bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knowledge graph prediction of unknown adverse drug reactions and validation in electronic health records
Authors: Bean Daniel M. , Wu Honghan , Iqbal Ehtesham , Dzahini Olubanke , Ibrahim Zina M. , Broadbent Matthew , Stewart Robert , Dobson Richard J. B. 
Published: November 2017

AbstractUnknown adverse reactions to drugs available on the market present a significant health risk and limit accurate judgement of the cost/benefit trade-off for medications. Machine learning has the potential to predict unknown adverse reactions from current knowledge. We constructed a knowledge graph containing four types of node: drugs, protein targets, indications and adverse reactions. Using this graph, we developed a machine learning algorithm based on a simple enrichment test and first demonstrated this method performs extremely well at classifying known causes of adverse reactions (AUC 0.92). A cross validation scheme in which 10% of drug-adverse reaction edges were systematically deleted per fold showed that the method correctly predicts 68% of the deleted edges on average. Next, a subset of adverse reactions that could be reliably detected in anonymised electronic health records from South London and Maudsley NHS Foundation Trust were used to validate predictions from the model that are not currently known in public databases. High-confidence predictions were validated in electronic records significantly more frequently than random models, and outperformed standard methods (logistic regression, decision trees and support vector machines). This approach has the potential to improve patient safety by predicting adverse reactions that were not observed during randomised trials.
The computations that support simple decision-making: A comparison between the diffusion and urgency-gating models
Authors: Evans Nathan J. , Hawkins Guy E. , Boehm Udo , Wagenmakers Eric-Jan , Brown Scott D. 
Published: November 2017

AbstractWe investigate a question relevant to the psychology and neuroscience of perceptual decision-making: whether decisions are based on steadily accumulating evidence, or only on the most recent evidence. We report an empirical comparison between two of the most prominent examples of these theoretical positions, the diffusion model and the urgency-gating model, via model-based qualitative and quantitative comparisons. Our findings support the predictions of the diffusion model over the urgency-gating model, and therefore, the notion that evidence accumulates without much decay. Gross qualitative patterns and fine structural details of the data are inconsistent with the notion that decisions are based only on the most recent evidence. More generally, we discuss some strengths and weaknesses of scientific methods that investigate quantitative models by distilling the formal models to qualitative predictions.
5D proteomic approach for the biomarker search in plasma: Acute myeloid leukaemia as a case study
Authors: Raza Syed Kashif , Saleem Mahwish , Shamsi Tahir , Choudhary M. Iqbal , Atta-ur-Rahman  , Musharraf Syed Ghulam 
Published: November 2017

AbstractAcute myeloid leukaemia (AML) is a type of cancer affecting all ages but it is more common in adults, as compared to children. Recent advancements in proteomics and mass spectrometry tools, offer a comprehensive solution to study the molecular complexity of diseases, such as cancers. This study is focused on the proteomic profiling of AML in comparison to healthy control for which, a systematic 5D proteomic approach for the fractionation of pooled plasma samples was used. Methodology includes depletion of Top-7 abundant proteins, ZOOM-isoelectric focusing (ZOOM-IEF), two-dimensional gel electrophoresis (2-DGE), and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis followed by the validation of identified biomarker proteins using enzyme linked immunosorbent assay (ELISA). Up-/down-fold changes in concentration of proteins were observed in 2-DGE of AML in comparison with the healthy control and a total of 34 proteins were identified in fractioned plasma. Among them, fifteen proteins were significantly differentiated and five proteins; SAA1, complement factor C7, ApoE, plasminogen, and ApoA1 were later verified by ELISA in individual samples, which showed that SAA1 and plasminogen could be used as potential biomarker for AML.
Serum Uric Acid is Independently Associated with Enlarged Perivascular Spaces
Authors: Yang Shuna , Zhang Xiaoyu , Yuan Junliang , Yin Jiangmei , Hu Wenli 
Published: November 2017

AbstractEnlarged perivascular spaces (EPVS) are reported to be associated with impaired cognitive function and sleep disorders. It is of clinical importance to understand the risk factors for EPVS. Hyperuricemia increases the risk of hypertension and endothelial dysfunction, which are well recognized to be associated with EPVS. Therefore, we postulated that serum uric acid (SUA) might be associated with EPVS. A total of 665 lacunar stroke patients were enrolled in this study. The SUA concentrations of patients with severe EPVS were much higher than those of patients with mild EPVS (for basal ganglia: 5.25 ± 1.40 mg/dl vs. 4.75 ± 1.40 mg/dl, p < 0.001; for white matter: 5.31 ± 1.41 mg/dl vs. 4.88 ± 1.37 mg/dl, p = 0.009). The percentage of subjects with severe EPVS tended to be higher in the highest quartile of SUA (chi-square test: P = 0.002 for basal ganglia and 0.006 for white matter). Spearman correlation analysis indicated that the SUA concentrations were positively correlated with the severity of EPVS (rho > 0, p < 0.05). Multivariate logistic regression analysis showed that high normal SUA was independently associated with a higher severity of EPVS. This finding suggests that high SUA levels might be an independent risk factor for EPVS in lacunar stroke patients.
NumtS colonization in mammalian genomes
Authors: Calabrese F. M. , Balacco D. L. , Preste R. , Diroma M. A. , Forino R. , Ventura M. , Attimonelli M. 
Published: November 2017

AbstractThe colonization of the nuclear genome by mitochondrial DNA is an ongoing process in eukaryotes and plays an important role in genomic variability. Notwithstanding the DNA sequence availability of about 100 complete eukaryotic genomes, up to now NumtS distribution has been fully reported for a small number of sequenced eukaryotic species. With the aim to clarify the time and way of NumtS evolution, we explored the genomic distribution of NumtS in 23 eukaryotic species using an intra/interspecies in silico approach based on a cross-species similarity search and deeply investigate the evolution of NumtS in mammals. The intra- and interspecies analysis underlined how some mitochondrial regions that populated nuclear genomes can be considered as hotspots. Considering the large amount of NumtS we found in platypus and opossum genomes, we hypothesized the occurrence of an earlier colonization that happened prior to the Prototherian/Therian mammal divergence, approximately 160–210 million years ago. These events are still detectable due to the species-specific dynamics that have affected these genomes. Phylogenetic analyses of NumtS derived from two different mitochondrial DNA loci allowed us to recognize the unusual NumtS evolution that acted differently on primate and non-primate species’ genomes.
Colour discrimination thresholds in type 1 Bipolar Disorder: a pilot study
Authors: Fernandes Thiago Monteiro Paiva , Andrade Suellen Marinho , de Andrade Michael Jackson Oliveira , Nogueira Renata Maria Toscano Barreto Lyra , Santos Natanael Antonio 
Published: November 2017

AbstractAlthough some studies have reported perceptual changes in psychosis, no definitive conclusions have been drawn about visual disturbances that are related to bipolar disorder (BPD). The purpose of the present study was to evaluate colour vision in BPD patients. Data were recorded from 24 participants: healthy control group (n = 12) and type 1 BPD group (n = 12). The participants were 20–45 years old and they were free from neurological disorders and identifiable ocular disease and had normal or corrected-to-normal visual acuity. Colour discrimination was evaluated using the Lanthony D-15d, Trivector and Ellipse tests, using a psychophysical forced-choice method. The relationship of visual measures to mood state and cognitive function was also investigated. The results showed that BPD patients had higher colour discrimination thresholds in the D15d (p < 0.001), Trivector (p < 0.001) and Ellipse (p < 0.01) tests compared with healthy controls. Linear regression analysis showed that mood state was related to colour discrimination. BPD individuals were not impaired in cognitive tasks. The present study provided new evidence of potential links between type 1 BPD and visual processing impairments. This research suggests a new direction for studies and the need for research in this field of study.
In situ investigation of phase transformations in Ti-6Al-4V under additive manufacturing conditions combining laser melting and high-speed micro-X-ray diffraction
Authors: Kenel C. , Grolimund D. , Li X. , Panepucci E. , Samson V. A. , Sanchez D. Ferreira , Marone F. , Leinenbach C. 
Published: November 2017

AbstractWe present combined in situ X-ray diffraction and high-speed imaging to monitor the phase evolution upon cyclic rapid laser heating and cooling mimicking the direct energy deposition of Ti-6Al-4V in real time. Additive manufacturing of the industrially relevant alloy Ti-6Al-4V is known to create a multitude of phases and microstructures depending on processing technology and parameters. Current setups are limited by an averaged measurement through the solid and liquid parts. In this work the combination of a micro-focused intense X-ray beam, a fast detector and unidirectional cooling provide the spatial and temporal resolution to separate contributions from solid and liquid phases in limited volumes. Upon rapid heating and cooling, the β ↔ α′ phase transformation is observed repeatedly. At room temperature, single phase α′ is observed. Secondary β-formation upon formation of α′ is attributed to V partitioning to the β-phase leading to temporary stabilization. Lattice strains in the α′-phase are found to be sensitive to the α′ → β phase transformation. Based on lattice strain of the β-phase, the martensite start temperature is estimated at 923 K in these experiments. Off-axis high speed imaging confirms a technically relevant solidification front velocity and cooling rate of 10.3 mm/s and 4500 K/s, respectively.
A Route to Terahertz Metamaterial Biosensor Integrated with Microfluidics for Liver Cancer Biomarker Testing in Early Stage
Authors: Geng Zhaoxin , Zhang Xiong , Fan Zhiyuan , Lv Xiaoqing , Chen Hongda 
Published: November 2017

AbstractEngineered Terahertz (THz) metamaterials presented an unique characteristics for biosensing application due to their accurately tunable resonance frequency, which is in accord with vibrational frequency of some important biomolecules such as cancer biomarker. However, water absorption in THz regime is an obstacle to extend application in trace biomolecules of cancer antibody or antigen. Here, to overcome water absorption and enhance the THz biosensing sensitivity, two kinds of THz metamaterials biosensor integrated with microfluidics were fabricated and used to detect the Alpha fetoprotein (AFP) and Glutamine transferase isozymes II (GGT-II) of liver cancer biomarker in early stage. There were about 19 GHz resonance shift (5 mu/ml) and 14.2 GHz resonance shift (0.02524 μg/ml) for GGT-II and AFP with a two-gap-metamaterial, respectively, which agreed with simulation results. Those results demonstrated the power and usefulness of metamaterial-assisted THz spectroscopy in trace cancer biomarker molecular detection for biological and chemical sensing. Moreover, for a particular cancer biomarker, the sensitivity could be further improved by optimizing the metamaterial structure and decreasing the permittivity of the substrate. This method might be powerful and potential for special recognition of cancer molecules in the early stage.
Rational design of cholesterol oxidase for efficient bioresolution of cholestane skeleton substrates
Authors: Qin Hui-Min , Zhu Zhangliang , Ma Zheng , Xu Panpan , Guo Qianqian , Li Songtao , Wang Jian-Wen , Mao Shuhong , Liu Fufeng , Lu Fuping 
Published: November 2017

AbstractCholesterol oxidase catalyzes the oxidation and isomerization of the cholestane substrates leading to the addition of a hydroxyl group at the C3 position. Rational engineering of the cholesterol oxidase from Pimelobacter simplex (PsChO) was performed. Mutagenesis of V64 and F70 improved the catalytic activities toward cholestane substrates. Molecular dynamics simulations, together with structure-activity relationship analysis, revealed that both V64C and F70V increased the binding free energy between PsChO mutants and cholesterol. F70V and V64C mutations might cause the movement of loops L56-P77, K45-P49 and L350-E354 at active site. They enlarged the substrate-binding cavity and relieved the steric interference with substrates facilitating recognition of C17 hydrophobic substrates with long side chain substrates.
Radio signatures of shock-accelerated electron beams in the solar corona
Authors: Mann G. , Melnik V. N. , Rucker H. O. , Konovalenko A. A. , Brazhenko A. I. 
Published: November 2017

Context.The Sun’s activity can appear in terms of radio bursts. In the frequency range 8−33 MHz the radio telescope URAN-2 observed special fine structures appearing as a chain of stripes of enhanced radio emission in the dynamic radio spectrum. The chain drifts slowly from 26 to 23 MHz within 4 min. The individual structures consist of a “head” at the high-frequency edge and a “tail” rapidly drifting from the “head” to lower frequencies over an extent of ≈10 MHz within 8 s. Since they resemble the well-known “herring bones” in type II radio bursts, they are interpreted as shock accelerated electron beams.Aims.The electron beams generating these fine structures are considered to be produced by shock drift acceleration (SDA). The beam electrons excite Langmuir waves which are converted into radio waves by nonlinear wave-plasma processes. That is called plasma emission. The aim of this paper is to link the radio spectral data of these fine structures to the theoretical results in order to gain a better understanding of the generation of energetic electrons by shocks in the solar corona.Methods.Adopting SDA for generating energetic electrons, the accelerated electrons establish a beam-like velocity distribution. Plasma emission requires the excitation of Langmuir waves, which is efficient if the velocity of the beam electrons exceeds a few times thermal electron speed. That is the case if the angle between the shock normal and the upstream magnetic field is nearly perpendicular. Hence, the Rankine-Hugoniot relationships, which describe the shock transition in the framework of magnetohydrodynamics, are evaluated for the special case of nearly perpendicular shocks under coronal circumstances.Results.The radio data deduced from the dynamic radio spectrum can be related in the best way to the theoretical results, if the electron beams, which generate these fine structures, are generated via SDA at an almost perpendicular shock, which is traveling nearly horizontally to the surface of the Sun.
Supergiants and their shells in young globular clusters
Authors: Szécsi Dorottya , Mackey Jonathan , Langer Norbert 
Published: November 2017

Context. Anomalous surface abundances are observed in a fraction of the low-mass stars of Galactic globular clusters, that may originate from hot-hydrogen-burning products ejected by a previous generation of massive stars.
Aims. We aim to present and investigate a scenario in which the second generation of polluted low-mass stars can form in shells around cool supergiant stars within a young globular cluster.
Methods. Simulations of low-metallicity massive stars (Mi ~ 150−600 M⊙) show that both core-hydrogen-burning cool supergiants and hot ionizing stellar sources are expected to be present simulaneously in young globular clusters. Under these conditions, photoionization-confined shells form around the supergiants. We have simulated such a shell, investigated its stability and analysed its composition.
Results. We find that the shell is gravitationally unstable on a timescale that is shorter than the lifetime of the supergiant, and the Bonnor-Ebert mass of the overdense regions is low enough to allow star formation. Since the low-mass stellar generation formed in this shell is made up of the material lost from the supergiant, its composition necessarily reflects the composition of the supergiant wind. We show that the wind contains hot-hydrogen-burning products, and that the shell-stars therefore have very similar abundance anomalies that are observed in the second generation stars of globular clusters. Considering the mass-budget required for the second generation star-formation, we offer two solutions. Either a top-heavy initial mass function is needed with an index of −1.71 to −2.07. Alternatively, we suggest the shell-stars to have a truncated mass distribution, and solve the mass budget problem by justifiably accounting for only a fraction of the first generation.
Conclusions. Star-forming shells around cool supergiants could form the second generation of low-mass stars in Galactic globular clusters. Even without forming a photoionizaton-confined shell, the cool supergiant stars predicted at low-metallicity could contribute to the pollution of the interstellar medium of the cluster from which the second generation was born. Thus, the cool supergiant stars should be regarded as important contributors to the evolution of globular clusters.
Charge exchange in galaxy clusters
Authors: Gu Liyi , Mao Junjie , de Plaa Jelle , Raassen A. J. J. , Shah Chintan , Kaastra Jelle S. 
Published: November 2017

Context. Though theoretically expected, the charge exchange emission from galaxy clusters has never been confidently detected. Accumulating hints were reported recently, including a rather marginal detection with the Hitomi data of the Perseus cluster. As previously suggested, a detection of charge exchange line emission from galaxy clusters would not only impact the interpretation of the newly discovered 3.5 keV line, but also open up a new research topic on the interaction between hot and cold matter in clusters.Aim. We aim to perform the most systematic search for the O VIII charge exchange line in cluster spectra using the RGS on board XMM-Newton.Methods. We introduce a sample of 21 clusters observed with the RGS. In order to search for O VIII charge exchange, the sample selection criterion is a >35σ detection of the O VIII Lyα line in the archival RGS spectra. The dominating thermal plasma emission is modeled and subtracted with a two-temperature thermal component, and the residuals are stacked for the line search. The systematic uncertainties in the fits are quantified by refitting the spectra with a varying continuum and line broadening.Results. By the residual stacking, we do find a hint of a line-like feature at 14.82 Å, the characteristic wavelength expected for oxygen charge exchange. This feature has a marginal significance of 2.8σ, and the average equivalent width is 2.5 × 10−4 keV. We further demonstrate that the putative feature can be barely affected by the systematic errors from continuum modeling and instrumental effects, or the atomic uncertainties of the neighboring thermal lines.Conclusions. Assuming a realistic temperature and abundance pattern, the physical model implied by the possible oxygen line agrees well with the theoretical model proposed previously to explain the reported 3.5 keV line. If the charge exchange source indeed exists, we expect that the oxygen abundance could have been overestimated by 8−22% in previous X-ray measurements that assumed pure thermal lines. These new RGS results bring us one step forward to understanding the charge exchange phenomenon in galaxy clusters.
Role of Drug Anesthesia and Cancer
Authors: Moradkhani Mahmoud , Karimi Arash 
Published: November 2017

AbstractMortality and morbidity rate among cancer patients is at an alarming rate and its ratio of incidence is increasing as a result of its effects of metastasis and recurrence in its patients. Anesthetists are faced with the challenges daily of handling and treating cancer patients, for surgical resection to removal of the primary tumor. Retrospective analyses and studies have proposed a link between anesthetic technique and cancer outcomes. In this mini-review, we will give a summary of some of the available effects of anesthetic and analgesic techniques on cancer metastasis as derived from experimental cell culture and live animal data and also from clinical studies.
A comparison of outcomes between a lumen-apposing metal stent with electrocautery-enhanced delivery system and a bi-flanged metal stent for drainage of walled-off pancreatic necrosis
Authors: Bekkali Noor , Nayar Manu , Leeds John , Charnley Richard , Huggett Matthew , Oppong Kofi 
Published: November 2017

Abstract
Background and study aims Bi-flanged metal stents (BFMS) have shown promise in the drainage of walled-off pancreatic necrosis (WON), but their placement requires multiple steps and the use of other devices. More recently, a novel device consisting of a combined lumen-apposing metal stent (LAMS) and electrocautery-enhanced delivery system has been introduced. The aim of this study was to compare the placement and outcomes of the two devices.
Patients and methods This was a retrospective review of consecutive patients undergoing endoscopic ultrasound-guided placement of BFMS or LAMS for drainage of symptomatic WON. Data from procedures between October 2012 and December 2016 were taken from a prospectively maintained database. We compared technical and clinical success, procedure time, costs, and composite end point of significant events (adverse events, stent migration, additional percutaneous drainage) between BFMS and LAMS.
Results 72 consecutive patients underwent placement of BFMS (40 patients, 44 stents) or LAMS (32 patients, 33 stents). Technical success was 91 % for BFMS and 97 % for LAMS. Clinical success was 65 % vs. 78 %, respectively. Median in-room procedure time was significantly shorter in the LAMS group (45 minutes [range 30 – 80]) than in the BFMS group (62.5 minutes [range 35 – 135]; P < 0.001) and fewer direct endoscopic necrosectomies (DEN) were performed (median 1 [0 – 2.0] vs. 2 [0 – 3.7], respectively; P = 0.005). If only inpatients were considered (35 BFMS and 19 LAMS), there was no significant difference in DEN 2 (range 0 – 11) and 2 (range 0 – 8), respectively. The composite end point of 32 % vs. 24 % was not significantly different. Median procedural costs for all patients with successful stent placement for WON treatment was €4427 (range 1630 – 12 926) for BFMS vs. €3500 (range 2509 – 13 393) for LAMS (P = 0.10).
Conclusion LAMS was superior to BFMS in terms of procedure time, with comparable adverse events, success, and costs.