bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between metabolic syndrome and increased risk of Barrett's esophagus: An Updated systematic review and meta-analysis
Authors: Karimian Mohammad , Salamati Majid , Azami Milad 
Published: January 2020

Abstract
Background: The relationship between metabolic syndrome ( MetS) and Barrett's esophagus (BE) is still a challenging issue, and inconsistent results have been reported in different studies. Therefore, this study was conducted to determine the relationship between MetS and BE. Methods : In this study, we followed the MOOSE protocol and the PRISMA guidelines for reporting the results. All study steps were performed independently by two authors. If necessary, the dispute was resolved by consultation with a third author. The search strategy is designed to find published studies. Comprehensive search was done in the following biomedical databases until July 2019: Cochrane Library, PubMed/Medline, Web of Science, Science Direct, EMBASE, Scopus, CINAHL, EBSCO, and Google Scholar search engine. All analyses were performed using Comprehensive Meta-Analysis Software Ver.2, while p-value lower than 0.05 was considered significant. Results : In 14 studies with a sample size of 108416, MetS significantly increased the risk of BE (OR=1.315; 95% CI: 1.110-1.558; P<0.001; Heterogeneity: I 2 = 81.55; P<0.001). Sensitivity analysis by omitting one study showed that overall estimates are still robust. Subgroup analysis was significant for continent (P<0.001) and MetS diagnostic criteria (P=0.043), but was not significant for variables of study type (P=0.899), study setting (P=0.115), control groups (P=0.671) and quality of studies (P=0.603). The Begg (P=0.912) and Egger's (P=0.094) tests were not significant; therefore, the publication bias did not play a role in the results. Conclusion: MetS increases the risk of BE compared to control groups. Future studies should examine whether treatment for metabolic syndrome reduces the risk of BE.
The Importance of Stroke as a Risk Factor of Cognitive Decline in Community Dwelling Older and Oldest peoples : The SONIC Study
Authors: Srithum Werayuth , Kabayama Mai , Gondo Yasuyuki , Masui Yukie , Akagi Yuya , Klinpudtan Nonglak , Kiyoshige Eri , Godai Kayo , Sugimoto Ken , Akasaka Hiroshi , Takami Yoichi , Takeya Yasushi , Yamamoto Koichi , Ikebe Kazunori , Ogawa Madoka , Inagaki Hiroki , Ishizaki Tatsuro , Arai Yasumichi , Rakugi Hiromi , Kamide Kei 
Published: January 2020

Abstract
Background: Cognitive impairment is a major health concern among older and oldest people.Moreover, stroke is a relevant contributor for cognitive decline and development of dementia. The study of cognitive decline focused on stroke as the important risk factor by recruiting older and oldest is still lagging behind. Therefore, the aim of this study was to investigate the importance of stroke as a risk factor of cognitive decline during three years in community dwelling older and oldest people.
Methods: This study was longitudinal study with a 3-year follow-up in Japan. The participants were 1,333community dwelling older and oldest people (70 years old = 675, 80 years old = 589, and 90 years old = 69). Data collected included basic data (age, sex, and history of stroke), vascular risk factors (hypertension, diabetes mellitus, dyslipidemia, atrial fibrillation, and current smoking), and social factors (educational level, frequency of going outdoors, long-term care (LTC) service used, and residential area). The Japanese version of the Montreal Cognitive Assessment (MoCA-J) was decline of ≥ 2 points was defined as cognitive decline. Multiple logistic regression analysis was used to investigate the association between stroke and other risk factors with cognitive decline during a 3-year follow-up.
Results: The fit of the hypothesized model by multiple logistic regression showed that a history of stroke, advanced age, and greater MoCA-J score at the baseline were important risk factors, while the presence of dyslipidemia and a higher educational level were protective factors that were significantly correlated with cognitive decline during the 3-year follow-up.
Conclusions: The cognitive decline after the 3-year follow-up was influenced by the history of stroke and advanced age, while greater MoCA-J score at the baseline was positively associated with subsequent 3 years cognitive decline. The protective factors were the presence of dyslipidemia and a higher educational level. Therefore, these factors are considered important and should be taken into consideration when searching for creative solutions to prevent cognitive decline after stroke in community dwelling older and oldest people.
neoANT-HILL: an integrated tool for identification of potential neoantigens
Authors: Coelho Ana Carolina , Fonseca Andre , Martins Danilo , Lins Paulo , Cunha Lucas da , de Souza Sandro 
Published: January 2020

Abstract
Background Cancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations on the original protein. Neoantigens identification remains a challenging task due largely to a high rate of false-positives.Results We have developed an efficient and automated pipeline for the identification of potential neoantigens. neoANT-HILL integrates several immunogenomic analyses to improve neoantigen detection from Next Generation Sequence (NGS) data. The pipeline has been compiled in a pre-built Docker image such that minimal computational background is required for download and setup. NeoANT-HILL was applied in the The Cancer Genome Atlas (TCGA) melanoma dataset and found several putative neoantigens including ones derived from the recurrent RAC1:P29S and SERPINB3:E250K mutations. neoANT-HILL was also used to identify potential neoantigens in RNA-Seq data with a high sensitivity and specificity.Conclusion neoANT-HILL is a user-friendly tool with a graphical interface that performs neoantigens prediction efficiently. neoANT-HILL is able to process multiple samples, provides several binding predictors, enables quantification of tumor-infiltrating immune cells and considers RNA-Seq data for identifying potential neoantigens. The software is available on github at https://github.com/neoanthill/neoANT-HILL .
Internal ammonium excess induces ROS-mediated reaction and causes carbon scarcity in rice
Authors: Yang Shunying , Hao Dongli , Jin Man , Li Yi , Liu Zengtai , Huang Yanan , Chen Tianxiang , Su Yanhua 
Published: January 2020

Abstract
Background: Overuse of nitrogen fertilizers is often applied to satisfy strong nitrogen demand of high–yielding rice, leading to persistent NH4+ excess in the plant. However, the mechanisms constraining the effectiveness of elevated plant NH4+ in plant growth and grain yield of rice are not sufficiently addressed. The current study analyses the early performance of such internal NH4+ excess in rice, aiming at finding out constraints against compromised nitrogen use efficiency Results: By mimicking a rapid accumulation of plant NH4+ and an RNA-Seq analysis, the present work reveals that internal NH4+ excess in rice plant initiates a burst of reactive oxygen species (ROS) and triggers probably specifically the activation of glutathione transferase (GST)–mediated glutathione cycling for ROS cleavage. Meanwhile, the suppression of the expression of genes involved in photon caption and the activity of primary CO2 fixation enzymes (Rubisco), provides implications of a reduction in photosynthetic carbon income.Along the progress of NH4+/ROS stresses, enhanced energy–producing processes (carbon breakdown) take place as indicated by strong induction of glycolysis related genes to meet the demand of energy consuming activation of ROS–cleavaging systems. The development of these defensive reactions causes a sugar scarcity in the plant that accumulatively leads to growth inhibition. To the opposite direction, a sucrose feeding treatment to the roots renders the accumulation of free NH4+ and ROS, partly restores the activities of photosynthetic CO2 fixation and thus alleviates the scarcity in active carbon source. Conclusion: Our results indicate that carbon scarcity is probably a major constraint in rice plant that limits the performance of nitrogen under overuse of N fertilizers. Keywords: rice, NH4+ excess, ROS, GSH cycle, carbon scarcity, sucrose feeding.
Oleic acid-based nanosystems for mitigating acute respiratory distress syndrome in mice through neutrophil suppression: how the particulate size affects therapeutic efficiency
Authors: Yu Huang-Ping , Liu Fu-Chao , Umoro Ani , Lin Zih-Chan , Elzoghby Ahmed O. , Hwang Tsong-Long , Fang Jia-You 
Published: January 2020

Abstract
Background: Oleic acid (OA) is reported to show anti-inflammatory activity toward activated neutrophils. It is also an important material in nanoparticles for increased stability and cellular internalization. We aimed to evaluate the anti-inflammatory activity of injectable OA-based nanoparticles for treating lung injury. Different sizes of nanocarriers were prepared to explore the effect of nanoparticulate size on inflammation inhibition.
Results: The nanoparticles were fabricated with the mean diameters of 105, 153, and 225 nm. The nanocarriers were ingested by isolated human neutrophils during a 5-min period, with the smaller sizes exhibiting greater uptake. The size reduction led to the decrease of cell viability and the intracellular calcium level. The OA-loaded nanosystems dose-dependently suppressed the superoxide anion and elastase produced by the stimulated neutrophils. The inhibition level was comparable for the nanoparticles of different sizes. In the ex vivo biodistribution study, the pulmonary accumulation of nanoparticles increased following the increase of particle size. The nanocarriers were mainly excreted by the liver and bile clearance. Mice were exposed to intratracheal lipopolysaccharide (LPS) to induce acute respiratory distress syndrome (ARDS), like lung damage. The lipid-based nanocarriers mitigated myeloperoxidase (MPO) and cytokines more effectively as compared to OA solution. The larger nanoparticles displayed greater reduction on MPO, TNF-α, and IL-6 than the smaller ones. The histology confirmed the decreased pulmonary neutrophil recruitment and lung-architecture damage after intravenous administration of larger nanoparticles.
Conclusions: Nanoparticulate size, an essential property governing the anti-inflammatory effect and lung-injury therapy, had different effects on activated neutrophil inhibition and in vivo therapeutic efficacy.
Increased PD-1-positive macrophages in the tissue of gastric cancer are closely associated with poor prognosis in gastric cancer patients.
Authors: Kono Yusuke , Saito Hiroaki , Miyauchi Wataru , Shimizu Shota , Murakami Yuki , Shishido Yuji , Miyatani Kozo , Matsunaga Tomoyuki , Fukumoto Yoji , Nakayama Yuji , Sakurai Chiye , Hatsuzawa Kiyotaka , Fujiwara Yoshiyuki 
Published: January 2020

Abstract
Background: Programmed cell death 1 (PD-1) is one of the immune checkpoint molecules that negatively regulate the function of T cells. Although recent studies indicate that PD-1 is also expressed on other immune cells besides T cells, its role remains unclear. This study aims to evaluate PD-1 expression on macrophages and examine its effect on anti-tumor immunity in gastric cancer (GC) patients.
Methods : The frequency of PD-1 + macrophages obtained from GC tissue was determined by multicolor flow cytometry (n = 15). Double immunohistochemistry staining of PD-1 and CD68 was also performed to evaluate the correlations among the frequency of PD-1 + macrophages, clinicopathological characteristicus, and prognosis in GC patients (n = 102).
Results: The frequency of PD-1 + macrophages was significantly higher in GC tissue than in non-tumor gastric tissue. The phagocytotic activity of PD-1 + macrophages was severely impaired compared with that of PD-1 - macrophages. The 5-year disease specific survival rates in patients with PD-1 + macrophage Low (the frequency of PD-1 + macrophages; < 0.85%) and those with PD-1 + macrophage High (the frequency of PD-1 + macrophages; ≥ 0.85%) were 85.9% and 65.8%, respectively ( P = 0.008). Finally, multivariate analysis showed the frequency of PD-1 + macrophage to be an independent prognostic factor.
Conclusions: The function of PD-1 + macrophage was severely impaired and increased frequency of PD-1 + macrophage worsened the prognosis of GC patients. PD-1–PD-L1 therapies may function through a direct effect on macrophages in GC.
Identification of stable reference genes for qPCR studies in common wheat (Triticum aestivum L.) seedlings under short-term drought stress
Authors: Dudziak Karolina , Sozoniuk Magdalena , Szczerba Hubert , Kuzdraliński Adam , Kowalczyk Krzysztof , Börner Andreas , Nowak Michał 
Published: January 2020

Abstract
Background
Quantitative PCR (qPCR) is one of the most common and accurate methods of gene expression analysis. However, the biggest challenge for this kind of examinations is normalization of the results, which requires the application of dependable internal controls. The selection of appropriate reference genes (RGs) is one of the most crucial points in qPCR data analysis and for correct assessment of gene expression. Because of the fact that many reports indicate that the expression profiles of typically used RGs can be unstable in certain experimental conditions, species or tissues, reference genes with stable expression levels should be selected individually for each experiment. In this study, we analysed a set of ten candidate RGs for wheat seedlings under short-term drought stress. Our tests included five ‘traditional’ RGs (GAPDH, ACT, UBI, TUB, and TEF1) and five novel genes developed by the RefGenes tool from the Genevestigator database.
Results
Expression stability was assessed using five different algorithms: geNorm, NormFinder, BestKeeper, RefFinder and the delta Ct method. In the final ranking, we identified three genes: CJ705892, ACT, and UBI, as the best candidates for housekeeping genes. However, our data indicated a slight variation between the different algorithms that were used. We revealed that the novel gene CJ705892, obtained by means of in silico analysis, showed the most stable expression in the experimental tissue and condition.
Conclusions
Our results support the statement, that novel genes selected for certain experimental conditions have a more stable level of expression in comparison to routinely applied RGs, like genes encoding actin, tubulin or GAPDH. Selected CJ705892 gene can be used as a housekeeping gene in the expression analysis in wheat seedlings under short-term drought. The results of our study will be useful for subsequent analyses of gene expression in wheat tissues subjected to drought.
DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features
Authors: Deng Lei , Lin Wei , Wang Jiacheng , Zhang Jingpu 
Published: January 2020

Abstract
Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that circRNAs are involved in the regulation of various diseases and cancers. Determining the functions of circRNAs in mammalian cells is of great significance for revealing their mechanism of action in physiological and pathological processes, diagnosis and treatment of diseases. However, determining the functions of circRNAs on a large scale is a challenging task because of the high experimental costs.

In this paper, we present a hierarchical deep learning model, DeepciRGO, which can effectively predict gene ontology functions of circRNAs. We build a heterogeneous network containing circRNA co-expressions, protein-protein interactions (PPIs) and protein-circRNA interactions. The topology features of proteins and circRNAs are calculated using a novel representation learning approach Hin2vec across the heterogeneous network. Then, a deep multi-label hierarchical classification model is trained with the topology features to predict the biological process (BP) function in the Gene Ontology (GO) for each circRNA. In particular, we manually curated a benchmark dataset containing 185 GO annotations for 62 circRNAs, namely, circRNA2GO-62. The DeepciRGO achieves promising performance on the circRNA2GO-62 dataset with a maximum F-measure of 0.412, a recall score of 0.4, and an accuracy of 0.4, which are significantly better than other state-of-the-art RNA function prediction methods. In addition, we demonstrate the considerable potential of integrating multiple interactions and association networks.
Evaluating Neonatal Resuscitation Skills of Practicing Nurses and Midwives in Selected Hospitals in Central Uganda​
Authors: Namuguzi Mary , Drake Karen , Ekong Elizabeth Namukombe , Asuquo Ekaete FRANCIS 
Published: January 2020

Abstract
Background: Uganda has a high neonatal mortality rate (27 per 1,000 live births), with birth asphyxia as one of the major contributor. Helping babies breathe (HBB) is an evidence-based program that aims to reduce neonatal mortality in resource-limited settings. Successful resuscitation depends on nurses’ and midwives’ knowledge and skills in neonatal resuscitation, and access to functional neonatal resuscitation equipment. This study aimed to evaluate knowledge and skills retention in neonatal resuscitation after HBB training among nurses and midwives, and the state/availability of neonatal resuscitation equipment. Methods: This study used a cross sectional design. Participants were 75 nurses and midwives from two hospitals in Central Uganda. Data were collected using questionnaires and observation checklists. Ethics approval was obtained from the Uganda Christian University and the research and ethics committees of the two hospital hospitals. Results: Nurses and midwives showed a high level of knowledge (92%). However, neonatal resuscitation skills among 44 observed participants were poor, as 68.2% failed to check equipment and select the correct mask and 45.5% did not make a firm seal when applying the mask. In addition, about 72% of participants did not ventilate at a rate of 40 breaths per minute, and 18.2% failed to assess chest movement. Observation of 44 resuscitations to evaluate the state/availability of neonatal resuscitation equipment showed that 27.3% did not have a suction device, 59.1% did not have a heat source/pre-warmed towels to warm the babies, 50% did not have appropriate self-inflating bags and masks for term and preterm babies, 72.7% had no clock/watch to count heart rate and determine the length of time ventilation was required, and 36.4% did not document that resuscitation was performed. Conclusions: To address Uganda’s neonatal mortality rate, it is necessary to implement regulatory policies for neonatal resuscitation, building nurses and midwives skills for active interventions during neonatal resuscitation as well as regular refresher courses to enhance skills. Key words: helping babies breathe (HBB), neonatal resuscitation, knowledge, skills and equipment
Control of JE vector by organic compounds isolated and green nanoparticles synthesised from leaf extract of Holoptelea integrifolia (Roxb.)
Authors: Singha Someshwar , Chandra Goutam 
Published: January 2020

Abstract
Background: Japanese encephalitis (JE) is a dreadful disease transmitted by Culex vishnui group of mosquitoes. Control of JE vectors at the larval stage is one of the effective approaches in controlling JE. Methods: Leaves of Holoptelea integrifolia were subjected to petroleum ether, ethyl acetate, acetone and absolute alcohol solvent extraction by Soxhlet apparatus. As the ethyl acetate extract showed best mosquito larvicidal activity against Culex vishnui, it extract was selected and processed further for isolation of active principle through column chromatography and TLC and then characterization of the active principle by FTIR and GC-MS was done. Results: Ethyl acetate extract was found to be the most potent larvicide. In the active fraction of isolated compounds from ethyl acetate extract, N-methyl-1-adamantaneacetamide was the major constituent responsible for larvicidal activity of Culex vishnui. Green nanoparticles were synthesised by treating silver nitrate with leaf extract of H. integrifolia and were examined for larvicidal activity. Nanoparticles were characterised by UV-VIS spectral analysis, XRD study, TEM, SEM and FTIR spectral analysis. Synthesised nanoparticles were 40-50 nm in size and showed good larvicidal activity on Cx. vishnui mosquitoes at 1.25, 2.25, 5, 7.5 and 10 ppm concentrations. Active principle of plant extract and green nanoparticles showed eco-friendly effect on non-target organisms like Chironomus circumdatus, Daphnia sp, Diplonychus anulatum and Tadpole larvae. Conclusion: Thus it can be concluded that active ingredient as well as green synthesized nano particles from H. integrifolia can be a good alternative of presently used chemical insecticides.
Effect of laser moxibustion for knee osteoarthritis: a multi-site double-blind randomized controlled trial
Authors: Zhao Ling , Cheng Ke , Wu Fan , Du Jiong , Chen Yue , Tan Ming T. , Lao Lixing , Shen Xueyong 
Published: January 2020

Abstract
Background A laser device that mimics traditional moxibustion without smoke may be effective and safe for treating patients with knee osteoarthritis.Methods A double-blind randomized clinical trial was conducted. A total of 392 patients with osteoarthritis of the knee were randomly assigned to receive laser treatment or sham control three times a week for 4 weeks with 20-week follow-up. Primary outcomes were changes in the WOMAC pain scores at week 4. Results Among the 392 randomized participants, 364 (92.86%) completed the trial. The median WOMAC pain score significantly decreased at week 4 in the active group than in the sham group (2.2; 95% CI, 1.7 to 2.8; P < .01). At week 24, compared to the sham laser, active laser treatment resulted in significant pain reduction and function improvement (3.3; 95% CI, 2.7 to 3.9; P < 0.01, and 15.7; 95% CI, 12.8 to 18.8; P < .01, respectively). The physical component of the quality of life significantly improved in the active group than in the sham control at week 4 (3.0; 95% CI, 1.1 to 4.9; P = 0.002) up to week 24 (5.1; 95% CI, 3.2 to 7.0; P < .001). No serious adverse effects were reported. Conclusion Laser moxibustion resulted in statistically and clinically significant pain reduction and function improvement following a 4-week treatment in patients with knee osteoarthritis.