bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel circRNA-miRNA-mRNA network identifies circ-YOD1 as a biomarker for coronary artery disease
Authors: Miao Liu , Yin Rui-Xing , Zhang Qing-Hui , Liao Pei-Juan , Wang Yong , Nie Rong-Jun , Li Hui 
Published: December 2019

AbstractCircular RNAs (circRNAs) are involved in many physiological functions. Whether circulating circRNAs serve as markers for coronary artery disease (CAD) is unknown. Seven CAD-related microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database and were analyzed using clustering and functional enrichment to identify hub mRNAs and miRNAs. StarBase V3.0 and circinteractome databases were used to predict interactions between circRNAs and miRNAs whereas miRwalk and DIANA TOOLS were used to predict interactions between miRNAs and mRNAs. Altogether, this helped establish a circRNA-miRNA-mRNA triple network for diagnosis of CAD. Five non-coding RNAs (ncRNAs) were identified in our study population with the use of quantitative real-time PCR (RT-PCR). The prognostic values of circYOD1, hsa-miR-21-3p and hsa-miR-296-3p were evaluated using a receiver operating characteristic (ROC) curve. A CAD circRNA-miRNA-mRNA network was established from our analyses containing one circRNA, four miRNAs and thirteen mRNAs. After performing RT-PCR validation between CAD and non-CAD samples, only three ncRNAs of five ncRNAs showed significance for further analysis. The area under ROC curve (AUC) of circ-YOD1 was 0.824, the AUC of hsa-miR-21-3p was 0.731 and hsa-miR-296-3p was 0.776. The pairwise comparison results showed that circ-YOD1 had statistical significance (PYOD1-21 < 0.01 and PYOD1-296 < 0.05). The results of functional enrichment analysis of interacting genes and microRNAs showed that the shared circ-YOD1 may act as a new biomarker for CAD. Our investigation of the triple regulatory networks of circRNA-miRNA-mRNA in CAD revealed circ-YOD1 as a potential biomarker for CAD.
Male-Specific Protein Disulphide Isomerase Function is Essential for Plasmodium Transmission and a Vulnerable Target for Intervention
Authors: Angrisano Fiona , Sala Katarzyna A. , Tapanelli Sofia , Christophides George K. , Blagborough Andrew M. 
Published: December 2019

AbstractInhibiting transmission of Plasmodium is an essential strategy in malaria eradication, and the biological process of gamete fusion during fertilization is a proven target for this approach. Lack of knowledge of the mechanisms underlying fertilization have been a hindrance in the development of transmission-blocking interventions. Here we describe a protein disulphide isomerase essential for malarial transmission (PDI-Trans/PBANKA_0820300) to the mosquito. We show that PDI-Trans activity is male-specific, surface-expressed, essential for fertilization/transmission, and exhibits disulphide isomerase activity which is up-regulated post-gamete activation. We demonstrate that PDI-Trans is a viable anti-malarial drug and vaccine target blocking malarial transmission with the use of PDI inhibitor bacitracin (98.21%/92.48% reduction in intensity/prevalence), and anti-PDI-Trans antibodies (66.22%/33.16% reduction in intensity/prevalence). To our knowledge, these results provide the first evidence that PDI function is essential for malarial transmission, and emphasize the potential of anti-PDI agents to act as anti-malarials, facilitating the future development of novel transmission-blocking interventions.
Self-Assembly in ultrahigh molecular weight sphere-forming diblock copolymer thin films under strong confinement
Authors: Cao Wei , Xia Senlin , Appold Michael , Saxena Nitin , Bießmann Lorenz , Grott Sebastian , Li Nian , Gallei Markus , Bernstorff Sigrid , Müller-Buschbaum Peter 
Published: December 2019

AbstractUltrahigh molecular weight (UHMW) diblock copolymers (DBCs) have emerged as a promising template for fabricating large-sized nanostructures. Therefore, it is of high significance to systematically study the influence of film thickness and solvent vapor annealing (SVA) on the structure evolution of UHMW DBC thin films. In this work, spin coating of an asymmetric linear UHMW polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) DBC is used to fabricate thin films, which are spherically structured with an inter-domain distance larger than 150 nm. To enhance the polymer chain mobility and facilitate approaching equilibrium nanostructures, SVA is utilized as a post-treatment of the spin coated films. With increasing film thickness, a local hexagonal packing of PMMA half-spheres on the surface can be obtained, and the order is improved at larger thickness, as determined by grazing incidence small angle X-ray scattering (GISAXS). Additionally, the films with locally hexagonal packed half-spherical morphology show a poor order-order-poor order transition upon SVA, indicating the realization of ordered structure using suitable SVA parameters.
Highly specific Electrochemical Sensing of Pseudomonas aeruginosa in patients suffering from corneal ulcers: A comparative study
Authors: Khalifa Marwa M. , Elkhawaga Amal A. , Hassan Mona A. , Zahran Asmaa M. , Fathalla Ahmed M. , El-Said Waleed A. , El-Badawy Omnia 
Published: December 2019

AbstractPseudomonas aeruginosa is the most common pathogenic gram-negative bacteria causing corneal ulcers globally. In severe cases, often after trauma and eye injury, corneal destruction progresses rapidly and may be completed within 24–48 h causing blindness. In our preliminary work, we have established an ultrasensitive polyaniline (PANI)/gold nanoparticles (Au NPs)/indium tin oxide (ITO) modified sensor for rapid detection of pyocyanin (PYO) in P. aeruginosa infections with a linear range from 238 μM to 1.9 μM and a detection limit of 500 nM. In the present study, we evaluated the efficiency of the established modified electrochemical sensor in the diagnosis of P. aeruginosa in 50 samples collected from patients suffering from corneal ulcers. The obtained results were compared with the results gained by the screen-printed electrode, conventional techniques, automated identification method, and the amplification of the 16 s rRNA gene by PCR as a gold standard test for P. aeruginosa identification. We have found that the electrochemical detection of PYO by square wave voltammetry technique using PANI/Au NPs modified ITO electrode was the only technique showing 100% agreement with the molecular method in sensitivity, specificity, positive and negative predictive values when compared with the SPE, conventional and automated methods.
Effects of Long-term Cotton Continuous Cropping on Soil Microbiome
Authors: Xi Hui , Shen Jili , Qu Zheng , Yang Dingyi , Liu Shiming , Nie Xinhui , Zhu Longfu 
Published: December 2019

AbstractVerticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.
Angiopoietin-2 predicts morbidity in adults with Fontan physiology
Authors: Shirali Aditya S. , Lluri Gentian , Guihard Pierre J. , Conrad Miles B. , Kim Helen , Pawlikowska Ludmila , Boström Kristina I. , Iruela-Arispe M. Luisa , Aboulhosn Jamil A. 
Published: December 2019

AbstractMorbidity in patients with single-ventricle Fontan circulation is common and includes arrhythmias, edema, and pulmonary arteriovenous malformations (PAVM) among others. We sought to identify biomarkers that may predict such complications. Twenty-five patients with Fontan physiology and 12 control patients with atrial septal defects (ASD) that underwent cardiac catheterization were included. Plasma was collected from the hepatic vein and superior vena cava and underwent protein profiling for a panel of 20 analytes involved in angiogenesis and endothelial dysfunction. Ten (40%) of Fontan patients had evidence of PAVM, eighteen (72%) had a history of arrhythmia, and five (20%) were actively in arrhythmia or had a recent arrhythmia. Angiopoietin-2 (Ang-2) was higher in Fontan patients (8,875.4 ± 3,336.9 pg/mL) versus the ASD group (1,663.6 ± 587.3 pg/mL, p < 0.0001). Ang-2 was higher in Fontan patients with active or recent arrhythmia (11,396.0 ± 3,457.7 vs 8,118.2 ± 2,795.1 pg/mL, p < 0.05). A threshold of 8,500 pg/mL gives Ang-2 a negative predictive value of 100% and positive predictive value of 42% in diagnosing recent arrhythmia. Ang-2 is elevated among adults with Fontan physiology. Ang-2 level is associated with active or recent arrhythmia, but was not found to be associated with PAVM.
Identification of QTL for Target Leaf Spot resistance in Sorghum bicolor and investigation of relationships between disease resistance and variation in the MAMP response
Authors: Kimball Jennifer , Cui Yaya , Chen Dongqin , Brown Pat , Rooney William L. , Stacey Gary , Balint-Kurti Peter J. 
Published: December 2019

AbstractTarget leaf spot (TLS) of sorghum, a foliar disease caused by the necrotrophic fungus Bipolaris cookei (also known as Bipolaris sorghicola), can affect grain yield in sorghum by causing premature drying of leaves and defoliation. Two sorghum recombinant inbred line (RIL) populations, BTx623/BTx642 and BTx623/SC155-14E, were assessed for TLS resistance in replicated trials. Using least square mean trait data, four TLS resistance QTL were identified, two in each population. Of these, three were previously unidentified while a major QTL on chromosome 5 in the BTx623/BTx642 RIL population corresponded to the previously identified TLS resistance gene ds1. A set of sorghum lines were assessed for production of reactive oxygen species induced by treatment with the microbe-associated molecular pattern (MAMP) flg22 (a derivative of flagellin). Flg22-induced ROS production varied between lines in a consistent fashion. One QTL associated with variation in the flg22 response was detected in the RIL populations. No evidence was found to link variation in the MAMP response to variation in TLS resistance
Tailoring parameter distributions to specific germplasm: impact on crop model-based ideotyping
Authors: Paleari Livia , Movedi Ermes , Vesely Fosco Mattia , Confalonieri Roberto 
Published: December 2019

AbstractCrop models are increasingly used to identify promising ideotypes for given environmental and management conditions. However, uncertainty must be properly managed to maximize the in vivo realizability of ideotypes. We focused on the impact of adopting germplasm-specific distributions while exploring potential combinations of traits. A field experiment was conducted on 43 Italian rice varieties representative of the Italian rice germplasm, where the following traits were measured: light extinction coefficient, radiation use efficiency, specific leaf area at emergence and tillering. Data were used to derive germplasm-specific distributions, which were used to re-run a previous modelling experiment aimed at identifying optimal combinations of plant trait values. The analysis, performed using the rice model WARM and sensitivity analysis techniques, was conducted under current conditions and climate change scenarios. Results revealed that the adoption of germplasm-specific distributions may markedly affect ideotyping, especially for the identification of most promising traits. A re-ranking of some of the most relevant parameters was observed (radiation use efficiency shifted from 4th to 1st), without clear relationships between changes in rankings and differences in distributions for single traits. Ideotype profiles (i.e., values of the ideotype traits) were instead more consistent, although differences in trait values were found.
GWAS studies reveal a possible genetic link between cancer and suicide attempt
Authors: Voskarides Konstantinos , Chatzittofis Andreas 
Published: December 2019

AbstractInuit is the population with the highest incidence of suicide attempt and cancer in the world. Previous studies reported that people attempted suicide have a higher future risk for cancer. In view of these data, the largest available genome wide association studies (GWAS) for four major mental disorder groups were screened here for any common genes with all known cancer associated genes and oncogenes/tumor suppressor genes. A common genetic background came out only between suicide attempt and cancer (cancer associated genes analysis: RR = 1.64, p = 7.83 × 10−5; oncogenes/tumor suppressor genes analysis: RR = 2.55, p = 2.82 × 10−22), this supporting existing epidemiological data. Incidence/prevalence of both conditions was found to correlate with extreme cold geographical regions (adjusted R2 = 0.135, p = 3.00 × 10−4); this is not the case for other mental disorders. Our results show a possible genetic link between suicide attempt and cancer and a possible evolutionary connection of both diseases with extreme cold environments. These data are useful for future molecular studies or even for investigation of possible therapeutic protocols.
Heparin Forms Polymers with Cell-free DNA Which Elongate Under Shear in Flowing Blood
Authors: de Vries Joost C. , Barendrecht Arjan D. , Clark Chantal C. , Urbanus Rolf T. , Boross Peter , de Maat Steven , Maas Coen 
Published: December 2019

AbstractHeparin is a widely used anticoagulant which inhibits factor Xa and thrombin through potentiation of antithrombin. We recently identified that the nucleic acid stain SYTOX reacts with platelet polyphosphate due to molecular similarities, some of which are shared by heparin. We attempted to study heparin in flowing blood by live-cell fluorescence microscopy, using SYTOX for heparin visualisation. Immunostaining was performed with monoclonal antibodies directed against various heparin-binding proteins. In addition, we studied modulation of heparin activity in coagulation assays, as well its effects on fibrin formation under flow in recalcified whole blood. We found that SYTOX-positive polymers appear in heparinised blood under flow. These polymers typically associate with platelet aggregates and their length (reversibly) increases with shear rate. Immunostaining revealed that of the heparin-binding proteins assessed, they only contain histones. In coagulation assays and flow studies on fibrin formation, we found that addition of exogenous histones reverses the anticoagulant effects of heparin. Furthermore, the polymers do not appear in the presence of DNase I, heparinase I/III, or the heparin antidote protamine. These findings suggest that heparin forms polymeric complexes with cell-free DNA in whole blood through a currently unidentified mechanism.
Structural consequences of BMPR2 kinase domain mutations causing pulmonary arterial hypertension
Authors: Chaikuad Apirat , Thangaratnarajah Chancievan , von Delft Frank , Bullock Alex N. 
Published: December 2019

AbstractBone morphogenetic proteins (BMPs) are secreted ligands of the transforming growth factor-β (TGF-β) family that control embryonic patterning, as well as tissue development and homeostasis. Loss of function mutations in the type II BMP receptor BMPR2 are the leading cause of pulmonary arterial hypertension (PAH), a rare disease of vascular occlusion that leads to high blood pressure in the pulmonary arteries. To understand the structural consequences of these mutations, we determined the crystal structure of the human wild-type BMPR2 kinase domain at 2.35 Å resolution. The structure revealed an active conformation of the catalytic domain that formed canonical interactions with the bound ligand Mg-ADP. Disease-associated missense mutations were mapped throughout the protein structure, but clustered predominantly in the larger kinase C-lobe. Modelling revealed that the mutations will destabilize the protein structure by varying extents consistent with their previously reported functional heterogeneity. The most severe mutations introduced steric clashes in the hydrophobic protein core, whereas those found on the protein surface were less destabilizing and potentially most favorable for therapeutic rescue strategies currently under clinical investigation.
Unprecedented efficient electron transport across Au nanoparticles with up to 25-nm insulating SiO2-shells
Authors: Li Chuanping , Xu Chen , Cahen David , Jin Yongdong 
Published: December 2019

AbstractQuantum tunneling is the basis of molecular electronics, but often its electron transport range is too short to overcome technical defects caused by downscaling of electronic devices, which limits the development of molecular-/nano-electronics. Marrying electronics with plasmonics may well present a revolutionary way to meet this challenge as it can manipulate electron flow with plasmonics at the nanoscale. Here we report on unusually efficient temperature-independent electron transport, with some photoconductivity, across a new type of junction with active plasmonics. The junction is made by assembly of SiO2 shell-insulated Au nanoparticles (Au@SiO2 NPs) into dense nanomembranes of a few Au@SiO2 layers thick and transport is measured across these membranes. We propose that the mechanism is plasmon-enabled transport, possibly tunneling (as it is temperature-independent). Unprecedentedly ultra-long-range transport across one, up to even three layers of Au@SiO2 in the junction, with a cumulative insulating (silica) gap up to 29 nm/NP layer was achieved, well beyond the measurable limit for normal quantum mechanical tunneling across insulators (~2.5 nm at 0.5–1 V). This finding opens up a new interdisciplinary field of exploration in nanoelectronics with wide potential impact on such areas as electronic information transfer.
Overexpression of the HECT ubiquitin ligase PfUT prolongs the intraerythrocytic cycle and reduces invasion efficiency of Plasmodium falciparum
Authors: Jankowska-Döllken Monika , Sanchez Cecilia P. , Cyrklaff Marek , Lanzer Michael 
Published: December 2019

AbstractThe glms ribozyme system has been used as an amenable tool to conditionally control expression of genes of interest. It is generally assumed that insertion of the ribozyme sequence does not affect expression of the targeted gene in the absence of the inducer glucosamine-6-phosphate, although experimental support for this assumption is scarce. Here, we report the unexpected finding that integration of the glms ribozyme sequence in the 3′ untranslated region of a gene encoding a HECT E3 ubiquitin ligase, termed Plasmodium falciparum ubiquitin transferase (PfUT), increased steady state RNA and protein levels 2.5-fold in the human malaria parasite P. falciparum. Overexpression of pfut resulted in an S/M phase-associated lengthening of the parasite’s intraerythrocytic developmental cycle and a reduced merozoite invasion efficiency. The addition of glucosamine partially restored the wild type phenotype. Our study suggests a role of PfUT in controlling cell cycle progression and merozoite invasion. Our study further raises awareness regarding unexpected effects on gene expression when inserting the glms ribozyme sequence into a gene locus.
Response surface methodological (RSM) approach for optimizing the removal of trihalomethanes (THMs) and its precursor’s by surfactant modified magnetic nanoadsorbents (sMNP) - An endeavor to diminish probable cancer risk
Authors: Kumari Minashree , Gupta Sunil Kumar 
Published: December 2019

AbstractResponse surface methodology (RSM) approach was used for optimization of the process parameters and identifying the optimal conditions for the removal of both trihalomethanes (THMs) and natural organic matter (NOM) in drinking water supplies. Co-precipitation process was employed for the synthesis of magnetic nano-adsorbent (sMNP), and were characterized by field emission scanning electron microscopy (SEM), trans-emission electron microscopy (TEM), BET (Brunauer-Emmett-Teller), energy dispersive X-ray (EDX) and zeta potential. Box-Behnken experimental design combined with response surface and optimization was used to predict THM and NOM in drinking water supplies. Variables were concentration of sMNP (0.1 g to 5 g), pH (4–10) and reaction time (5 min to 90 min). Statistical analysis of variance (ANOVA) was carried out to identify the adequacy of the developed model, and revealed good agreement between the experimental data and proposed model. The experimentally derived RSM model was validated using t-test and a range of statistical parameters. The observed R2 value, adj. R2, pred. R2 and “F-values” indicates that the developed THM and NOM models are significant. Risk analysis study revealed that under the RSM optimized conditions, a marked reduction in the cancer risk of THMs was observed for both the groups studied. Therefore, the study observed that the developed process and models can be efficiently applied for the removal of both THM and NOM from drinking water supplies.
Bidirectional association between asthma and migraines in adults: Two longitudinal follow-up studies
Authors: Kim So Young , Min Chanyang , Oh Dong Jun , Lim Jae-Sung , Choi Hyo Geun 
Published: December 2019

AbstractThe objective of this study was to evaluate the bidirectional association between asthma and migraines using control subjects matched by demographic factors. The Korean Health Insurance Review and Assessment Service - National Sample Cohort from 2002 to 2013 was used. In study I, 113,059 asthma participants were matched with 113,059 control I participants. In study II, 36,044 migraine participants were matched with 114,176 control II participants. The hazard ratios (HRs) of migraines in the asthma patients (study I) and asthma in the migraine patients (study II) were analyzed using stratified Cox proportional hazard models after adjusting for depression and the Charlson comorbidity index. In study I, 5.3% (6,017/ 113,059) of the asthma group and 3.4% (3,806/ 113,059) of the control I group had migraines (P < 0.001). The asthma group demonstrated an adjusted HR of 1.47 for migraine (95% confidence interval (CI) = 1.41–1.53, P < 0.001). In study II, 15.4% (5,548/36,044) of the migraine group and 10.6% (15,271/144,176) of the control group had asthma (P < 0.001). The migraine group showed an adjusted HR of 1.37 for asthma (95% CI = 1.33–1.41, P value < 0.001). Asthma and migraines are reciprocally associated.