bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of long non-coding RNA expression profiles in vascular endothelial cells with hyperglycemia-induced damage
Authors: Xu Erqin , Hu Xiaolei , Li Xiaoli , Jin Guoxi , Zhuang Langen , Wang Qiong , Pei Xiaoyan 
Published: December 2019

Abstract
Background: Diabetes mellitus is often associated with microvascular and macrovascular lesions, and hyperglycemia-induced vascular endothelial cell damage is a key factor. Methods: We investigated long non-coding RNAs (lncRNAs) and mRNAs that are affected by hyperglycemia-induced damage using human umbilical vein endothelial cells (HUVECs) as a model. HUVECs were cultured under high (25 mmol/L) or normal (5 mmol/L) glucose conditions for 6 d, and then lncRNAs and protein-coding transcripts were profiled by RNA-seq. Results: Among 40,379 lncRNAs screened, 214 were upregulated (log2 [fold-change] > 1, FDR < 0.05) and 197 were downregulated (log2 [fold-change] < −1, FDR < 0.05) in response to high-glucose. Furthermore, among 28,431 protein-coding genes screened, 778 were upregulated and 998 were downregulated. A total of 945 lncRNA/mRNA pairs were identified, including 126 differentially expressed lncRNAs predicted to target 201 mRNAs, among which 26 were cis-regulatory interactions. The corresponding lncRNA-mRNA network was composed of 354 lncRNA nodes, 1,167 mRNA nodes and 9,735 edges. Dozens of lncRNAs with high degree may play important roles in high-glucose-induced HUVEC damage, including ENST00000600527, NONHSAT037576.2, NONHSAT135706.2, ENST00000602127, NONHSAT200243.1, NONHSAT217282.1, NONHSAT176260.1, NONHSAT199075.1, NONHSAT067063.2, NONHSAT058417.2. Conclusion: These observations may provide novel insights into the regulatory molecules and pathways of hyperglycemia-related endothelial dysfunction in diabetes-associated vascular disease. Keywords：lncRNA, diabetes mellitus, HUVECs, expression profiling, hyperglycemia, RNA-seq
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
Authors: Muñoz-Benavent Maria , Hartkopf Felix , Bossche Tim Van Den , Piro Vitor C. , García-Ferris Carlos , Latorre Amparo , Renard Bernhard Y. , Muth Thilo 
Published: December 2019

Abstract
Background The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared towards human microbiomes. Microbiota are better understood when analyzed in their biological context, which is together with their host or environment, but this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Results Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics, and metaproteomics in an integrative manner. The pipeline has been developed using the Snakemake framework in order to obtain an automated and reproducible workflow. One of the key features is the on-the-fly creation of a tailored proteogenomic database based on metagenomics and metatranscriptomics data, leading to improved protein identification, taxonomic and functional analysis. gNOMO combines meta-omics analysis of the host with its bacterial population and allows to investigate both host and microbiome of non-model organisms with commonly insufficiently complete reference databases. Conclusions Using experimental datasets of the German cockroach Blattella germanica , a non-model organism with very complex gut microbiome, we show the capabilities of gNOMO with regard to meta-omics data integration, expression ratio comparison, taxonomic and functional analysis as well as intuitive output visualization. gNOMO includes functional information of metagenomics, metatranscriptomics, and metaproteomics data of the microbiome in the same visualization facilitating the interpretation of the results. Moreover, host data can be analyzed in parallel to obtain an equivalent output that allows to study the metabolic situation of the whole symbiotic system. Finally, the metaproteomics identification and annotation are optimized using a tailored proteogenomics database automatically obtained within the gNOMO workflow. In conclusion, gNOMO is a fully automated pipeline, for integrating and analyzing multiple meta-omics data and for producing useful output visualizations. In addition, it is specifically designed for data from non-model organisms. The gNOMO pipeline is freely available under the Apache 2.0 open-source license and can be downloaded from https://gitlab.com/rki_bioinformatics/gnomo .
Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating peel cracking in Akebia trifoliata fruit
Authors: Niu Juan , Shi Yaliang , Huang Kunyong , Zhong Yicheng , Chen Jing , Sun Zhimin , Luan Mingbao , Chen Jianhua 
Published: December 2019

Abstract
Background Akebia trifoliata (Thunb.) Koidz, can be used as a new potential candidate biofuel and bioenergy crop due to its high productivity, adaptability and tolerance to cultivation conditions. However, the pericarp of A. trifoliata cracks open longitudinally and disperses its seeds along the ventral suture during fruit ripening, which is a serious problem that limits the usefulness of its biofuel feedstocks and causes significant losses of yield and commercial value. However, there have been no known previous investigations of the fruit cracking and its molecular mechanisms in A. trifoliata.Results The dynamic structural changes of the fruit peels were observed. In the non-cracking stage of growth, the exocarp was dense, had an orderly arrangement, and the cuticle was complete and distributed continuously. However, the cells became thinner, had reduced integrity, lost cell wall structures, and there was cell wall break down, in the fruit cracking stage. Moreover, analysis of the complementary RNA sequencing based transcriptomes and tandem mass tag based proteomes at different development stages of the fruit ripening, were performed to detect the genes and proteins related to the fruit cracking in A. trifoliata. A total of 20 differentially expressed genes and 17 differentially abundant proteins were identified from the transcriptomics and proteomics data that contribute to the fruit cracking, by participating in the biosynthesis of the phenylpropanoid pathway, galactose metabolism, pentose, and glucuronate interconversions, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Several candidate genes and proteins related to pentose and glucuronate interconversions (pectate lyases and pectinesterase) and galactose metabolism (β-galactosidases 1 and β-galactosidases 2) may play key roles in A. trifoliata fruit cracking.Conclusions Complementary transcriptome and proteome level analyses indicated that a complex molecular network was controlling the fruit cracking process. This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits. The candidate genes/proteins identified in this study may be useful for the genetic improvement of A. trifoliata and other crops.
Identifying Leading Indicators of System Resilience and the Strategy for Developing Them: A Review of Reviews
Authors: Pereira Nichole , Churruca Kate , Egan Rylan , Ellis Louise A. , Braithwaite Jeffrey , Nizamani Sundus , Austin Elizabeth E. , Long Janet C. , Clay-Williams Robyn 
Published: December 2019

Abstract
Background: System resilience describes the performance or capacity of a system to absorb and adapt in response to stressors and perturbations. This protocol outlines the search strategy to identify indicators or metrics of system resilience from across diverse fields and examine the methods/processes for developing these indicators or metrics.Methods: This protocol is grounded in the Joanna Briggs Institute (JBI) Scoping Review methodology. We will search Web of Science and Scopus for reviews that report on system resilience assessment and measurement techniques. We will also employ snowball sampling techniques. Due to the breadth of the topic, this search will be limited to systematic reviews, meta-analyses, or literature reviews with a structured, documented search strategy reporting on primary research studies published in the English language. We will not limit the search by date or discipline. Reviews that report on psychological resilience or resilience at the level of an individual will be excluded. Discussion: The ability to assess or measure resilience is important to identify risks, opportunities, and strategies to influence sustained, reliable, and predictable sy­stem operations. We hypothesise that there are commonalities in the types of indicators used and how they are developed. These patterns may have relevance to other fields, like healthcare. The findings from this review may help others develop their own indicators and assessment strategies for understanding resilience within their own systems. Ethics and Dissemination: This study is ethics exempt. We will disseminate the results of this work at national and international quality and safety conferences, and through publication of a manuscript.
A visualized pulmonary arterial thrombus by using a new echocardiographic view in an intermediate-risk a cute pulmonary embolism patient: a case report
Authors: Mu Guanyu , Li Feixue , Chen Xiaolin , Zhao Bo , Li Guangping , Fu Huaying 
Published: December 2019

Abstract
BackgroundAcute pulmonary embolism (APE) is a life-threatening disease with nonspecific clinical signs and symptoms. Rapid and accurate diagnosis is crucial for the clinical management of patients with acute pulmonary embolism. A new recommended echocardiography view may be of further help in the diagnosis, evaluate the change of the thrombosis and treatment effect.Case presentationWe report a case of a 74-year-old man with a 12-day history of decreased exercise capacity and dyspnoea. The patient was diagnosed intermediate-risk APE as several pulmonary emboli in pulmonary artery were seen in multidetector computed tomographic pulmonary angiography with normal blood pressure and echocardiographic right ventricular overload. And we found a pulmonary artery clot in the right pulmonary artery through transthoracic echocardiography. After 11-days anticoagulation, the patient underwent a reassessment, showed decrease in RV diameter and pulmonary artery thrombus. ConclusionThis case highlights the significant role that echocardiography played in a patient who presented pulmonary embolism with a stable hemodynamic situation and normal blood pressure. The new echocardiographic view could provide correct diagnoses by identifying the clot size and location visually. Knowledge of the echocardiography results of APE would aid the diagnosis.
Seq-SymRF: A random forest model predict potential miRNA-disease associations based on information of sequences and clinical symptoms
Authors: Li Jinlong , Chen Xingyu , Huang Qixing , Wang Yang , Xie Yun , Dai Zong , Zou Xiaoyong , Li Zhanchao 
Published: December 2019

Abstract
Background: MicroRNA (MiRNA) plays a vital role in biological processes and closely relate with various human diseases. Research on the miRNA-disease associations contributes to the prevention, diagnosis and treatment of diseases, as well as the identification of new drugs and the discovery of lead compounds. Since traditional experiment methods are time-consuming and expensive, it is necessary to develop an efficient and accurate theoretical approach to identify potential miRNA-disease associations. Results: In this study, a sequence- and symptom-based random forest classifier model (Seq-SymRF) was constructed to identify the potential associations between miRNA and disease. Compared with existing methods, features derived from only sequence information were used to characterize miRNA. More importantly, clinical symptoms were utilized to represent disease. Moreover, the clustering method by calculating the Euclidean distance was implemented to construct the reliable negative sample. Based on the five-fold cross-validation, the model achieved the accuracy, specificity, sensitivity, precision and Matthews correlation coefficient of 98.00%, 99.43%, 96.58%, 99.40% and 0.9604, respectively. The areas under receiver operating characteristic curve and precision recall curve were 0.9967 and 0.9975, respectively. Additionally, case study was implemented with leukemia, breast neoplasms and hsa-mir-21. Most of top-25 predicted disease-related miRNAs (36/50 for leukemia; 33/50 for breast neoplasms) and 32 of top-50 predicted miRNA-related diseases were verified by literature and dbDEMC database. Conclusion: We proposed a new method, named Seq-SymRF, for predicting miRNA-disease associations, which could be regarded as a powerful high-throughput virtual screening tool for drug research and development.
From Plasmodium vivax outbreak to elimination: lessons learnt from a retrospective analysis of data from Guantang
Authors: Yang Guo-Jing , Liu Ying , Shang Le-Yuan , Zhang Hong-Wei , Zhou Xiao-Nong , Penny Melissa A. , Smith Thomas A. 
Published: December 2019

Abstract
Background: Malaria was once a serious public health problem in China with Plasmodium vivax the major species responsible for more than 90% of local transmission. Following significant integrated malaria control and elimination programs, malaria burden declined, and by 2017 China recorded no indigenous cases. To understand the historical malaria transmission patterns and epidemic characteristics in China and insights useful to guide P. vivax malaria control and elimination elsewhere, a retrospective study was carried out. Materials and Methods: Historical data from a pilot study conducted in Guantang, Luyi in central China from 1971-1995, were digitised. The data included monthly numbers of reported cases, febrile cases, parasite carriage rates, the neonatal infection rate, and entomological data from Anopheles sinensis. Results: Following 25 years of continuous integrated malaria control activities, malaria incidence in Guantang decreased from 4,333 cases per 10,000 in 1970 before integrated implementation to 0.23 cases per 10,000 in 1991, and no cases in 1992-1995. Some fluctuations in incidence were observed between 1977 and 1981. During the period parasite rates, antibody levels and the neonatal infection rate also decreased. The pattern of seasonality confirmed that P. vivax in Henan Province was primarily of long incubation type (temperate) during non-transmission period. The findings retrospectively provide a scientific basis for the implementation of mass campaigns of liver stage hypnozoite clearance. Entomological studies indicated that An. sinensis was the only vector, and it preferred bovine to human hosts, predominantly biting and resting outdoors. Mosquito densities declined between 1971 and 1984.Conclusion: The integrated malaria control approach in Guantang effectively controlled malaria and achieved elimination. Analysis of the effectiveness of the program can provide guidance to other regions or countries with similar ecological settings aiming to move from malaria control to elimination. There is a potential challenge in the maintenance of non-transmission status owing to imported cases and the long dormancy of liver stage hypnozoites.
One-step RT-qPCR assay for ZIKV RNA detection in Aedes aegypti samples: A protocol to study infection &amp; gene expression during ZIKV infection
Authors: Araujo Ricardo Vieira , Feitosa-Suntheimer Fabiana , Gold Alexander S. , Londono-Renteria Berlin , Colpitts Tonya Michelle 
Published: December 2019

Abstract
Background: Zika virus (ZIKV) is transmitted to humans during the bite of an infected mosquito. In a scenario of globalization and climate change, the frequency of outbreaks has and will increase in areas with competent vectors, revealing a need for continuous improvement of ZIKV detection tools in vector populations. A simple, rapid and sensitive assay for viral detection is qRT-PCR, yet oligos optimized for ZIKV detection in mammalian cells and samples have repeatedly shown high background when used on mosquito RNA. In this work we present a one-step qRT-PCR protocol that allows for the detection of ZIKV in mosquitoes and for the evaluation of gene expression from the same mosquito sample and RNA. This assay is a less expensive qRT-PCR approach than that most frequently used in the literature and has a much lower background, allowing for confident detection.Methods: Our new oligo design to detect ZIKV RNA included in silicoanalysis of both viral and mosquito (Ae. aegyptiand Ae. albopictus)genomes, targeting sequences conserved between Asian and African ZIKV lineages, but not matching Aedesgenomes. This assay will allow researchers to avoid nonspecific amplification in insect samples due to viral integration into the mosquito genome, a phenomenon known to happen in wild and colonized populations of mosquitoes.Standard curves constructed with in vitrotranscribed ZIKV RNA were used to optimize the sensitivity, efficiency and reproducibility of the assay.Results: Finally, the assay was used with success to detect both ZIKV RNA in infected mosquitoes and to detect expression of the Defensin A gene, an antimicrobial peptide (AMP) involved in Aedes aegyptiimmune response to virus infection.Conclusions: The experimental approach to detect ZIKV RNA in Aedes aegyptipresented here has demonstrated to be specific, sensitive and reliable, and additionally it allows for the analysis of mosquito gene expression during ZIKV infection.
Risk factors of tractional retinal detachment in non-silicone oil tamponade eyes after vitrectomy for proliferative diabetic retinopathy
Authors: Chen Qiulu , Wang Wenying , Hu Liting , Zhang Lina , Ma Yuna , Du Zhaodong , Zhao Guiqiu 
Published: December 2019

Abstract
BackgroundTraction retinal detachment is one of the serious complications of proliferative diabetic retinopathy (PDR) and poses a serious threat to the visual acuity of patients.The purpose of this paper is to investigated the risk factors of tractional retinal detachment (TRD) in non-silicone oil tamponade eyes after vitrectomy for PDR.MethodsWe performed a retrospective review of patients with postoperative TRD who underwent vitrectomy with non -silicone oil tamponade (C3F8, sterilized air or BSS) for PDR. The clinical information, including laboratory tests and the history of ocular treatment, was determined and compared to the control group to analyze their significance.ResultsThe control group consisted of 28 patients who underwent vitrectomy with non-silicone oil tamponade for PDR immediately one proceeding and one following the surgery of each of the 14 patients (TRD group) with postoperative TRD. The history of photocoagulation, serum albumin, blood urea nitrogen and serum creatinine were significantly associated with TRD. The logistic regression analysis indicated that lower serum albumin concentration was the major systemic risk factor for the occurrence of TRD (P = 0.027).ConclusionThe main systemic risk factor related to TRD was serum albumin in patients with PDR who underwent vitrectomy with non-silicone oil tamponade. Preoperative albumin supplementation may reduce the risk of postoperative TRD.
The Accuracy of Different Generation Intraocular Lens Power Formulas in Eyes with Axial Length Lower than 22 millimeter
Authors: Yildiz Aydın , Arikan Sedat 
Published: December 2019

Abstract
Background:To investigate the accurate formulas for eyes with axial length (AL) lower than 22 millimeters among usually used six intraocular lens (IOL) calculation formulas. MethodsA total of 122 eyes with short ALs that is lower than 22 mm of 122 patients who underwent phacoemulsification surgery with the same type of IOL implantation were included in this retrospective study. The biometric values of the patients were obtained by using optical low coherence reflectometry (OLCR) for six formulas involving Hoffer Q, SRK-T, Haigis, Barett Universal II, Holladay 2 and Hill-RBF. All patients had a postoperative best corrected visual acuity level that is equal or higher than 20/40. While comparing the accuracy of these six IOL calculation formulas, the mean absolute error (MAE), and the median absolute error (MedAE) values were taken into account.ResultsThe MAE values for Hoffer Q, SRK-T, Haigis, Holladay 2, Hill-RBF and Barrett Universal II formulas were 0.390, 0.390, 0.324, 0.327, 0.331 and 0.208 respectively. Also the rank of MedAE values for the mentioned formulas was 0.245, 0.310, 0.310, 0.250, 0.255 and 0.190. The lowest MAE and MedAE value was found in Barrett Universal II formula, whereas the highest one was in the SRK/T formula with a statistical significance (p<0.001). After Bonferroni correction, there were no statistically significant difference between Barret Universal II formula and the other formulas except SRK/T (p>0.01). Three patients (2.5%) were in the ±0.75 D range, 15 patients (12.3%) were in the ±0.50 D, and the remaining 104 (85.2%) patients were in the ±0.25 D at the first month follow-up. ConclusionsAlthough Barrett Universal II appears to be the most accurate IOL calculation formula, third, fourth and other newer generation formulas have also a good predictive value for accurate estimation of IOL power in short eyes.
A combination of Spearmint and flaxseed extract improved endocrine and histomorphology of ovary in experimental PCOS
Authors: Mina Mehraban , Gholamali Jelodar , Farhad Rahmanifar 
Published: December 2019

Abstract
BackgroundPolycystic ovary syndrome (PCOS) is a complex reproduction and endocrine disorder of women in the reproductive age. Spearmint (Mentha Spicata L.) has anti-androgenic activity and flaxseed (Linum Usitatissimum L.) contains phytoestrogen and was reported to improve PCOS conditions. This study aimed to evaluate PCOS conditions following administration of a mixture of these two plants.MethodsTwenty-four rats with regular cycles were randomly divided into four groups as control (C) and treatment-control (TC) received a combination of spearmint extract (SE) + flaxseed extract (FE). PCOS was induced in PCOS and treatment (T) groups by a single intramuscular injection of estradiol valerate. The treatment group received a combination of SE and FE for 30 days, 7 weeks after injection of estradiol valerate. Estrous cycles were monitored for 10 days and in the last day animals were sacrificed, ovaries were collected for the histomorphometric study and the serum levels of progesterone, testosterone, estradiol, and dehydroepiandrosterone (DHEA) were measured. ResultSignificant rise in progesterone and a decrease in testosterone and estradiol with no significant change of DHEA in the T group, was observed in comparison with the PCOS group (P<0.05). No significant difference noticed between T and control groups (C &CT) regarding evaluated hormones. A significant increase in primary, pre-antral and antral follicles noticed in the T group compared to the PCOS group. The number of cystic follicles decreased in the T group compared with the PCOS group. Granulosa layer thickness increased while the thickness of theca decreased significantly in the T group compared to the PCOS group (P<0.05). No significant endocrine or histological differences noticed between C and TC groups.ConclusionA combination of flaxseed and spearmint extract improved the endocrine profile and the histomorphometric features of the ovary in the T group compared to the PCOS group.