bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cycling hypoxia promotes a pro-inflammatory phenotype in macrophages via JNK/p65 signaling pathway
Authors: Delprat Victor , Tellier Céline , Demazy Catherine , Raes Martine , Feron Olivier , Michiels Carine 
Published: January 2020

AbstractCycling hypoxia (cyH), also called intermittent hypoxia, occurs in solid tumors and affects different cell types in the tumor microenvironment and in particular the tumor-associated macrophages (TAMs). As cyH and TAMs both favor tumor progression, we investigated whether cyH could drive the pro-tumoral phenotype of macrophages. Here, the effects of cyH on human THP-1 macrophages and murine bone marrow-derived macrophages (BMDM), either unpolarized M0, or polarized in M1 or M2 phenotype were studied. In M0 macrophages, cyH induced a pro-inflammatory phenotype characterized by an increase in TNFα and IL-8/MIP-2 secretion. CyH amplified the pro-inflammatory phenotype of M1 macrophages evidenced by an increased pro-inflammatory cytokine secretion and pro-inflammatory gene expression. Furthermore, cyH increased c-jun activation in human M0 macrophages and highly increased c-jun and NF-κB activation in M1 macrophages. C-jun and p65 are implicated in the effects of cyH on M0 and M1 macrophages since inhibition of their activation prevented the cyH pro-inflammatory effects. In conclusion, we demonstrated that cyH induces or amplifies a pro-inflammatory phenotype in M0 and M1 macrophages by activating JNK/p65 signaling pathway. These results highlight a specific role of cyH in the amplification of tumor-related inflammation by modulating the inflammatory phenotype of macrophages.
Predictive factors of postoperative infection-related complications in adult patients with cerebral cavernous malformations
Authors: Ding Chen-Yu , Lian Bao-Qiang , Ge Hong-Liang , He Qiu , Li Ang , Chen Xiao-Yong , Xu Jia-Heng , Lin Fu-Xin , Lin Yuan-Xiang , Kang De-Zhi 
Published: January 2020

AbstractPostoperative infection is an important factor contributing to poor prognosis after surgical treatment of cerebral cavernous malformations (CCM). However, the predictive factors of postoperative infection-related complications in adult patients with CCM have still not been well established. To identify possible predictive factors of postoperative infection after CCM surgery, we retrospectively evaluated the data of CCM patients who were enrolled into our prospective registry database. The relationship between preoperative characteristics of patients and postoperative infection-related complications was analyzed. A total of 167 CCM patients were included in this study. The average age was 39.69 ± 15.27 years old, and 21 of them had postoperative infection. For patients with postoperative infection, the Glasgow Coma Scale (GCS), Modified Rankin Scale (mRS), white blood cell (WBC) count, and neutrophil (NEU) count were all significantly higher than those of the group without infection. Our preliminary results showed that NEU count might have significant predictive value of intracranial infection, and GCS, mRS and CCM presenting with hemorrhage were all factors significantly related to postoperative pneumonia. Preoperative GCS, mRS and CCM presenting with hemorrhage might be used as predictive factors for postoperative pneumonia after CCM surgery, while preoperative NEU count can be used as an important predictive factor for postoperative intracranial infection after CCM surgery. Further large-scale studies are still needed to confirm this finding.
Induction of left ventricular hypoplasia by occluding the foramen ovale in the fetal lamb
Authors: Wong Flora Y. , Veldman Alex , Sasi Arun , Teoh Mark , Edwards Andrew , Chan Yuen , Graupner Oliver , Enzensberger Christian , Axt-Fliedner Roland , Black Mary Jane , Schranz Dietmar 
Published: January 2020

AbstractDisturbed fetal haemodynamics often affects cardiac development and leads to congenital cardiac defects. Reduced left ventricular (LV) preload in the fetus may result in hypoplastic LV, mitral and aortic valve, mimicking a moderate form of hypoplastic left heart complex. We aimed to induce LV hypoplasia by occluding the foramen ovale (FO) to reduce LV preload in the fetal sheep heart, using percutaneous trans-hepatic catheterisation. Under maternal anaesthesia and ultrasound guidance, hepatic venous puncture was performed in six fetal lambs (0.7–0.75 gestation). A coronary guidewire was advanced into the fetal inferior vena cava, right and left atrium. A self-expandable stent was positioned across the FO. An Amplatzer Duct Occluder was anchored within the stent for FO occlusion. Euthanasia and post-mortem examination was performed after 3 weeks. Nine fetuses were used as age-matched controls. Morphometric measurements and cardiac histopathology were performed. Compared with controls, fetal hearts with occluded FO had smaller LV chamber, smaller mitral and aortic valves, lower LV-to-RV ratio in ventricular weight and wall volume, and lower number of LV cardiomyocyte nuclei. We conclude that fetal FO occlusion leads to a phenotype simulating LV hypoplasia. This large animal model may be useful for understanding and devising therapies for LV hypoplasia.
Silencing of SENP2 in Multiple Myeloma Induces Bortezomib Resistance by Activating NF-κB Through the Modulation of IκBα Sumoylation
Authors: Xie Hongyi , Gu Yuanliang , Wang Wenjuan , Wang Xuyao , Ye Xiaojuan , Xin Chao , Lu Mengjiao , Reddy B. Ashok , Shu Peng 
Published: January 2020

AbstractThe proteasome inhibitor bortezomib is the most successfully applied chemotherapeutic drug for treating multiple myeloma. However, its clinical efficacy reduced due to resistance development. The underlying molecular mechanisms of bortezomib resistance are poorly understood. In this study, by combining in silico analysis and sgRNA library based drug resistance screening assay, we identified SENP2 (Sentrin/SUMO-specific proteases-2) as a bortezomib sensitive gene and found its expression highly downregulated in bortezomib resistant multiple myeloma patient’s samples. Furthermore, down regulation of SENP2 in multiple myeloma cell line RPMI8226 alleviated bortezomib induced cell proliferation inhibition and apoptosis, whereas, overexpression of SENP2 sensitized these cells to bortezomib treatment. We further demonstrate that knockdown of SENP2 in RPMI8226 cells increased SUMO2 conjugated IκBα that resulted in the activation of NF-κB. Taken together, we report that silencing of SENP2 and consequent activation of NF-κB through the modulation of IκBα sumoylation as a novel mechanism inducing bortezomib resistance in multiple myeloma.
Regulation of histamine and diamine oxidase in patients undergoing orthotopic liver transplantation
Authors: Schiefer Judith , Baron-Stefaniak Joanna , Boehm Thomas , Wadowski Patricia , Berlakovich Gabriela , Kuessel Lorenz , Mühlbacher Jakob , Jilma-Stohlawetz Petra , Schwameis Michael , Jilma Bernd , Faybik Peter 
Published: January 2020

AbstractIncreased concentrations of the vasodilator histamine have been observed in patients undergoing abdominal surgery. The role of histamine during orthotopic liver transplantation (OLT) has only been studied in animals. The aim of this study was to measure plasma concentrations of histamine and its degrading enzyme diamine oxidase (DAO) in patients undergoing orthotopic liver transplantation, and assess whether histamine or DAO correlate with intraoperative noradrenaline requirements. Histamine and DAO concentrations were measured in 22 adults undergoing liver transplantation and 22 healthy adults. Furthermore, norepinephrine requirements during liver transplantation were recorded. Baseline concentrations of histamine and DAO were greater in patients, who underwent liver transplantation, than in healthy individuals (Histamine: 6.4 nM, IQR[2.9–11.7] versus 4.3 nM, IQR[3.7–7.1], p = 0.029; DAO: 2.0 ng/mL, IQR[1.5–4.1] versus <0,5 ng/mL, IQR[<0.5–1.1], p < 0.001). During liver transplantation, histamine concentrations decreased to 1.8 nM, IQR[0.5–4.9] in the anhepatic phase (p < 0.0001 versus baseline), and to 1.5 nM, IQR[0.5–2.9] after reperfusion (p < 0.0001 versus baseline). In contrast, DAO concentrations increased to 35.5 ng/ml, IQR[20–50] in the anhepatic phase (p = 0.001 versus baseline) and to 39.5 ng/ml, IQR[23–64] after reperfusion (p = 0.001 versus baseline), correlating inversely with histamine. Norepinephrine requirements during human liver transplantation correlated significantly with DAO concentrations in the anhepatic phase (r = 0.58, p = 0.011) and after reperfusion (r = 0.56; p = 0.022). In patients undergoing orthotopic liver transplantation, histamine concentrations decrease whereas DAO concentrations increase manifold. Diamine oxidase correlates with intraoperative norepinephrine requirements in patients undergoing OLT.
Effects of metazachlor and its major metabolite metazachlor OA on early life stages of marbled crayfish
Authors: Velisek Josef , Stara Alzbeta , Kubec Jan , Zuskova Eliska , Buric Milos , Kouba Antonin 
Published: January 2020

AbstractThe effects of the herbicide metazachlor and its major metabolite metazachlor OA at two concentrations, including environmentally relevant concentrations of metazachlor (0.0115 µmol/l and 0.0790 µmol/l) and metazachlor OA (0.0117 µmol/l and 0.0805 µmol/l), respectively, were evaluated on early ontogeny, growth, behaviour, oxidative stress, antioxidant enzyme levels, histology, and mortality of marbled crayfish Procambarus virginalis. Both tested concentrations of metazachlor and metazachlor OA were associated with significantly lower growth and delayed ontogenetic development compared to controls. Exposure of metazachlor at 0.0115 µmol/l and metazachlor OA at 0.0117 µmol/l and 0.0805 µmol/l resulted in significantly lower activity of total superoxide dismutase (SOD), catalase (CAT), glutathione s-transferase (GST), glutathione reductase (GR), and reduced glutathione (GSH) compared with control and resulted in gill anomalies ranging from wall thinning to focal disintegration of branchial structure. Metazachlor at the environmentally relevant concentration of 0.0790 µmol/l was associated with significant alterations of crayfish distance moved and walking speed. The potential risk associated with metazachlor use in agriculture related to effects on non-target aquatic organisms.
Lack of maintenance of motorway fences works against their intended purpose with potential negative impacts on protected species
Authors: Farfán Miguel A. , Fa Julia E. , Martín-Taboada Adrián , García-Carrasco José María , Duarte Jesús 
Published: January 2020

AbstractLinear infrastructure intrusions into natural ecosystems, such as motorways and high-speed railways, causes direct loss of habitat but also impacts fauna through collisions. Wildlife road mortality is well documented and extensive conservation legislation exists in many countries to minimise the negative impact of these infrastructures. However, although these measures are implemented because of legislation, these structures are often not adequately maintained. Here we present data on the functionality of perimeter fences along two motorways in Malaga province (southern Spain) erected to prevent collisions with the common chameleon (Chamaeleo chamaeleon). We sampled the fences along the 14 km of the two motorways included in the 17 1 × 1 km squares of the study area. Our results show that the reptile fence is permeable throughout at those points where the metal sheeting was absent and where the vegetation had overgrown around the fence, hence allowing chameleons to cross. Given our results, we conclude that this situation is likely to be similar in other regions of Spain and in other countries. This is because construction/concessionary companies do not consider the environmental impact of construction projects in the medium and long term, and environmental authorities do not ensure that companies comply with the legislation.
Pharmacological enrichment of polygenic risk for precision medicine in complex disorders
Authors: Reay William R. , Atkins Joshua R. , Carr Vaughan J. , Green Melissa J. , Cairns Murray J. 
Published: January 2020

AbstractIndividuals with complex disorders typically have a heritable burden of common variation that can be expressed as a polygenic risk score (PRS). While PRS has some predictive utility, it lacks the molecular specificity to be directly informative for clinical interventions. We therefore sought to develop a framework to quantify an individual’s common variant enrichment in clinically actionable systems responsive to existing drugs. This was achieved with a metric designated the pharmagenic enrichment score (PES), which we demonstrate for individual SNP profiles in a cohort of cases with schizophrenia. A large proportion of these had elevated PES in one or more of eight clinically actionable gene-sets enriched with schizophrenia associated common variation. Notable candidates targeting these pathways included vitamins, antioxidants, insulin modulating agents, and cholinergic drugs. Interestingly, elevated PES was also observed in individuals with otherwise low common variant burden. The biological saliency of PES profiles were observed directly through their impact on gene expression in a subset of the cohort with matched transcriptomic data, supporting our assertion that this gene-set orientated approach could integrate an individual’s common variant risk to inform personalised interventions, including drug repositioning, for complex disorders such as schizophrenia.
Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for the analysis of CAGE data
Authors: Georgakilas Georgios K. , Perdikopanis Nikos , Hatzigeorgiou Artemis 
Published: January 2020

AbstractCap Analysis of Gene Expression (CAGE) has emerged as a powerful experimental technique for assisting in the identification of transcription start sites (TSSs). There is strong evidence that CAGE also identifies capping sites along various other locations of transcribed loci such as splicing byproducts, alternative isoforms and capped molecules overlapping introns and exons. We present ADAPT-CAGE, a Machine Learning framework which is trained to distinguish between CAGE signal derived from TSSs and transcriptional noise. ADAPT-CAGE provides highly accurate experimentally derived TSSs on a genome-wide scale. It has been specifically designed for flexibility and ease-of-use by only requiring aligned CAGE data and the underlying genomic sequence. When compared to existing algorithms, ADAPT-CAGE exhibits improved performance on every benchmark that we designed based on both annotation- and experimentally-driven strategies. This performance boost brings ADAPT-CAGE in the spotlight as a computational framework that is able to assist in the refinement of gene regulatory networks, the incorporation of accurate information of gene expression regulators and alternative promoter usage in both physiological and pathological conditions.
MTAP-deficiency could predict better treatment response in advanced lung adenocarcinoma patients initially treated with pemetrexed-platinum chemotherapy and bevacizumab
Authors: Jing Wang , Zhu Hui , Liu Wenjuan , Zhai Xiaoyang , Tian Hairong , Yu Jinming 
Published: January 2020

AbstractTo investigate the predictive value of methylthioadenosine phosphorylase (MTAP) on treatment response and survival in advanced lung adenocarcinoma. MTAP expression was detected by immunohistochemistry. Treatment response and survival were compared according to MTAP expression level. The results indicated MTAP-low expression was observed in 61.2% (101/165) of all patients. The objective response rate and disease control rate improved in the MTAP-low group (64.4% vs 46.9%, p = 0.035; 92.1% vs. 79.7%, p = 0.03; respectively). The median progression-free survival and survival time in the MTAP-low group were significantly lower than that in the MTAP-high group (8.1 vs. 13.1 months, p = 0.002; 22 vs. 32 months, p = 0.044). Multivariate analysis demonstrated that brain metastasis (HR 1.55, p = 0.046), thoracic radiation (HR 0.52, p = 0.026), and MTAP-low expression (HR 1.36, p = 0.038) were independent factors on survival. It is concluded that MTAP-low expression could predict improved treatment response but worsened survival in advanced lung adenocarcinoma.
Expression and functional analysis of the hydrogen peroxide biosensors HyPer and HyPer2 in C2C12 myoblasts/myotubes and single skeletal muscle fibres
Authors: Fernández-Puente Escarlata , Sánchez-Martín Manuel A. , de Andrés Jorge , Rodríguez-Izquierdo Lorena , Méndez Lucía , Palomero Jesús 
Published: January 2020

AbstractHydrogen peroxide (H2O2) is generated in cells and plays an important role as a signalling molecule. It has been reported that H2O2 is involved in physiological and pathological processes in skeletal muscle. However, H2O2 detection in cells with traditional techniques produces frequent artefacts. Currently, the HyPer biosensor detects intracellular H2O2 specifically in real time using fluorescence microscopy. The aim of this study was to develop and optimize approaches used to express the HyPer biosensor in different models of skeletal muscle cells, such as the C2C12 myoblast/myotube cell line and mature skeletal muscle fibres isolated from C57BL/6J mice, and to measure intracellular H2O2 in real time in these cells. The results show that the expression of the HyPer biosensor in skeletal muscle cells is possible. In addition, we demonstrate that HyPer is functional and that this biosensor detects changes and fluctuations in intracellular H2O2 in a reversible manner. The HyPer2 biosensor, which is a more advanced version of HyPer, presents improved properties in terms of sensitivity in detecting lower concentrations of H2O2 in skeletal muscle fibres. In conclusion, the expression of the HyPer biosensor in the different experimental models combined with fluorescence microscopy techniques is a powerful methodology to monitor and register intracellular H2O2 specifically in skeletal muscle. The innovation of the methodological approaches presented in this study may present new avenues for studying the role of H2O2 in skeletal muscle pathophysiology. Furthermore, the methodology may potentially be adapted to yield other specific biosensors for different reactive oxygen and nitrogen species or metabolites involved in cellular functions.
Structural Analysis and Optimization of Convolutional Neural Networks with a Small Sample Size
Authors: D’souza Rhett N. , Huang Po-Yao , Yeh Fang-Cheng 
Published: January 2020

AbstractDeep neural networks have gained immense popularity in the Big Data problem; however, the availability of training samples can be relatively limited in specific application domains, particularly medical imaging, and consequently leading to overfitting problems. This “Small Data” challenge may need a mindset that is entirely different from the existing Big Data paradigm. Here, under the small data scenarios, we examined whether the network structure has a substantial influence on the performance and whether the optimal structure is predominantly determined by sample size or data nature. To this end, we listed all possible combinations of layers given an upper bound of the VC-dimension to study how structural hyperparameters affected the performance. Our results showed that structural optimization improved accuracy by 27.99%, 16.44%, and 13.11% over random selection for a sample size of 100, 500, and 1,000 in the MNIST dataset, respectively, suggesting that the importance of the network structure increases as the sample size becomes smaller. Furthermore, the optimal network structure was mostly determined by the data nature (photographic, calligraphic, or medical images), and less affected by the sample size, suggesting that the optimal network structure is data-driven, not sample size driven. After network structure optimization, the convolutional neural network could achieve 91.13% accuracy with only 500 samples, 93.66% accuracy with only 1000 samples for the MNIST dataset and 94.10% accuracy with only 3300 samples for the Mitosis (microscopic) dataset. These results indicate the primary importance of the network structure and the nature of the data in facing the Small Data challenge.
Identification of 13 novel USH2A mutations in Chinese retinitis pigmentosa and Usher syndrome patients by targeted next-generation sequencing
Authors: Qu Ling-hui , Jin Xin , Long Yan-ling , Ren Jia-yun , Weng Chuang-huang , Xu Hai-wei , Liu Yong , Meng Xiao-hong , Li Shi-ying , Yin Zheng-qin 
Published: January 2020

Abstract
Background: The USH2A gene encodes usherin, a basement membrane protein that is involved in the development and homeostasis of the inner ear and retina. Mutations in USH2A are linked to Usher syndrome type II (USH II) and non-syndromic retinitis pigmentosa (RP). Molecular diagnosis can provide insight into the pathogenesis of these diseases, facilitate clinical diagnosis, and identify individuals who can most benefit from gene or cell replacement therapy. Here, we report 21 pathogenic mutations in the USH2A gene identified in 11 Chinese families by using the targeted next-generation sequencing (NGS) technology.
Methods: In all, 11 unrelated Chinese families were enrolled, and NGS was performed to identify mutations in the USH2A gene. Variant analysis, Sanger validation, and segregation tests were utilized to validate the disease-causing mutations in these families.
Results: We identified 21 pathogenic mutations, of which 13, including 5 associated with non-syndromic RP and 8 with USH II, have not been previously reported. The novel variants segregated with disease phenotype in the affected families and were absent from the control subjects. In general, visual impairment and retinopathy were consistent between the USH II and non-syndromic RP patients with USH2A mutations.
Conclusions: These findings provide a basis for investigating genotype–phenotype relationships in Chinese USH II and RP patients and for clarifying the pathophysiology and molecular mechanisms of the diseases associated with USH2A mutations.
Short-chain fatty acids accompanying changes in the gut microbiome contribute to the development of hypertension in patients with preeclampsia
Authors: Chang Yanling , Chen Yunyan , Zhou Qiong , Wang Chuan , Chen Lei , Di Wen , Zhang Yu 
Published: January 2020

Abstract
Preeclampsia (PE) is regarded as a pregnancy-associated hypertension disorder that is related to excessive inflammatory responses. Although the gut microbiota (GM) and short-chain fatty acids (SCFAs) have been related to hypertension, their effects on PE remain unknown. We determined the GM abundance and faecal SCFA levels by 16S ribosomal RNA (rRNA) sequencing and gas chromatography, respectively, using faecal samples from 27 patients with severe PE and 36 healthy, pregnant control subjects. We found that patients with PE had significantly decreased GM diversity and altered GM abundance. At the phylum level, patients with PE exhibited decreased abundance of Firmicutes albeit increased abundance of Proteobacteria; at the genus level, patients with PE had lower abundance of Blautia, Eubacterium_rectale, Eubacterium_hallii, Streptococcus, Bifidobacterium, Collinsella, Alistipes, and Subdoligranulum, albeit higher abundance of Enterobacter and Escherichia_Shigella. The faecal levels of butyric and valeric acids were significantly decreased in patients with PE and significantly correlated with the above-mentioned differential GM abundance. We predicted significantly increased abundance of the lipopolysaccharide (LPS)-synthesis pathway and significantly decreased abundance of the G protein-coupled receptor (GPCR) pathway in patients with PE, based on phylogenetic reconstruction of unobserved states (PICRUSt). Finally, we evaluated the effects of oral butyrate on LPS-induced hypertension in pregnant rats. We found that butyrate significantly reduced the blood pressure (BP) in these rats. In summary, we provide the first evidence linking GM dysbiosis and reduced faecal SCFA to PE and demonstrate that butyrate can directly regulate BP in vivo, suggesting its potential as a therapeutic agent for PE.