bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of haptoglobin alleles in autism spectrum disorders
Authors: Cupaioli Francesca Anna , Mosca Ettore , Magri Chiara , Gennarelli Massimo , Moscatelli Marco , Raggi Maria Elisabetta , Landini Martina , Galluccio Nadia , Villa Laura , Bonfanti Arianna , Renieri Alessandra , Fallerini Chiara , Minelli Alessandra , Marabotti Anna , Milanesi Luciano , Fasano Alessio , Mezzelani Alessandra 
Published: May 2020

AbstractGene-environment interactions, by means of abnormal macromolecular intestinal adsorption, is one of the possible causes of autism spectrum disorders (ASD) predominantly in patients with gastrointestinal disorders. Pre-haptoglobin-2 (zonulin), encoded by theHaptoglobin(HP) allele-2 gene, enhances the intestinal permeability by modulation of intercellular tight junctions. The two alleles ofHP,HP1andHP2, differ for 2 extra exons inHP2that result in exon duplication undetectable by classic genome-wide association studies. To evaluate the role ofHP2in ASD pathogenesis and to set up a method to discriminateHPalleles, Italian subjects with ASD (n = 398) and healthy controls (n = 379) were genotyped by PCR analysis; subsequently, the PCR results were integrated with microarray genotypes (Illumina Human Omni 1S-8), obtained using a subset from the same subjects, and then we developed a computational method to predictHPalleles. On the contrary to our expectations, there was no association betweenHP2and ASD (P > 0.05), and there was no significant allele association in subjects with ASD with or without gastrointestinal disorders (P > 0.05). With the aid of bioinformatics analysis, from a window frame of ~2 Mb containing 314 SNPs, we obtain imputation accuracy (r2) between 0.4 and 0.9 (median 0.7) and correct predictions were between 70% and 100% (median 90%). The conclusions endorse that enhanced intestinal permeability in subjects with ASD should not be imputed toHP2but to other members of the zonulin family and/or to environmental factors.
Relevance of Caspase-1 and Nlrp3 Inflammasome on Inflammatory Bone Resorption in A Murine Model of Periodontitis
Authors: Rocha Fernanda R G. , Delitto Andrea E. , de Souza Joao A. Chaves , González-Maldonado Laura A. , Wallet Shannon M. , Rossa Junior Carlos 
Published: May 2020

AbstractThis study investigates the role of NLRP3 inflammasome and its main effector Caspase-1 in inflammation and alveolar bone resorption associated with periodontitis. Heat-killed Aggregatibacter actinomycetemcomitans (Aa) was injected 3x/week (4 weeks) into gingival tissues of wild-type (WT), Nlrp3-KO and Caspase1-KO mice. Bone resorption was measured by µCT and osteoclast number was determined by tartrate-resistant acid phosphatase (TRAP) staining. Inflammation was assessed histologically (H/E staining and immunofluorescence of CD45 and Ly6G). In vitro studies determined the influence of Nlrp3 and Caspase-1 in Rankl-induced osteoclast differentiation and activity and on LPS-induced expression of inflammation-associated genes. Bone resorption was significantly reduced in Casp1-KO but not in Nlrp3-KO mice. Casp1-KO mice had increased in osteoclast numbers, whereas the inflammatory infiltrate or on gene expression were similar to those of WT and Nlrp3-KO mice. Strikingly, osteoclasts differentiated from Nlrp3-deficient macrophages had increased resorbing activity in vitro. LPS-induced expression of Il-10, Il-12 and Tnf-α was significantly reduced in Nlrp3- and Casp1-deficient macrophages. As an inceptive study, these results suggest that Nlrp3 inflammasome does not play a significant role in inflammation and bone resorption in vivo and that Caspase-1 has a pro-resorptive role in experimental periodontal disease.
Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products
Authors: Srimongkol Grittaya , Ditmangklo Boonsong , Choopara Ilada , Thaniyavarn Jiraporn , Dean Deborah , Kokpol Sirirat , Vilaivan Tirayut , Somboonna Naraporn 
Published: May 2020

AbstractStaphylococcus aureus strains carrying enterotoxin A gene (sea) causes food poisoning and cannot be distinguished from non-pathogenic strains by the culture method. Here, we developed a rapid, specific and sensitive visual detection of sea using loop-mediated isothermal amplification (LAMP) combined with nanogold probe (AuNP) or styryl dye (STR). LAMP-AuNP and LAMP-STR can detect as low as 9.7 fg (3.2 sea copies) and 7.2 sea copies, respectively, which were lower than PCR (97 fg or 32 sea copies). The excellent performance of these new assays was demonstrated in food samples using crude DNA lysates. While the culture method detected 104 CFU/g in ground pork and 10 CFU/mL in milk in 5–7 days, LAMP-AuNP could detect down to 10 CFU/g for both samples in 27 minutes. Analyzing 80 pork and milk samples revealed that the LAMP-AuNP showed 100% sensitivity, 97–100% specificity and 97.5–100% accuracy, which were superior to the culture method, and comparable to PCR but without requirement of a thermal cycler. Furthermore, our LAMP-AuNP detect sea at a range below the food safety control (<100 CFU/g). The LAMP-STR quantitated sea in 10–1,000 CFU (7.2–720 copies). Our crude DNA lysis combined with LAMP-AuNP/STR present effective point-of-care detection and facilitate appropriate control strategies.
A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4
Authors: Nouri Hoda , Fouladiha Hamideh , Moghimi Hamid , Marashi Sayed-Amir 
Published: May 2020

AbstractZymomonas mobilis ZM4 has recently been used for a variety of biotechnological purposes. To rationally enhance its metabolic performance, a reliable genome-scale metabolic network model (GEM) of this organism is required. To this end, we reconstructed a genome-scale metabolic model (iHN446) for Z. mobilis, which involves 446 genes, 859 reactions, and 894 metabolites. We started by first reconciling the existing GEMs previously constructed for Z. mobilis to obtain a draft network. Next, recent gene annotations, up-to-date literature, physiological data and biochemical databases were used to upgrade the network. Afterward, the draft network went through a curative and iterative process of gap-filling by computational tools and manual refinement. The final model was evaluated using experimental data and literature information. We next applied this model as a platform for analyzing the links between transcriptome-flux and transcriptome-metabolome. We found that experimental observations were in agreement with the predicted results from our final GEM. Taken together, this comprehensive model (iHN446) can be utilized for studying metabolism in Z. mobilis and finding rational targets for metabolic engineering applications.
Novel approach for effective removal of methylene blue dye from water using fava bean peel waste
Authors: Bayomie Omar S. , Kandeel Haitham , Shoeib Tamer , Yang Hu , Youssef Noha , El-Sayed Mayyada M. H. 
Published: May 2020

AbstractFava bean peels, Vicia faba (FBP) are investigated as biosorbents for the removal of Methylene Blue (MB) dye from aqueous solutions through a novel and efficient sorption process utilizing ultrasonic-assisted (US) shaking. Ultrasonication remarkably enhanced sorption rate relative to conventional (CV) shaking, while maintaining the same sorption capacity. Ultrasonic sorption rate amounted to four times higher than its conventional counterpart at 3.6 mg/L initial dye concentration, 5 g/L adsorbent dose, and pH 5.8. Under the same adsorbent dose and pH conditions, percent removal ranged between 70–80% at the low dye concentration range (3.6–25 mg/L) and reached about 90% at 50 mg/L of the initial dye concentration. According to the Langmuir model, maximum sorption capacity was estimated to be 140 mg/g. A multiple linear regression statistical model revealed that adsorption was significantly affected by initial concentration, adsorbent dose and time. FBP could be successfully utilized as a low-cost biosorbent for the removal of MB from wastewater via US biosorption as an alternative to CV sorption. US biosorption yields the same sorption capacities as CV biosorption, but with significant reduction in operational times.
Label-free plasma proteomics identifies haptoglobin-related protein as candidate marker of idiopathic pulmonary fibrosis and dysregulation of complement and oxidative pathways
Authors: Saraswat Mayank , Joenväärä Sakari , Tohmola Tiialotta , Sutinen Eva , Vartiainen Ville , Koli Katri , Myllärniemi Marjukka , Renkonen Risto 
Published: May 2020

AbstractIdiopathic pulmonary fibrosis (IPF) is a lung parenchymal disease of unknown cause usually occurring in older adults. It is a chronic and progressive condition with poor prognosis and diagnosis is largely clinical. Currently, there exist few biomarkers that can predict patient outcome or response to therapies. Together with lack of markers, the need for novel markers for the detection and monitoring of IPF, is paramount. We have performed label-free plasma proteomics of thirty six individuals, 17 of which had confirmed IPF. Proteomics data was analyzed by volcano plot, hierarchical clustering, Partial-least square discriminant analysis (PLS-DA) and Ingenuity pathway analysis. Univariate and multivariate statistical analysis overlap identified haptoglobin-related protein as a possible marker of IPF when compared to control samples (Area under the curve 0.851, ROC-analysis). LXR/RXR activation and complement activation pathways were enriched in t-test significant proteins and oxidative regulators, complement proteins and protease inhibitors were enriched in PLS-DA significant proteins. Our pilot study points towards aberrations in complement activation and oxidative damage in IPF patients and provides haptoglobin-related protein as a new candidate biomarker of IPF.
Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing
Authors: Bandara H. M. H. N. , Wood D. L. A. , Vanwonterghem I. , Hugenholtz P. , Cheung B. P. K. , Samaranayake L. P. 
Published: May 2020

AbstractMicroorganisms employ quorum sensing (QS) mechanisms to communicate with each other within microbial ecosystems. Emerging evidence suggests that intraspecies and interspecies QS plays an important role in antimicrobial resistance in microbial communities. However, the relationship between interkingdom QS and antimicrobial resistance is largely unknown. Here, we demonstrate that interkingdom QS interactions between a bacterium, Pseudomonas aeruginosa and a yeast, Candida albicans, induce the resistance of the latter to a widely used antifungal fluconazole. Phenotypic, transcriptomic, and proteomic analyses reveal that P. aeruginosa’s main QS molecule, N-(3-Oxododecanoyl)-L-homoserine lactone, induces candidal resistance to fluconazole by reversing the antifungal’s effect on the ergosterol biosynthesis pathway. Accessory resistance mechanisms including upregulation of C. albicans drug-efflux, regulation of oxidative stress response, and maintenance of cell membrane integrity, further confirm this phenomenon. These findings demonstrate that P. aeruginosa QS molecules may confer protection to neighboring yeasts against azoles, in turn strengthening their co-existence in hostile polymicrobial infection sites.
Sero-epidemiological study of the rotavirus VP8* protein from different P genotypes in Valencia, Spain
Authors: Vila-Vicent Susana , Gozalbo-Rovira Roberto , Rubio-Del-Campo Antonio , Santiso-Bellón Cristina , Navarro-Lleó Noemí , Muñoz Carlos , Buesa Javier , Rodríguez-Díaz Jesús 
Published: May 2020

AbstractThe aims of the present work were to determine the prevalence and titer of serum antibodies against several rotavirus VP8* proteins from different P genotypes in children and adults in Valencia, Spain; and to determine the role of the secretor status (FUT2G428A polymorphism) in the antibody response. The VP8* protein from the P[4], P[6], P[8], P[9], P[11], P[14] and P[25] genotypes were produced in E. coli. These proteins were tested with 88 serum samples from children (n = 41, 3.5 years old in average) and from adults (n = 47, 58 years old in average) by ELISA. A subset of 55 samples were genotyped for the FUT2G428A polymorphism and the antibody titers compared. The same subset of samples was also analysed by ELISA using whole rotavirus Wa particles (G1P[8]) as antigen. Ninety-three per cent of the samples were positive for at least one of the VP8* antigens. Differences in the IgG seroprevalence were found between children and adults for the P[4], P[8] and P[11] genotypes. Similarly, significant differences were found between adults and children in their antibody titers against the P[4], P[8], and P[11] VP8* genotypes, having the children higher antibody titers than adults. Interestingly, positive samples against rare genotypes such as P[11] (only in children), P[14] and P[25] were found. While no statistical differences in the antibody titers between secretors and non-secretors were found for any of the tested P genotypes studied, a higher statistic significant prevalence for the P[25] genotype was found in secretors compared to non-secretors. Significant differences in the antibody titers between secretors and non-secretors were found when the whole viral particles from the Wa rotavirus strain (G1P[8]) were used as the antigen.
Direct exposure of the head to solar heat radiation impairs motor-cognitive performance
Authors: Piil Jacob F. , Christiansen Lasse , Morris Nathan B. , Mikkelsen C. Jacob , Ioannou Leonidas G. , Flouris Andreas D. , Lundbye-Jensen Jesper , Nybo Lars 
Published: May 2020

AbstractHealth and performance impairments provoked by thermal stress are societal challenges geographically spreading and intensifying with global warming. Yet, science may be underestimating the true impact, since no study has evaluated effects of sunlight exposure on human brain temperature and function. Accordingly, performance in cognitively dominated and combined motor-cognitive tasks and markers of rising brainstem temperature were evaluated during exposure to simulated sunlight (equal to ~1000 watt/m2). Acute exposure did not affect any performance measures, whereas prolonged exposure of the head and neck provoked an elevation of the core temperature by 1 °C and significant impairments of cognitively dominated and motor task performances. Importantly, impairments emerged at considerably lower hyperthermia levels compared to previous experiments and to the trials in the presents study without radiant heating of the head. These findings highlight the importance of including the effect of sunlight radiative heating of the head and neck in future scientific evaluations of environmental heat stress impacts and specific protection of the head to minimize detrimental effects.
Relative abundance of derelict fishing gear in the Hawaii-based pelagic longline fishery grounds as estimated from fishery observer data
Authors: Uhrin Amy V. , Walsh William A. , Brodziak Jon 
Published: May 2020

AbstractDerelict fishing gear (DFG) is abundant across the remote North Pacific Ocean, accumulating in convergence zones that coincide with the fishing grounds of the Hawai’i-based pelagic longline fishery. Longlines are prone to snagging DFG, providing an opportunistic, yet regular, reporting mechanism by longline fishery observers (fishery-dependent data). We apply a zero-inflated negative binomial model previously used to standardize catch per unit effort (CPUE) for bycatch and incidentally caught species in this fishery to estimate DFG relative abundance and qualitative trends within the longline fishing grounds. During 2008–2016, observers reported 1326 marine debris items intercepted by longlines, dominated by DFG at nearly 90%. Modeling results suggest that the relative abundance of DFG has declined ~66% from 2008–2016. DFG standardized CPUE was higher for longlines fished inside the North Pacific Subtropical Convergence Zone (versus outside) and increased moving eastward and northward toward the Great Pacific Garbage Patch. Despite substantially less effort in the shallow-set sector of the fishery (∼60 m depth), DFG standardized CPUE was four-fold greater than that of the deep-set sector (∼250 m) suggesting that marine debris observer reporting focused in this sector may be most effective. Some fishermen voluntarily stow snagged debris; incentivizing at-sea removal may elicit further cooperation.
Longitudinal optical imaging technique to visualize progressive axonal damage after brain injury in mice reveals responses to different minocycline treatments
Authors: Pernici Chelsea D. , Rowe Rachel K. , Doughty P. Timothy , Madadi Mahboubeh , Lifshitz Jonathan , Murray Teresa A. 
Published: May 2020

AbstractA high-resolution, three-dimensional, optical imaging technique for the murine brain was developed to identify the effects of different therapeutic windows for preclinical brain research. This technique tracks the same cells over several weeks. We conducted a pilot study of a promising drug to treat diffuse axonal injury (DAI) caused by traumatic brain injury, using two different therapeutic windows, as a means to demonstrate the utility of this novel longitudinal imaging technique. DAI causes immediate, sporadic axon damage followed by progressive secondary axon damage. We administered minocycline for three days commencing one hour after injury in one treatment group and beginning 72 hours after injury in another group to demonstrate the method’s ability to show how and when the therapeutic drug exerts protective and/or healing effects. Fewer varicosities developed in acutely treated mice while more varicosities resolved in mice with delayed treatment. For both treatments, the drug arrested development of new axonal damage by 30 days. In addition to evaluation of therapeutics for traumatic brain injury, this hybrid microlens imaging method should be useful to study other types of brain injury and neurodegeneration and cellular responses to treatment.
Enzymatic and genetic characterization of lignin depolymerization by Streptomyces sp. S6 isolated from a tropical environment
Authors: Riyadi Fatimah Azizah , Tahir Analhuda Abdullah , Yusof Nurtasbiyah , Sabri Nurul Syazwani Ahmad , Noor Megat Johari Megat Mohd , Akhir Fazrena Nadia M. D. , Othman Nor’azizi , Zakaria Zuriati , Hara Hirofumi 
Published: May 2020

AbstractThe conversion of lignocellulosic biomass into bioethanol or biochemical products requires a crucial pretreatment process to breakdown the recalcitrant lignin structure. This research focuses on the isolation and characterization of a lignin-degrading bacterial strain from a decaying oil palm empty fruit bunch (OPEFB). The isolated strain, identified as Streptomyces sp. S6, grew in a minimal medium with Kraft lignin (KL) as the sole carbon source. Several known ligninolytic enzyme assays were performed, and lignin peroxidase (LiP), laccase (Lac), dye-decolorizing peroxidase (DyP) and aryl-alcohol oxidase (AAO) activities were detected. A 55.3% reduction in the molecular weight (Mw) of KL was observed after 7 days of incubation with Streptomyces sp. S6 based on gel-permeation chromatography (GPC). Gas chromatography-mass spectrometry (GC-MS) also successfully highlighted the production of lignin-derived aromatic compounds, such as 3-methyl-butanoic acid, guaiacol derivatives, and 4,6-dimethyl-dodecane, after treatment of KL with strain S6. Finally, draft genome analysis of Streptomyces sp. S6 also revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin depolymerization, as well as for the mineralization of the lower molecular weight compounds, confirming the lignin degradation capability of the bacterial strain.
Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance
Authors: Uemura Takuya , Hachisu Masakazu , Desaki Yoshitake , Ito Ayaka , Hoshino Ryosuke , Sano Yuka , Nozawa Akira , Mujiono Kadis , Galis Ivan , Yoshida Ayako , Nemoto Keiichirou , Miura Shigetoshi , Nishiyama Makoto , Nishiyama Chiharu , Horito Shigeomi , Sawasaki Tatsuya , Arimura Gen-ichiro 
Published: May 2020

AbstractPlants respond to herbivory by perceiving herbivore danger signal(s) (HDS(s)), including “elicitors”, that are present in herbivores’ oral secretions (OS) and act to induce defense responses. However, little is known about HDS-specific molecules and intracellular signaling. Here we explored soybean receptor-like kinases (RLKs) as candidates that might mediate HDS-associated RLKs’ (HAKs’) actions in leaves in response to OS extracted from larvae of a generalist herbivore, Spodoptera litura. Fractionation of OS yielded Frα, which consisted of polysaccharides. The GmHAKs composed of their respective homomultimers scarcely interacted with Frα. Moreover, Arabidopsis HAK1 homomultimers interacted with cytoplasmic signaling molecule PBL27, resulting in herbivory resistance, in an ethylene-dependent manner. Altogether, our findings suggest that HAKs are herbivore-specific RLKs mediating HDS-transmitting, intracellular signaling through interaction with PBL27 and the subsequent ethylene signaling for plant defense responses in host plants.
Phase diagram of the two-dimensional Hubbard-Holstein model
Authors: Costa Natanael C. , Seki Kazuhiro , Yunoki Seiji , Sorella Sandro 
Published: May 2020

AbstractThe electron–electron and electron–phonon interactions play an important role in correlated materials, being key features for spin, charge and pair correlations. Thus, here we investigate their effects in strongly correlated systems by performing unbiased quantum Monte Carlo simulations in the square lattice Hubbard-Holstein model at half-filling. We study the competition and interplay between antiferromagnetism (AFM) and charge-density wave (CDW), establishing its very rich phase diagram. In the region between AFM and CDW phases, we have found an enhancement of superconducting pairing correlations, favouring (nonlocal) s-wave pairs. Our study sheds light over past inconsistencies in the literature, in particular the emergence of CDW in the pure Holstein model case.
Investigation of rotor strength and rotor dynamics for high‐speed high‐power switched reluctance machines
Authors: Gan Chun , Chen Yu , Cui Xiupeng , Sun Jianbo , Ni Kai , Qu Ronghai 
Published: May 2020

This study proposes an investigation scheme of the rotor strength and rotor dynamic characteristics for high‐speed high‐power switched reluctance machines (SRMs). The analytical model and finite element analysis model are established to predict the maximum stress and deformation in the rotor. The Mises yield criterion is employed to verify the strength of the rotor at 1.2 times the rated speed. For the rotor dynamics, critical speed, unbalance response, and stability of the shaft system are analysed in detail. In the developed critical speed calculation scheme, the gyroscopic effect and the impact of the rotation speed on the stiffness and damping are considered. Then, the critical speeds acquired by the developed scheme are compared with those derived by using the conventional method. The unbalance response curves at different nodes are adopted for the unbalance response calculation, while the stability of the shaft system is verified by calculating the logarithmic decrement rates. The critical speed measurement experiment is performed on a 160 kW and 18,000 r/min SRM prototype, and the proposed critical speed calculation scheme is proved to be effective and accurate. The effectiveness of the unbalance response calculation method and the stability judgement technique are also verified by experiment.