bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening and characterization of prophages in Desulfovibrio genomes
Authors: Crispim Josicelli Souza , Dias Roberto Sousa , Vidigal Pedro Marcus Pereira , de Sousa Maíra Paula , da Silva Cynthia Canêdo , Santana Mateus Ferreira , de Paula Sérgio Oliveira 
Published: June 2018

AbstractBacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due to their ability to microbiologically induce corrosion, biofilm formation and H2S production. Bacteriophages are an alternative control method for SRB, whose information for this group of bacteria however, is scarce. The present study developed a workflow for the identification of complete prophages in Desulfovibrio. Poly-lysogenesis was shown to be common in Desulfovibrio. In the 47 genomes analyzed 53 complete prophages were identified. These were classified within the order Caudovirales, with 69.82% belonging to the Myoviridade family. More than half the prophages identified have genes coding for lysozyme or holin. Four of the analyzed bacterial genomes present prophages with identity above 50% in the same strain, whose comparative analysis demonstrated the existence of colinearity between the sequences. Of the 17 closed bacterial genomes analyzed, 6 have the CRISPR-Cas system classified as inactive. The identification of bacterial poly-lysogeny, the proximity between the complete prophages and the possible inactivity of the CRISPR-Cas in closed bacterial genomes analyzed allowed the choice of poly-lysogenic strains with prophages belonging to the Myoviridae family for the isolation of prophages and testing of related strains for subsequent studies.
High-Performance Solid-State Thermionic Energy Conversion Based on 2D van der Waals Heterostructures: A First-Principles Study
Authors: Wang Xiaoming , Zebarjadi Mona , Esfarjani Keivan 
Published: June 2018

AbstractTwo-dimensional (2D) van der Waals heterostructures (vdWHs) have shown multiple functionalities with great potential in electronics and photovoltaics. Here, we show their potential for solid-state thermionic energy conversion and demonstrate a designing strategy towards high-performance devices. We propose two promising thermionic devices, namely, the p-type Pt-G-WSe2-G-Pt and n-type Sc-WSe2-MoSe2-WSe2-Sc. We characterize the thermionic energy conversion performance of the latter using first-principles GW calculations combined with real space Green’s function (GF) formalism. The optimal barrier height and high thermal resistance lead to an excellent performance. The proposed device is found to have a room temperature equivalent figure of merit of 1.2 which increases to 3 above 600 K. A high performance with cooling efficiency over 30% of the Carnot efficiency above 450 K is achieved. Our designing and characterization method can be used to pursue other potential thermionic devices based on vdWHs.
Vector competence of Haemaphysalis longicornis ticks for a Japanese isolate of the Thogoto virus
Authors: Talactac Melbourne Rio , Yoshii Kentaro , Hernandez Emmanuel Pacia , Kusakisako Kodai , Galay Remil Linggatong , Fujisaki Kozo , Mochizuki Masami , Tanaka Tetsuya 
Published: June 2018

AbstractThogoto virus (THOV), a tick-borne arbovirus not previously reported in East Asia, was recently isolated from Haemaphysalis longicornis in Kyoto, Japan. In this study, we investigated the vector competence of H. longicornis ticks for a Japanese isolate of the Thogoto virus using anal pore microinjection and experimental virus acquisition. Our results showed that anal pore microinjection can readily infect adult ticks, and THOV-infected ticks can successfully transmit the virus to mice. Blood feeding was also critical in the distribution of the virus in tick organs, most especially in the salivary glands. Furthermore, co-feeding between an infected adult and naïve nymphs can also produce infected molted adults that can horizontally transmit THOV to mice. Altogether, our results suggest that H. longicornis is a competent vector for the Japanese THOV isolate and could be the primary tick vector of the virus in Japan.
Presymptomatic change in microRNAs modulates Tau pathology
Authors: Sharma Salil , Khadimallah Ines , Corya Adam Williamson , Ali Yousuf Omar , Rao Xi , Liu Yunlong , Lu Hui-Chen 
Published: June 2018

AbstractMicroRNAs (miRs) are 18~23 nucleotides long non-coding RNAs that regulate gene expression. To explore whether miR alterations in tauopathy contribute to pathological conditions, we first determined which hippocampal miRs are altered at the presymptomatic and symptomatic stages of tauopathy using rTg4510 mice (Tau mice), a well-characterized tauopathy model. miR-RNA pairing analysis using QIAGEN Ingenuity Pathway Analysis (IPA) revealed 401 genes that can be regulated by 71 miRs altered in Tau hippocampi at the presymptomatic stage. Among several miRs confirmed with real-time qPCR, miR142 (−3p and −5p) in Tau hippocampi were significantly upregulated by two-weeks of age and onward. Transcriptome studies by RNAseq and IPA revealed several overlapping biological and disease associated pathways affected by either Tau or miR142 overexpression, including Signal Transducer and Activator of Transcription 3 (Stat3) and Tumor Necrosis Factor Receptor 2 (Tnfr2) signaling pathways. Similar to what was observed in Tau brains, overexpressing miR142 in wildtype cortical neurons augments mRNA levels of Glial Fibrillary Acidic Protein (Gfap) and Colony Stimulating Factor 1 (Csf1), accompanied by a significant increase in microglia and reactive astrocyte numbers. Taken together, our study suggests that miR alterations by Tau overexpression may contribute to the neuroinflammation observed in Tau brains.
Probiotic Lactobacillus paracasei A221 improves the functionality and bioavailability of kaempferol-glucoside in kale by its glucosidase activity
Authors: Shimojo Yosuke , Ozawa Yusuke , Toda Toshihiko , Igami Kentaro , Shimizu Takahiko 
Published: June 2018

AbstractThe interplay between food components and gut microbiota has been considered an important factor affecting the functionality of health-promoting foods. In this study, the effects of the probiotic Lactobacillus paracasei A221 on the functionality and bioavailability of kaempferol-3-o-sophroside (KP3S), a kaempferol-glucoside contained in kale, were investigated in vitro and in vivo. Unlike the type strain NBRC15889, the A221 strain converted standard KP3S as well as the kaempferol-glucosides in kale extract into kaempferol (KP). Using an intestinal barrier model, treatment with A221 significantly improved the effects of kale extract on the barrier integrity in vitro. KP, but not KP3S, clearly induced similar effects, suggesting that KP contributes to the functional improvement of the kale extract by A221. Pharmacokinetics analyses revealed that the co-administration of A221 and KP3S significantly enhanced the amount of deconjugated KP in murine plasma samples at 3 h post-administration. Finally, the oral administration of KP to Sod1-deficinet mice, which is a good mouse model of age-related disease, clearly ameliorated various pathologies, including skin thinning, fatty liver and anemia. These findings suggest that Lactobacillus paracasei A221 is effective for enhancing the anti-aging properties of kaempferol-glucosides by modulating their functionality and bioavailability through the direct bioconversion.
Spatio-temporal modelling of weekly malaria incidence in children under 5 for early epidemic detection in Mozambique
Authors: Colborn Kathryn L. , Giorgi Emanuele , Monaghan Andrew J. , Gudo Eduardo , Candrinho Baltazar , Marrufo Tatiana J. , Colborn James M. 
Published: June 2018

AbstractMalaria is a major cause of morbidity and mortality in Mozambique. We present a malaria early warning system (MEWS) for Mozambique informed by seven years of weekly case reports of malaria in children under 5 years of age from 142 districts. A spatio-temporal model was developed based on explanatory climatic variables to map exceedance probabilities, defined as the predictive probability that the relative risk of malaria incidence in a given district for a particular week will exceed a predefined threshold. Unlike most spatially discrete models, our approach accounts for the geographical extent of each district in the derivation of the spatial covariance structure to allow for changes in administrative boundaries over time. The MEWS can thus be used to predict areas that may experience increases in malaria transmission beyond expected levels, early enough so that prevention and response measures can be implemented prior to the onset of outbreaks. The framework we present is also applicable to other climate-sensitive diseases.
Purifying and positive selection in the evolution of stop codons
Authors: Belinky Frida , Babenko Vladimir N. , Rogozin Igor B. , Koonin Eugene V. 
Published: June 2018

AbstractModes of evolution of stop codons in protein-coding genes, especially the conservation of UAA, have been debated for many years. We reconstructed the evolution of stop codons in 40 groups of closely related prokaryotic and eukaryotic genomes. The results indicate that the UAA codons are maintained by purifying selection in all domains of life. In contrast, positive selection appears to drive switches from UAG to other stop codons in prokaryotes but not in eukaryotes. Changes in stop codons are significantly associated with increased substitution frequency immediately downstream of the stop. These positions are otherwise more strongly conserved in evolution compared to sites farther downstream, suggesting that such substitutions are compensatory. Although GC content has a major impact on stop codon frequencies, its contribution to the decreased frequency of UAA differs between bacteria and archaea, presumably, due to differences in their translation termination mechanisms.
Rate of recovery from perturbations as a means to forecast future stability of living systems
Authors: Ghadami Amin , Gourgou Eleni , Epureanu Bogdan I. 
Published: June 2018

AbstractAnticipating critical transitions in complex ecological and living systems is an important need because it is often difficult to restore a system to its pre-transition state once the transition occurs. Recent studies demonstrate that several indicators based on changes in ecological time series can indicate that the system is approaching an impending transition. An exciting question is, however, whether we can predict more characteristics of the future system stability using measurements taken away from the transition. We address this question by introducing a model-less forecasting method to forecast catastrophic transition of an experimental ecological system. The experiment is based on the dynamics of a yeast population, which is known to exhibit a catastrophic transition as the environment deteriorates. By measuring the system’s response to perturbations prior to transition, we forecast the distance to the upcoming transition, the type of the transition (i.e., catastrophic/non-catastrophic) and the future equilibrium points within a range near the transition. Experimental results suggest a strong potential for practical applicability of this approach for ecological systems which are at risk of catastrophic transitions, where there is a pressing need for information about upcoming thresholds.
PTPRS Regulates Colorectal Cancer RAS Pathway Activity by Inactivating Erk and Preventing Its Nuclear Translocation
Authors: Davis Thomas B. , Yang Mingli , Schell Michael J. , Wang Heiman , Ma Le , Pledger W. Jack , Yeatman Timothy J. 
Published: June 2018

AbstractColorectal cancer (CRC) growth and progression is frequently driven by RAS pathway activation through upstream growth factor receptor activation or through mutational activation of KRAS or BRAF. Here we describe an additional mechanism by which the RAS pathway may be modulated in CRC. PTPRS, a receptor-type protein tyrosine phosphatase, appears to regulate RAS pathway activation through ERK. PTPRS modulates ERK phosphorylation and subsequent translocation to the nucleus. Native mutations in PTPRS, present in ~10% of CRC, may reduce its phosphatase activity while increasing ERK activation and downstream transcriptional signaling.
The strategies and outcomes of left subclavian artery revascularization during thoracic endovascular repair for type B aortic dissection
Authors: Xiang Yuwei , Huang Bin , Zhao Jichun , Hu Hankui , Yuan Ding , Yang Yi 
Published: June 2018

AbstractThis study was to analyze the outcomes of left subclavian artery (LSA) revascularization during thoracic endovascular repair (TEVAR) for type B aortic dissections (TBAD). From 2011 to 2017, TBAD patients who underwent LSA revascularization during TEVAR were enrolled. Technical success, endoleaks, mortality, complication, reintervention, and patency of target vessels were analyzed. 38 patients were included, 14 underwent carotid-subclavian bypass (CSB), and 24 underwent chimney graft (CG) implantation. Technical success rates were 92.9% and 100% in CSB and CG group. Eleven immediate type I endoleak (EL-I) was detected, including one from CSB group and ten from CG group. Three immediate type II endoleak (EL-II) was detected in CSB group. Perioperative complications showed no difference, but CSB group had longer intensive care unit (ICU) stay time. Median follow-up time was 26.2 months, and overall mortality was 14.3% and 0% in each group. Three EL-I and one EL-II underwent reintervention. All the LSA showed good patency, except one suffered from CG collapse. Both CSB and CG were feasible strategies to preserve the antegrade blood flow of LSA, and each strategy had its advantages and disadvantages. Based on our current experience, we preferred CG for high-risk patients. However, the evidence was still not strong enough, further well-designed studies are necessary to identify the criteria for LSA revascularization strategy during TEVAR.
Controlling the impact of the managed honeybee on wild bees in protected areas
Authors: Henry Mickaël , Rodet Guy 
Published: June 2018

AbstractIn recent years, conservation biologists have raised awareness about the risk of ecological interference between massively introduced managed honeybees and the native wild bee fauna in protected natural areas. In this study, we surveyed wild bees and quantified their nectar and pollen foraging success in a rosemary Mediterranean scrubland in southern France, under different conditions of apiary size and proximity. We found that high-density beekeeping triggers foraging competition which depresses not only the occurrence (−55%) and nectar foraging success (−50%) of local wild bees but also nectar (−44%) and pollen (−36%) harvesting by the honeybees themselves. Overall, those competition effects spanned distances of 600–1.100 m around apiaries, i.e. covering 1.1–3.8km2 areas. Regardless the considered competition criterion, setting distance thresholds among apiaries appeared more tractable than setting colony density thresholds for beekeeping regulation. Moreover, the intraspecific competition among the honeybees has practical implications for beekeepers. It shows that the local carrying capacity has been exceeded and raises concerns for honey yields and colony sustainability. It also offers an effective ecological criterion for pragmatic decision-making whenever conservation practitioners envision progressively reducing beekeeping in protected areas. Although specific to the studied area, the recommendations provided here may help raise consciousness about the threat high-density beekeeping may pose to local nature conservation initiatives, especially in areas with sensitive or endangered plant or bee species such as small oceanic islands with high levels of endemism.
Directional emission of plastic luminescent films using photonic crystals fabricated by soft-X-ray interference lithography and reactive ion etching
Authors: Wu Qiang , Liu Bo , Zhu Zhichao , Gu Mu , Chen Hong , Xue Chaofan , Zhao Jun , Wu Yanqing , Tai Renzhong , Ouyang Xiaoping 
Published: June 2018

AbstractIn this report, a novel method to prepare photonic crystals based on the combination of soft-X-ray interference lithography (XIL) and reactive ion etching (RIE) with a bi-layer photoresist system was developed. XIL can be utilized to prepare periodic structures with high efficiency but the depth of etch is limited due to the strong absorption of photoresist for soft-X-ray. Based on the pattern prepared by XIL, RIE can be utilized to further etch a second layer of photoresist, so that one can obtain a large depth of etch. Controlling the dispersion relation of the prepared photonic crystals, strongly directional emission of plastic luminescent films was demonstrated. A wavelength-integrated enhancement of 2.64-folds enhancement in the range of 420 to 440 nm in the normal direction was obtained. Guided-mode resonance and Fabry-Perot resonance could be the critical factors to control the directional emission. Devices based on directional emission films have a variety of applications in such as detectors, optical communication and display screens.
Tunability of p- and n-channel TiOx thin film transistors
Authors: Peng Wu-Chang , Chen Yao-Ching , He Ju-Liang , Ou Sin-Liang , Horng Ray-Hua , Wuu Dong-Sing 
Published: June 2018

AbstractTo acquire device-quality TiOx films usually needs high-temperature growth or additional post-thermal treatment. However, both processes make it very difficult to form the p-type TiOx even under oxygen-poor growth condition. With the aid of high energy generated by high power impulse magnetron sputtering (HIPIMS), a highly stable p-type TiOx film with good quality can be achieved. In this research, by varying the oxygen flow rate, p-type γ-TiO and n-type TiO2 films were both prepared by HIPIMS. Furthermore, p- and n-type thin film transistors employing γ-TiO and TiO2 as channel layers possess the field-effect carrier mobilities of 0.2 and 0.7 cm2/Vs, while their on/off current ratios are 1.7 × 104 and 2.5 × 105, respectively. The first presented p-type γ-TiO TFT is a major breakthrough for fabricating the TiOx-based p-n combinational devices. Additionally, our work also confirms HIPIMS offers the possibility of growing both p- and n-type conductive oxides, significantly expanding the practical usage of this technique.
Climatic influence on anthrax suitability in warming northern latitudes
Authors: Walsh Michael G. , de Smalen Allard W. , Mor Siobhan M. 
Published: June 2018

AbstractClimate change is impacting ecosystem structure and function, with potentially drastic downstream effects on human and animal health. Emerging zoonotic diseases are expected to be particularly vulnerable to climate and biodiversity disturbance. Anthrax is an archetypal zoonosis that manifests its most significant burden on vulnerable pastoralist communities. The current study sought to investigate the influence of temperature increases on geographic anthrax suitability in the temperate, boreal, and arctic North, where observed climate impact has been rapid. This study also explored the influence of climate relative to more traditional factors, such as livestock distribution, ungulate biodiversity, and soil-water balance, in demarcating risk. Machine learning was used to model anthrax suitability in northern latitudes. The model identified climate, livestock density and wild ungulate species richness as the most influential features in predicting suitability. These findings highlight the significance of warming temperatures for anthrax ecology in northern latitudes, and suggest potential mitigating effects of interventions targeting megafauna biodiversity conservation in grassland ecosystems, and animal health promotion among small to midsize livestock herds.
The association between TNFR gene polymorphisms and the risk of Hepatitis B Virus-Related Liver Diseases in Chinese population
Authors: Ma Liping , Chen Siyuan , Mao Xiaohuan , Lu Yu , Zhang Xiaolian , Lao Xianjun , Qin Xue , Li Shan 
Published: June 2018

AbstractTumor necrosis factor receptor superfamily 2 (TNFR2) plays an important role in controlling the progression of antiviral and antitumorr. Evidence suggests that TNFR2 is involved in the pathogenesis of HBV-induced liver injury. We therefore examined whether TNFR2 polymorphisms are associated with the risk of HBV-related liver disease in Chinese population. In this case-control study, 115 chronic hepatitis B (CHB) patients, 86 HBV-related liver cirrhosis patients (LC), 272 HBV-related hepatocellular carcinoma patients (HCC) and 269 healthy controls were recruited. TNFR2 rs1061622 and rs1061624 polymorphisms were examined using a polymerase chain reaction-restriction fragment length polymorphism analysis. Binary logistic regression analyses revealed that the A allele of rs1061624 was positively associated with the risk of CHB (AA vs. GG, P = 0.026; AA vs. GA+GG, P = 0.021), LC (AA vs. GG, P = 0.027; AA+GA vs. GG, P = 0.036), and HCC (GA vs. GG, P = 0.046; GA+AA vs. GG, P = 0.031). Moreover, subgroup analysis indicated that male subjects have increased risk in developing CHB and LC. Nevertheless, no association was found between rs1061622 polymorphism and HBV-related liver diseases in the overall or subgroup analyses. Our retrospective study suggests that the TNFR2 rs1061624 polymorphism is associated with HBV-related CHB, LC, and HCC in Chinese population, particularly in males.
Global patterns of human and livestock respiration
Authors: Cai Qixiang , Yan Xiaodong , Li Yafei , Wang Leibin 
Published: June 2018

AbstractCarbon emissions from human and animals has been neglected by previous studies in estimating the carbon cycle of ecosystem. This study first estimates the spatial-temporal patterns of carbon emissions density from human and livestock respiration among countries around the world from 1960–2014. Then we simulate the soil heterotrophic respiration (Rh) to analyze the contribution of human and livestock respiration to total heterotrophic respiration of global ecosystem. Our results show that the respiration of human and livestock respectively contribute more than 1% of the total carbon output from heterotrophic respiration in most countries and affect more than 5% in almost half of the countries. Moreover, the effect of livestock respiration is slightly greater than that of human beings. Therefore, the estimation of heterotrophic respiration should not only consider Rh in these countries, human and livestock respiration are equally important in the research on regional carbon budget.
In-situ, time resolved monitoring of uranium in BFS:OPC grout. Part 2: Corrosion in water
Authors: Stitt C. A. , Paraskevoulakos C. , Banos A. , Harker N. J. , Hallam K. R. , Pullin H. , Davenport A. , Street S. , Scott T. B. 
Published: June 2018

AbstractTo reflect potential conditions in a geological disposal facility, uranium was encapsulated in grout and submersed in de-ionised water for time periods between 2–47 weeks. Synchrotron X-ray Powder Diffraction and X-ray Tomography were used to identify the dominant corrosion products and measure their dimensions. Uranium dioxide was observed as the dominant corrosion product and time dependent thickness measurements were used to calculate oxidation rates. The effectiveness of physical and chemical grout properties to uranium corrosion and mobilisation is discussed and Inductively Coupled Plasma Mass Spectrometry was used to measure 238U(aq) content in the residual water of several samples.