvasively image arrhythmic activation on the epicardium during VT to identify and localize key components of the arrhythmogenic pathway that can be effective targets for antiarrhythmic intervention.
Strathprints Institutional Repository Bayesian Latent Variable Models for Collaborative Item Rating Prediction. In: Acm Cikm, 2011-03-31. Bayesian Latent Variable Models for Collaborative Item Rating Prediction

Strathprints is designed to allow users to access the research output of the University of Strathclyde. Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (http://strathprints.strath.ac.uk/) and the content of this paper for research or study, educational, or not-for-profit purposes without prior permission or charge. ABSTRACT Collaborative filtering systems based on ratings make it easier for users to find content of interest on the Web and as such they constitute an area of much research. In this paper we first present a Bayesian latent variable model for rating prediction that models ratings over each user's latent interests and also each item's latent topics. We describe a Gibbs sampling procedure that can be used to estimate its parameters and show by experiment that it is competitive with the gradient descent SVD methods commonly used in state-of-the-art systems. We then proceed to make an important and novel extension to this model, enhancing it with user-dependent and item-dependant biases to significantly improve rating estimation. We show by experiment on a large set of real ratings data that these models are able to outperform 3 common base-lines, including a very competitive and modern SVD-based model. Furthermore we illustrate other advantages of our approach beyond simply its ability to provide more accurate ratings and show that it is able to perform better on the common and important case where the user profile is short. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee.
Helicobacter pyloriLipopolysaccharides Preferentially Induce CXC Chemokine Production in Human Monocytes

ABSTRACT Helicobacter pylori infection can cause duodenal ulcers and may also induce gastric adenocarcinoma. The bacteria colonize the gastric mucosa and areas of gastric metaplasia in the duodenum for decades, resulting in active chronic inflammation in the infected areas. A characteristic feature of the infection is the ongoing recruitment of neutrophils to the infected sites. To evaluate the role of H. pylori lipopolysaccharides (LPS) in the recruitment of leukocytes to the gastric mucosa, we have examined the cytokine and chemokine production from human monocytes stimulated with LPS isolated from different H. pylori strains, as well as from several other gram-negative bacteria. Our results show thatH. pylori LPS induce a large production of neutrophil-recruiting CXC chemokines (interleukin-8 and growth-related oncogene alpha) from purified human monocytes, to almost the same extent as Escherichia coli LPS. However, and in agreement with previous studies, H. pylori LPS was much less potent in inducing production of proinflammatory cytokines by purified human monocytes and was also a weak inducer of the CC chemokine RANTES. There was no difference between LPS preparations from different H. pylori strains in their ability to induce cytokines and chemokines. The preferential production of CXC chemokines after stimulation with H. pylori LPS indicates an important contribution of this molecule in maintaining neutrophil recruitment during the infection, irrespective of the infecting strain.