bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decaying turbulence and magnetic fields in galaxy clusters
Authors: Sur Sharanya 
Published: July 2019

Abstract
We explore the decay of turbulence and magnetic fields generated by fluctuation dynamo action in the context of galaxy clusters where such a decaying phase can occur in the aftermath of a major merger event. Using idealized numerical simulations that start from a kinetically dominated regime we focus on the decay of the steady state rms velocity and the magnetic field for a wide range of conditions that include varying the compressibility of the flow, the forcing wavenumber, and the magnetic Prandtl number. Irrespective of the compressibility of the flow, both the rms velocity and the rms magnetic field decay as a power law in time. In the subsonic case we find that the exponent of the power law is consistent with the −3/5 scaling reported in previous studies. However, in the transonic regime both the rms velocity and the magnetic field initially undergo rapid decay with an ≈t−1.1 scaling with time. This is followed by a phase of slow decay where the decay of the rms velocity exhibits an ≈−3/5 scaling in time, while the rms magnetic field scales as ≈−5/7. Furthermore, analysis of the Faraday rotation measure (RM) reveals that the Faraday RM also decays as a power law in time ≈t−5/7; steeper than the ∼t−2/5 scaling obtained in previous simulations of magnetic field decay in subsonic turbulence. Apart from galaxy clusters, our work can have potential implications in the study of magnetic fields in elliptical galaxies.
Peculiar motion of the Solar system derived from a dipole anisotropy in the redshift distribution of distant quasars
Authors: Singal Ashok K 
Published: July 2019

ABSTRACT
An observer stationary with respect to comoving coordinates of the expanding universe should find the redshift distribution to be isotropic. However, a peculiar motion of the observer would introduce a dipole anisotropy in the observed redshift distribution. Conversely, a dipole anisotropy in observed redshift distribution could be exploited to infer our peculiar motion, or rather of our Solar system. We determine here our peculiar velocity by studying the dipole anisotropy in the redshift distribution of a large sample of quasars. The magnitude of the peculiar velocity thus determined turns out to be 2350 ± 280 km s−1, not only much larger than 370 km s−1 determined from the dipole anisotropy in the cosmic microwave background radiation (CMBR), but also nearly in an opposite direction. Such large values for peculiar velocity have been found in a couple of radio surveys too, but with a direction along the CMBR dipole. Large genuine differences in the inferred motion, whether in magnitude or direction, are rather disconcerting since a solar peculiar velocity should not depend upon the method of its determination. Such discordant dipoles imply perhaps an anisotropic universe, violating the cosmological principle, a cornerstone of the modern cosmology.
Constraining a black hole companion for M87* through imaging by the Event Horizon Telescope
Authors: Safarzadeh Mohammadtaher , Loeb Abraham , Reid Mark 
Published: July 2019

ABSTRACT
The Event Horizon Telescope, a global very long baseline interferometric array observing at a wavelength of 1.3 mm, detected the first image of the M87 supermassive black hole (SMBH). M87 is a giant elliptical galaxy at the centre of the Virgo cluster, which is expected to have formed through merging of cluster galaxies. Consequently M87* hosted mergers of black holes through dynamical friction and could have one or multiple binary companions with a low mass ratio at large separations. We show that a long-term monitoring of the M87 SMBH image over ∼1 yr with absolute positional accuracy of 1 ≈ $\mu$as could detect such binary companions and exclude a large parameter space in semimajor axis (a0) and mass ratio (q), which is currently not constrained. Moreover, the presence of the accretion disc around M87* excludes a binary companion with a0 ≈ of the order of a milliparsec, as otherwise the accretion disc would have been tidally disrupted.
XPD/ERCC2 mutations interfere in cellular responses to oxidative stress
Authors: Lerner Leticia K , Moreno Natália C , Rocha Clarissa R R , Munford Veridiana , Santos Valquíria , Soltys Daniela T , Garcia Camila C M , Sarasin Alain , Menck Carlos F M 
Published: July 2019

AbstractNucleotide excision repair (NER) is a conserved, flexible mechanism responsible for the removal of bulky, helix-distorting DNA lesions, like ultraviolet damage or cisplatin adducts, but its role in the repair of lesions generated by oxidative stress is still not clear. The helicase XPD/ERCC2, one of the two helicases of the transcription complex IIH, together with XPB, participates both in NER and in RNA pol II-driven transcription. In this work, we investigated the responses of distinct XPD-mutated cell lines to the oxidative stress generated by photoactivated methylene blue (MB) and KBrO3 treatments. The studied cells are derived from patients with XPD mutations but expressing different clinical phenotypes, including xeroderma pigmentosum (XP), XP and Cockayne syndrome (XP-D/CS) and trichothiodystrophy (TTD). We show by different approaches that all XPD-mutated cell lines tested were sensitive to oxidative stress, with those from TTD patients being the most sensitive. Host cell reactivation (HCR) assays showed that XP-D/CS and TTD cells have severely impaired repair capacity of oxidised lesions in plasmid DNA, and alkaline comet assays demonstrated the induction of significantly higher amounts of DNA strand breaks after treatment with photoactivated MB in these cells compared to wild-type cells. All XPD-mutated cells presented strong S/G2 arrest and persistent γ-H2AX staining after photoactivated MB treatment. Taken together, these results indicate that XPD participates in the repair of lesions induced by the redox process, and that XPD mutations lead to differences in the response to oxidatively induced damage.
Visualization and analysis of RNA-Seq assembly graphs
Authors: Nazarie Fahmi W , Shih Barbara , Angus Tim , Barnett Mark W , Chen Sz-Hau , Summers Kim M , Klein Karsten , Faulkner Geoffrey J , Saini Harpreet K , Watson Mick , Dongen Stijn van , Enright Anton J , Freeman Tom C 
Published: July 2019

AbstractRNA-Seq is a powerful transcriptome profiling technology enabling transcript discovery and quantification. Whilst most commonly used for gene-level quantification, the data can be used for the analysis of transcript isoforms. However, when the underlying transcript assemblies are complex, current visualization approaches can be limiting, with splicing events a challenge to interpret. Here, we report on the development of a graph-based visualization method as a complementary approach to understanding transcript diversity from short-read RNA-Seq data. Following the mapping of reads to a reference genome, a read-to-read comparison is performed on all reads mapping to a given gene, producing a weighted similarity matrix between reads. This is used to produce an RNA assembly graph, where nodes represent reads and edges similarity scores between them. The resulting graphs are visualized in 3D space to better appreciate their sometimes large and complex topology, with other information being overlaid on to nodes, e.g. transcript models. Here we demonstrate the utility of this approach, including the unusual structure of these graphs and how they can be used to identify issues in assembly, repetitive sequences within transcripts and splice variants. We believe this approach has the potential to significantly improve our understanding of transcript complexity.
Durable superamphiphobic silica aerogel surfaces for the culture of 3D cellular spheroids
Authors: Xu Lianyi , Chen Shuangshuang , Lu Xuemin , Lu Qinghua 
Published: July 2019

Abstract
The 3D multicellular spheroids with intact cell–cell junctions have major roles in biological research by virtue of their unique advantage of mimicking the cellular physiological environments. In this work, a durable superamphiphobic silica aerogel surface (SSAS) has been fabricated for the upward culture of 3D multicellular spheroids. Poly(3,4-ethylenedioxythiophene) (PEDOT) was first electrodeposited on a conductive steel mesh as a first template for porous silica coating. Soot particles were then applied as a second template to construct a cauliflower-like silica aerogel nanostructure. After fluorination, a hierarchical structure with re-entrant curvature was finally fabricated as a durable superamphiphobic surface. This superamphiphobic surface also presented excellent antifouling towards biomacromolecules and cells, which has been demonstrated by the successful upward culture of cell spheroids. The upward culture makes the observation of cellular behavior in situ possible, holding great potential for 3D cellular evaluation in vitro.
Automated sleep stage scoring of the Sleep Heart Health Study using deep neural networks
Authors: Zhang Linda , Fabbri Daniel , Upender Raghu , Kent David 
Published: July 2019

AbstractStudy ObjectivesPolysomnography (PSG) scoring is labor intensive and suffers from variability in inter- and intra-rater reliability. Automated PSG scoring has the potential to reduce the human labor costs and the variability inherent to this task. Deep learning is a form of machine learning that uses neural networks to recognize data patterns by inspecting many examples rather than by following explicit programming.MethodsA sleep staging classifier trained using deep learning methods scored PSG data from the Sleep Heart Health Study (SHHS). The training set was composed of 42 560 hours of PSG data from 5213 patients. To capture higher-order data, spectrograms were generated from electroencephalography, electrooculography, and electromyography data and then passed to the neural network. A holdout set of 580 PSGs not included in the training set was used to assess model accuracy and discrimination via weighted F1-score, per-stage accuracy, and Cohen’s kappa (K).ResultsThe optimal neural network model was composed of spectrograms in the input layer feeding into convolutional neural network layers and a long short-term memory layer to achieve a weighted F1-score of 0.87 and K = 0.82.ConclusionsThe deep learning sleep stage classifier demonstrates excellent accuracy and agreement with expert sleep stage scoring, outperforming human agreement on sleep staging. It achieves comparable or better F1-scores, accuracy, and Cohen’s kappa compared to literature for automated sleep stage scoring of PSG epochs. Accurate automated scoring of other PSG events may eventually allow for fully automated PSG scoring.
Ticagrelor Reduces Ischemia-Reperfusion Injury Through the NF-κB–Dependent Pathway in Rats
Authors: Liu Xiaogang , Wang Yuting , Zhang Mingjing , Liu Yufeng , Hu Liqun , Gu Ye 
Published: July 2019

Abstract:
We recently showed that ticagrelor reduced myocardial ischemia-reperfusion injury (IRI) and downregulated galectin-3 in the ischemic myocardium. This study tested the hypothesis that ticagrelor could reduce IRI through the NF-κB pathway. Rats were randomly divided into sham-operated group, placebo group (gastric administration of saline after IRI), ticagrelor group (gastric administration of ticagrelor after left anterior descending artery ligation), dextran sodium sulfate (DSS) group (DSS was added to drinking water 7 days before IRI), and DSS + ticagrelor group (DSS was added to drinking water 7 days before IRI and gastric administration of ticagrelor after left anterior descending artery ligation). Ticagrelor significantly reduced the infarct size and plasma cTnI at 3 and 7 days after IRI, significantly downregulated protein and mRNA expressions of NF-κB and galectin-3, and mRNA expressions of IL-6 and TNF-α in the ischemic area at 24 hours, 3 and 7 days after IRI. Ticagrelor also significantly decreased plasma high-sensitivity C-reactive protein and NT-proBNP levels at 24 hours and 3 days after IRI. Furthermore, pretreatment with DSS blocked the beneficial effects of ticagrelor. Our study indicates that the cardioprotective effect of ticagrelor might be partly mediated by inhibiting the NF-κB pathway in this rat model of IRI.
Physcion 8-O-β-Glucopyranoside Alleviates Oxidized Low-Density Lipoprotein-Induced Human Umbilical Vein Endothelial Cell Injury by Inducing Autophagy Through AMPK/SIRT1 Signaling[RETRACTED]
Authors: Yang Xiuli , Yin Guotian , Sun Haiyan , Zhao Guoan 
Published: July 2019

Aim:
Vascular endothelial cell dysfunction plays a crucial role in the initiation and development of atherosclerosis. Physcion 8-O-β-glucopyranoside (PG), an anthraquinone extracted from Polygonum cuspidatum, has a number of pharmacological functions. The aim of this study was to elucidate the protective effects of PG against oxidized low-density lipoprotein (ox-LDL) in VECs.

Methods and Materials:
Human umbilical vein endothelial cells (HUVECs) were used as the in vitro model. Cell viability and apoptosis were, respectively, assessed by CCK-8 assay and Annexin-V/PI staining. Formation of autophagosomes was visualized by acridine orange staining, and the autophagy flux was tracked after infecting the cells with the mRFP-GFP-LC3 adenovirus. The expression levels of various apoptosis and autophagy-associated marker proteins were detected by Western blotting.

Results:
Pretreatment with PG protected the HUVECs from ox-LDL–induced apoptosis. In addition, PG promoted autophagy in HUVECs, which was responsible for its antiapoptotic effects. Finally, activation of AMPK/SIRT1 signaling was upstream of PG-induced autophagy.

Conclusions:
PG has potential pharmacological effects against oxidative damage–induced HUVEC injury through inducing AMPK/SIRT1-mediated autophagy.
miR-3188 (rs7247237-C>T) Single-Nucleotide Polymorphism Is Associated With the Incidence of Vascular Complications in Chinese Patients With Type 2 Diabetes
Authors: Wu Bin , Liu Guojing , He Fazhong , Liu Rong , Wang Zhenmin , Wang Youhong , Zhou Honghao , Zhang Wei 
Published: July 2019

Abstract:
miR-3188, one of the earliest discovered microRNAs, is involved in regulating the mTOR-p-PI3K/AKT pathway, thus affecting the progression of diabetic complications. In this study, we observed that the miR-3188 (rs7247237-C>T) polymorphism not only affected the production of nitric oxide (NO) production in endothelial cells, but also significantly associated with the incidence of vascular complications in Chinese patients with type 2 diabetes. Mechanistic analyses indicate that miR-3188 (rs7247237-T) polymorphism inhibited its own expression and upregulated the expression of gstm1 and trib3, which impairs NO production in human endothelial cells through inactivating AKT/eNOS signal transduction pathway. In addition, our clinical retrospective study indicated that, compared with patients with the CC genotype (n = 351), patients with rs7247237 TT + CT genotypes (n = 580) exhibited an increased risk of major vascular events during intensive glucose control treatment (hazard ratio = 1.560; 95% CI: 1.055–2.307, P = 0.025). Simultaneously, the risk of major vascular events was marginally decreased in patients with the CC genotype during intensive glucose control treatment compared with standard treatment (hazard ratio = 0.666; 95% CI: 0.433–1.016, P = 0.053). Our findings indicate that the miR-3188 (rs7247237-C>T) polymorphism is associated with the incidence of vascular complications in Chinese patients with type 2 diabetes, likely due to its remarkable effect on miR-3188 expression.
Duodenal obstruction due to chronic pancreatitis of the pancreas tail treated by surgical intervention
Authors: Tomioka Atsushi , Shimizu Tetsunosuke , Asakuma Mitsuhiro , Inoue Yoshihiro , Taniguchi Kohei , Hirokawa Fumitoshi , Hayashi Michihiro , Uchiyama Kazuhisa 
Published: July 2019

Abstract

Rationale:
Duodenal obstruction (DO) sometimes induces the groove pancreatitis. However, the case of DO due to chronic pancreatitis in pancreas tail (CPPT) is extremely rare. Therefore, the managements of DO caused by CPPT have not been established yet.

Patient concerns:
A 68-year-old man, who was under the treatment of chronic pancreatitis, presented to our hospital with nausea and abdominal pain. He was diagnosed as DO caused by CPPT. The Conservative treatment, including the nasogastric aspiration and intravenous infusion under the absence of food, was performed. The drainage fluid from naso-gastric tube had been more than 2000 ml per a day although continuing treatment for 14 days. Hence, we decided that the conservative therapy was failed and the surgical intervention was required.

Diagnosis:
Computed tomography showed gastroduodenal expansion due to stenosis at the horizontal portion of the duodenum with increasing pancreatic pseudocyst. The contrast radiography of the duodenum showed severe stenosis around Treitz ligament. His pre-surgical diagnosis was DO due to CPPT through exclusion of other etiologies for DO such as annular pancreas, SMA syndrome, duodenal diaphragm and Crohn disease.

Intervention:
Spleen preserving distal pancreatectomy (Warshaw operation) was performed with gastrojejunostomy. During surgery, marked redness and thickness of the mesenteric serosa around Treiz ligament were observed. His surgical findings were supported our preoperative prediction.

Outcomes:
The patient was successfully treated and discharged uneventfully after postoperative day 14. At the 9 months follow-up visit, the patient is still doing well without any symptoms.

Conclusion:
Combination of gastrojejunostomy and Warshaw operation is one of the ideal surgical procedures for patients of DO due to CPPT.
Preventing deoxygenation with high flow nasal cannula oxygen during induction of general anesthesia for rigid bronchoscopy
Authors: Min Ji Young , Jo Haedeun , Roh Kyungmoon , Chung Mee Young 
Published: July 2019

Abstract

Rationale:
Rigid bronchoscopy under general anesthesia enables performing diagnostic and/or therapeutic procedures in the tracheobronchial tree. As most patients undergoing rigid bronchoscopy have moderate to severe respiratory disease or central airway obstruction, the operators often face the risk of hypoxemia when inserting the rigid bronchoscope into the patients’ airway. Applying high flow nasal cannula (HFNC) oxygen therapy before the insertion of the bronchoscope allows to maintain high fractional inspired oxygen (FiO2) and thus leading to maximizing apnea time before desaturation.

Patient concerns and diagnosis:
Case 1: A 70-year-old female patient was diagnosed with lung cancer in the left lower lobe and a tracheal mass of about 2.6 cm ∗ 0.8 cm in size.
Case 2: A male patient, 77 years old, 55.7 kg and 157.3 cm in height, had been diagnosed with chronic obstructive pulmonary disease, and was scheduled for the bronchoscopic volume reduction surgery upon exacerbation of his symptoms of dyspnea and cough with sputum.

Interventions:
Preoxygenation was performed with HFNC (Fisher&Paykel Optiflow ThriveTM, New Zealand) for 3 minutes before the administration of anesthetic medications. The oxygen flow was set at 50 L/min and the FiO2 at 1.0. SpO2 increased to 100%.

Outcomes:
The HFNC oxygen has shown its effectiveness in safely maintaining the patients’ SpO2 during the prolonged apneic period of inserting bronchoscope.

Lessons:
HFNC oxygen is an effective tool in oxygenating the patients during the induction of rigid bronchoscopy, and that it may be a superior alternative to the conventional method of preoxygenation.
IMP3 is a biomarker for non-muscle-invasive urothelial carcinoma of the bladder associated with an aggressive phenotype
Authors: Yang Feiya , Zhou Qiang , Meng Lingquan , Xing Nianzeng 
Published: July 2019

Abstract
Bladder cancer is one of the most common malignancies of urinary tract. The current study aimed to investigate the role of insulin-like growth factor II messenger RNA binding protein 3 (IMP3) expression in the prognostic evaluation of non-muscle- invasive urothelial carcinoma of the bladder.
Immunohistochemistry (IHC) was carried out to examine IMP3 protein expression in specimens from 183 cases of non-muscle-invasive urothelial carcinoma, 20 cases of muscle-invasive urothelial carcinoma and 20 benign tissues adjacent to cancer tissue.
The expression of IMP3 was not detected in the adjacent benign tissues. The expression intensity of IMP3 in muscle-invasive samples was significantly higher than that in non-muscle-invasive urothelial carcinoma specimens (P = .008). IMP3 expression was significantly related with advanced tumor stage (P < .001), advanced tumor grade (P = .004), and tumor recurrence (P < .001) in non-muscle-invasive urothelial carcinomas. Kaplan–Meier analysis showed that IMP3-positive patients had much lower disease-free (P < .001), progression-free (P = .002) and metastasis-free (P = .019) survival rates compared with those with IMP3-negative tumors. By multivariable Cox analysis, we also found that IMP3 expression in non-muscle- invasive urothelial carcinomas proved to be an independent unfavorable prognostic factor of disease-free survival (HR: 2.52; 95% CI, 1.39–4.56; P = .002), progression- free survival (HR: 5.19; 95% CI, 1.54–17.46; P = .008) and metastasis-free survival (HR: 4.87; 95% CI, 1.08–22.02; P = .040).
Our results demonstrate that the expression of IMP3 in non-muscle- invasive bladder cancer can serve as an independent predictor that will help recognize the subgroup of patients with a high ability to relapse, progress, and metastasize and who might get the maximum benefit from an early and more aggressive treatment strategy.
Efficacy of different probiotic protocols in irritable bowel syndrome
Authors: Liang Ding , Longgui Ning , Guoqiang Xu 
Published: July 2019

AbstractBackground:Probiotics is a prevalence therapeutic method for irritable bowel syndrome (IBS), but there is lack of comparison in different protocols. We aim to differentiate the reasonable protocols by assessing the efficacy and safety through the combined way of traditional and network meta-analysis.Method:PubMed, Medline, EMBASE, Web of Science, and Cochrane Central Register of Controlled Trials databases were searched from January 2006 to April 2019. The relative risk (RR) with a 95% confidence interval (CI) was used to combine dichotomous data of responders.Result:Among 14 studies included 1695 patients were identified as suitable for inclusion. The proportion of responders was associated with the administration of multispecies probiotics (RR: 1.39; 95% CI: 1.19–1.61) and the dose of 109∼1010(RR: 2.08; 95% CI: 1.59–2.71). In network meta-analysis, the protocol of DUO had a significant effect for diarrhea type of IBS compared with placebo (RR: 7.46; 95% CI: 2.00–32.23). In the rest of 4 protocols, no significant difference was found in each other except F19 which appears inferior when compared with Pro (RR: 0.16; 95% CI: 0.03–0.88). Meanwhile, Pro showed a superior effect for undifferentiated-type IBS compared with placebo (RR: 7.16; 95% CI: 1.72–29.89). No probiotics-associated severe adverse event was reported in included studies.Conclusion:Probiotics is a safety choice to improve the overall symptoms for IBS patient. The protocols with suitable dose combined ofLactobacillusandBifidobacteriumcan have prepotent effects compared with single species or over-dosage protocols. Network meta-analysis shows that DUO may be the first recommendation for diarrhea-type IBS. In the remaining 4 regimes of this study, Pro has a high rank for undifferentiated-type IBS.