bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scrapie susceptibility-associated indel polymorphism of shadow of prion protein gene (SPRN) in Korean native black goats
Authors: Kim Yong-Chan , Kim Seon-Kwan , Jeong Byung-Hoon 
Published: October 2019

AbstractPrion diseases in sheep and goats are called scrapie and belong to a group of transmissible spongiform encephalopathies (TSEs) caused by the abnormal misfolding of the prion protein encoded by the prion protein gene (PRNP). The shadow of the prion protein gene (SPRN) is the only prion gene family member that shows a protein expression profile similar to that of the PRNP gene in the central nervous system. In addition, genetic susceptibility of the SPRN gene has been reported in variant Creutzfeldt–Jakob disease (CJD), bovine spongiform encephalopathy (BSE) and scrapie. However, genetic studies of the SPRN gene have not been carried out in Korean native black goats. Here, we investigated the genotype and allele frequencies of SPRN polymorphisms in 213 Korean native black goats and compared these polymorphisms with those previously reported for scrapie-affected animals. We found a total of 6 polymorphisms including 1 nonsynonymous single nucleotide polymorphism (SNP) and 1 synonymous SNP in the open reading frame (ORF) region and 3 SNPs and 1 indel polymorphism (c.495_496insCTCCC) in the 3′ untranslated region (UTR) by direct DNA sequencing. A significant difference in the allele frequency of the c.495_496insCTCCC indel polymorphism was found between the Italian scrapie-affected goats and the Korean native black goats (P < 0.001). Furthermore, there was a significant difference in the allele frequencies of the c.495_496insCTCCC indel polymorphism between Italian healthy goats and Korean native black goats (P < 0.001). To evaluate the biological impact of the novel nonsynonymous SNP c.416G > A (Arg139Gln), we carried out PROVEAN analysis. PROVEAN predicted the SNP as ‘Neutral’ with a score of −0.297. To the best of our knowledge, this is the first genetic study of the SPRN gene in Korean native black goats.
Predicting the Dispersion Relations of One-Dimensional Phononic Crystals by Neural Networks
Authors: Liu Chen-Xu , Yu Gui-Lan 
Published: October 2019

AbstractIn this paper, deep back propagation neural networks (DBP-NNs) and radial basis function neural networks (RBF-NNs) are employed to predict the dispersion relations (DRs) of one-dimensional (1D) phononic crystals (PCs). The data sets generated by transfer matrix method (TMM) are used to train the NNs and detect their prediction accuracy. In our work, filling fractions, mass density ratios and shear modulus ratios of PCs are considered as the input values of NNs. The results show that both the DBP-NNs and the RBF-NNs exhibit good performances in predicting the DRs of PCs. For one-parameter prediction, the RBF-NNs have shorter training time and remarkable prediction accuracy, for two- and three-parameter prediction, the DBP-NNs have more stable performance. The present work confirms the feasibility of predicting the DRs of PCs by NNs, and provides a useful reference for the application of NNs in the design of PCs and metamaterials.
Slow freezing versus vitrification for the cryopreservation of zebrafish (Danio rerio) ovarian tissue
Authors: Marques Lis S. , Fossati Ana A. N. , Rodrigues Rômulo B. , Da Rosa Helen T. , Izaguirry Aryele P. , Ramalho Juliana B. , Moreira José C. F. , Santos Francielli Weber , Zhang Tiantian , Streit Danilo P. 
Published: October 2019

AbstractThe aim of the present study was to compare the efficiency of vitrification and slow freezing techniques for the cryopreservation of zebrafish ovarian tissue containing immature follicles. In Experiment 1, assessment of cell membrane integrity by trypan blue exclusion staining was used to select the best cryoprotectant solution for each cryopreservation method. Primary growth (PG) oocytes showed the best percentage of membrane integrity (63.5 ± 2.99%) when SF4 solution (2 M methanol + 0.1 M trehalose + 10% egg yolk solution) was employed. The vitrification solution, which presented the highest membrane integrity (V2; 1.5 M methanol + 5.5 M Me2SO + 0.5 M sucrose + 10% egg yolk solution) was selected for Experiment 2. Experiment 2 aimed to compare the vitrification and slow freezing techniques in the following parameters: morphology, oxidative stress, mitochondrial activity, and DNA damage. Frozen ovarian tissue showed higher ROS levels and lower mitochondrial activity than vitrified ovarian tissue. Ultrastructural observations of frozen PG oocytes showed rupture of the plasma membrane, loss of intracellular contents and a large number of damaged mitochondria, while vitrified PG oocytes had intact mitochondria and cell plasma membranes. We conclude that vitrification may be more effective than slow freezing for the cryopreservation of zebrafish ovarian tissue.
Mayaro Virus Induction of Oxidative Stress is Associated With Liver Pathology in a Non-Lethal Mouse Model
Authors: da Silva Caetano Camila Carla , Camini Fernanda Caetano , Almeida Letícia Trindade , Ferraz Ariane Coelho , da Silva Tales Fernando , Lima Rafaela Lameira Souza , de Freitas Carvalho Mayara Medeiros , de Freitas Castro Thalles , Carneiro Cláudia Martins , de Mello Silva Breno , de Queiroz Silva Silvana , de Magalhães José Carlos , de Brito Magalhães Cintia Lopes 
Published: October 2019

AbstractMayaro virus (MAYV) causes Mayaro fever in humans, a self-limiting acute disease, with persistent arthralgia and arthritis. Although MAYV has a remerging potential, its pathogenic mechanisms remain unclear. Here, we characterized a model of MAYV infection in 3–4-week BALB/c mice. We investigated whether the liver acts as a site of viral replication and if the infection could cause histopathological alterations and an imbalance in redox homeostasis, culminating with oxidative stress. MAYV-infected mice revealed lower weight gain; however, the disease was self-resolving. High virus titre, neutralizing antibodies, and increased levels of aspartate and alanine aminotransferases were detected in the serum. Infectious viral particles were recovered in the liver of infected animals and the histological examination of liver tissues revealed significant increase in the inflammatory infiltrate. MAYV induced significant oxidative stress in the liver of infected animals, as well as a deregulation of enzymatic antioxidant components. Collectively, this is the first study to report that oxidative stress occurs in MAYV infection in vivo, and that it may be crucial in virus pathogenesis. Future studies are warranted to address the alternative therapeutic strategies for Mayaro fever, such as those based on antioxidant compounds.
Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii
Authors: Nardini Luisa , Holm Inge , Pain Adrien , Bischoff Emmanuel , Gohl Daryl M. , Zongo Soumanaba , Guelbeogo Wamdaogo M. , Sagnon N’Fale , Vernick Kenneth D. , Riehle Michelle M. 
Published: October 2019

AbstractEnhancers are cis-regulatory elements that control most of the developmental and spatial gene expression in eukaryotes. Genetic variation of enhancer sequences is known to influence phenotypes, but the effect of enhancer variation upon enhancer functional activity and downstream phenotypes has barely been examined in any species. In the African malaria vector, Anopheles coluzzii, we identified candidate enhancers in the proximity of genes relevant for immunity, insecticide resistance, and development. The candidate enhancers were functionally validated using luciferase reporter assays, and their activity was found to be essentially independent of their physical orientation, a typical property of enhancers. All of the enhancers segregated genetically polymorphic alleles, which displayed significantly different levels of functional activity. Deletion mutagenesis and functional testing revealed a fine structure of positive and negative regulatory elements that modulate activity of the enhancer core. Enhancer polymorphisms segregate in wild A. coluzzii populations in West Africa. Thus, enhancer variants that modify target gene expression leading to likely phenotypic consequences are frequent in nature. These results demonstrate the existence of naturally polymorphic A. coluzzii enhancers, which may help explain important differences between individuals or populations for malaria transmission efficiency and vector adaptation to the environment.
Occurence of microplastics in the hyporheic zone of rivers
Authors: Frei S. , Piehl S. , Gilfedder B. S. , Löder M. G. J. , Krutzke J. , Wilhelm L. , Laforsch C. 
Published: October 2019

AbstractAlthough recent studies indicate that fluvial systems can be accumulation areas for microplastics (MPs), the common perception still treats rivers and streams primarily as pure transport vectors for MPs. In this study we investigate the occurrence of MPs in a yet unnoticed but essential compartment of fluvial ecosystems - the hyporheic zone (HZ). Larger MP particles (500–5,000 µm) were detected using attenuated total reflectance (ATR) - Fourier-transform infrared (FTIR) spectroscopy. Our analysis of MPs (500–5,000 µm) in five freeze cores extracted for the Roter Main River sediments (Germany) showed that MPs were detectable down to a depth of 0.6 m below the streambed in low abundances (≪1 particle per kg dry weight). Additionally, one core was analyzed as an example for smaller MPs (20–500 µm) with focal plane array (FPA)- based µFTIR spectroscopy. Highest MP abundances (~30,000 particles per kg dry weight) were measured for pore scale particles (20–50 µm). The detected high abundances indicate that the HZ can be a significant accumulation area for pore scale MPs (20–50 µm), a size fraction that yet is not considered in literature. As the HZ is known as an important habitat for invertebrates representing the base of riverine food webs, aquatic food webs can potentially be threatened by the presence of MPs in the HZ. Hyporheic exchange is discussed as a potential mechanism leading to a transfer of pore scale MPs from surface flow into streambed sediments and as a potential vector for small MPs to enter the local aquifer. MPs in the HZ therefore may be a potential risk for drinking water supplies, particularly during drinking water production via river bank filtration.
Characterization, expression profiling, and functional analysis of a Populus trichocarpa defensin gene and its potential as an anti-Agrobacterium rooting medium additive
Authors: Wei Hui , Movahedi Ali , Xu Chen , Sun Weibo , Li Lingling , Li Dawei , Zhuge Qiang 
Published: October 2019

AbstractThe diverse antimicrobial properties of defensins have attracted wide scientific interest in recent years. Also, antimicrobial peptides (AMPs), including cecropins, histatins, defensins, and cathelicidins, have recently become an antimicrobial research hotspot for their broad-spectrum antibacterial and antifungal activities. In addition, defensins play important roles in plant growth, development, and physiological metabolism, and demonstrate tissue specificity and regulation in response to pathogen attack or abiotic stress. In this study, we performed molecular cloning, characterization, expression profiling, and functional analysis of a defensin from Populus trichocarpa. The PtDef protein was highly expressed in the prokaryotic Escherichia coli system as a fusion protein (TrxA–PtDef). The purified protein exhibited strong antibacterial and antifungal functions. We then applied PtDef to rooting culture medium as an alternative exogenous additive to cefotaxime. PtDef expression levels increased significantly following both biotic and abiotic treatment. The degree of leaf damage observed in wild-type (WT) and transgenic poplars indicates that transgenic poplars that overexpress the PtDef gene gain enhanced disease resistance to Septotis populiperda. To further study the salicylic acid (SA) and jasmonic acid (JA) signal transduction pathways, SA- and JA-related and pathogenesis-related genes were analyzed using quantitative reverse-transcription polymerase chain reaction; there were significant differences in these pathways between transgenic and WT poplars. The defensin from Populus trichocarpa showed significant activity of anti-bacteria and anti-fungi. According to the results of qRT-PCR and physiological relevant indicators, the applied PtDef to rooting culture medium was chosen as an alternative exogenous additive to cefotaxime. Overexpressing the PtDef gene in poplar improve the disease resistance to Septotis populiperda.
The whole-genome sequence analysis of Morchella sextelata
Authors: Mei-Han  , Qingshan-Wang  , Baiyintala  , Wuhanqimuge  
Published: October 2019

AbstractMorchella are macrofungi and are also called morels, as they exhibit a morel-like upper cap structure. Morels contain abundant essential amino acids, vitamins and biologically active compounds, which provide substantial health benefits. Approximately 80 species of Morchella have been reported, and even more species have been isolated. However, the lack of wild Morchella resources and the difficulties associated with culturing Morchella have caused a shortage in the morels available for daily consumption. Additionally, in-depth genomic and morphological studies are still needed. In this study, to provide genomic data for further investigations of culturing techniques and the biological functions of Morchella sextelata (M. sextelata), de novo genome sequencing was carried out on the Illumina HiSeq. 4000 platform using both the Illumina 150 and PacBio systems. The final estimated genome size of M. sextelata was 52.93 Mb, containing 59 contigs and a GC content of 47.37%. A total of 9,550 protein-coding genes were annotated. In addition, the repeat sequences, gene components and gene functions were analyzed using various databases. Furthermore, the secondary metabolite gene clusters and the predicted structures of their products were analyzed. Finally, a genomic comparison of different species of Morchella was performed.
Extracellular adenosine triphosphate is associated with airflow limitation severity and symptoms burden in patients with chronic obstructive pulmonary disease
Authors: Hlapčić Iva , Hulina-Tomašković Andrea , Somborac-Bačura Anita , Rajković Marija Grdić , Dugac Andrea Vukić , Popović-Grle Sanja , Rumora Lada 
Published: October 2019

AbstractExtracellular adenosine triphosphate (eATP)-driven inflammation was observed in chronic obstructive pulmonary disease (COPD) but was not investigated in patients’ blood. Therefore, this study aimed to investigate eATP concentration in plasma of COPD patients and its association with disease severity and smoking. Study included 137 patients with stable COPD and 95 control subjects. eATP concentration was determined in EDTA plasma by luminometric method, and mRNA expression of eATP receptors P2X7R and P2Y2R was analysed by quantitative polymerase chain reaction (qPCR). eATP concentration was increased in COPD patients compared to controls (P < 0.001). Moreover, it was increasing with disease severity (GOLD 2–4) as well as symptoms burden and exacerbations history (GOLD A–D) (P < 0.05). eATP in healthy smokers differed from healthy non-smokers (P < 0.05) but was similar to GOLD 2 and GOLD A patients. eATP showed great diagnostic performances (OR = 12.98, P < 0.001) and correctly classified 79% of study participants. It demonstrated association with FEV1 and multicomponent indices (ADO, BODEx, BODCAT, CODEx, DOSE). Regarding gene expression, P2Y2R was increased in the blood of COPD patients. Plasma eATP could become a diagnostic and/or prognostic biomarker in COPD, as it seems to be associated with patients’ condition, quality of life and disease progression.
Influence of Pichia pastoris X-33 produced in industrial residues on productive performance, egg quality, immunity, and intestinal morphometry in quails
Authors: Gaboardi Giana Carla , Alves Débora , Gil de los Santos Diego , Xavier Eduardo , Nunes Ana Paula , Finger Paula , Griep Emili , Roll Victor , Oliveira Patrícia , Silva Arthur , Moreira Ângela , Conceição Fabricio 
Published: October 2019

AbstractThis study was conducted in quails to evaluate the probiotic potential of Pichia pastoris X-33, cultivated in parboiled rice effluent supplemented with biodiesel glycerol or in standard medium Yeast Extract–Peptone–Dextrose (YPD). Forty-days-old female quails were divided into three treatments: T1 (Control) received a basal diet without P. pastoris; T2 (Pichia Effluent) received a basal diet supplemented with P. pastoris grown in parboiled rice effluent and biodiesel glycerol, and T3 (Pichia YPD) received a basal diet supplemented with P. pastoris produced in YPD. The birds were vaccinated against Newcastle Disease (NDV), Avian Infectious Bronchitis (IBV), and Gumboro Disease on days 1 and 28. The following parameters were analyzed: performance, egg quality, humoral immune response to the vaccines, organ weight, and intestinal morphometry. P. pastoris grown in YPD increased egg weight (p < 0.05). The lowest liver weight on day 14 was obtained in Pichia Effluent, whereas both P. pastoris supplemented groups had the lowest duodenum weights on day 14. Besides that, livers and duodenums presented no morphological changes in any of the three treatments. Supplementation of P. pastoris modulated the immune system of the birds, increasing anti-IBV, anti-NDV, and anti-Gumboro antibodies levels compared to the Control (p < 0.05). In conclusion, quail’s immune response was improved by Pichia pastoris X-33, either it was grown in YPD or industrial residues, and the egg weight increased with Pichia pastoris X-33 grown in YPD, thereby demonstrating to be a promising probiotic for poultry.
Efficacy and tolerability of granulocyte colony-stimulating factors in cancer patients after chemotherapy: A systematic review and Bayesian network meta-analysis
Authors: Wang Yong , Chen Lin , Liu Fen , Zhao Ning , Xu Liyao , Fu Biqi , Li Yong 
Published: October 2019

AbstractThe optimum granulocyte colony-stimulating factor (G-CSF) treatment for cancer patients after being treated with cytotoxic chemotherapy remains unknown. Therefore, a systematic review and Bayesian network meta-analysis were performed to assess the efficacy and tolerability of 11 G-CSF drugs on patients after chemotherapy. A total of 73 randomized controlled trials (RCTs) containing 15,124 cancer patients were included for the final network meta-analysis. Compared with pegfilgrastim, there were a higher risk with filgrastim for incidence of febrile neutropenia (FN) (OR [95% CI]: 1.63 [1.07, 2.46]), and a higher risk with short-acting G-CSF (S-G-CSF) biosimilar and lenograstim for incidence of bone pain (BP) (OR [95% CI]: 6.45 [1.10, 65.73], 5.12 [1.14, 26.12], respectively). Mecapegfilgrastim, lipegfilgrastim and balugrastim were best G-CSF drugs in reducing FN (cumulative probabilities: 58%, 15%, 11%, respectively). S-G-CSF biosimilar, empegfilgrastim, and long-acting G-CSF (L-G-CSF) biosimilar were best G-CSF drugs in reducing severe neutropenia (SN) (cumulative probabilities: 21%, 20%, 15%, respectively). Mecapegfilgrastim, balugrastim, lipegfilgrastim and L-G-CSF biosimilar were best G-CSF drugs in reducing BP (cumulative probabilities: 20%, 14%, 8%, 8%, respectively). Mecapegfilgrastim, lipegfilgrastim and balugrastim might be the most appreciate G-CSF drugs with both good efficacy and tolerability when treating cancer patients after cytotoxic chemotherapy.
Urban warming and future air-conditioning use in an Asian megacity: importance of positive feedback
Authors: Takane Yuya , Kikegawa Yukihiro , Hara Masayuki , Grimmond C. Sue B. 
Published: October 2019

AbstractThe impact of feedback between urban warming and air-conditioning (AC) use on temperatures in future urban climates is explored in this study. Pseudo-global warming projections are dynamically downscaled to 1 km using a regional climate model (RCM) coupled to urban canopy and building energy models for current and six future global warming (ΔTGW) climates based on IPCC RCP8.5. Anthropogenic heat emissions from AC use is projected to increase almost linearly with ΔTGW, causing additional urban warming. This feedback on urban warming reaches 20% of ΔTGW in residential areas. This further uncertainty in future projections is comparable in size to that associated with: a selection of emission scenarios, RCMs, and urban planning scenarios. Thus this feedback should not be neglected in future urban climate projections, especially in hot cities with large AC use. The impact of the feedback during the July 2018 Japanese heat waves is calculated to be 0.11 °C.
Voltage fade mitigation in the cationic dominant lithium-rich NCM cathode
Authors: Chandan Prem , Chang Chung-Chieh , Yeh Kuo-Wei , Chiu Chui-Chang , Wu Dong-Ze , Huang Tzu-Wen , Wu Phillip M. , Chi Po-Wei , Hsu Wei-Fan , Su Kai-Han , Lee Yu-Wen , Chang Hua-Shu , Wang Ming-Jye , Wu Heng-Liang , Tang Horng-Yi , Wu Maw-Kuen 
Published: October 2019

AbstractIn the archetypal lithium-rich cathode compound Li1.2Ni0.13Co0.13Mn0.54O2, a major part of the capacity is contributed from the anionic (O2−/−) reversible redox couple and is accompanied by the transition metal ions migration with a detrimental voltage fade. A better understanding of these mutual interactions demands for a new model that helps to unfold the occurrences of voltage fade in lithium-rich system. Here we present an alternative approach, a cationic reaction dominated lithium-rich material Li1.083Ni0.333Co0.083Mn0.5O2, with reduced lithium content to modify the initial band structure, hence ~80% and ~20% of capacity are contributed by cationic and anionic redox couples, individually. A 400 cycle test with 85% capacity retention depicts the capacity loss mainly arises from the metal ions dissolution. The voltage fade usually from Mn4+/Mn3+ and/or On−/O2− reduction at around 2.5/3.0 V seen in the typical lithium-rich materials is completely eliminated in the cationic dominated cathode material.
Non-hermitian topology as a unifying framework for the Andreev versus Majorana states controversy
Authors: Avila J. , Peñaranda F. , Prada E. , San-Jose P. , Aguado R. 
Published: October 2019

AbstractZero-energy Andreev levels in hybrid semiconductor-superconductor nanowires mimic all expected Majorana phenomenology, including $$2{e}^{2}/h$$
2

e

2

∕
h
conductance quantisation, even where band topology predicts trivial phases. This surprising fact has been used to challenge the interpretation of various transport experiments in terms of Majorana zero modes. Here we show that the Andreev versus Majorana controversy is clarified when framed in the language of non-Hermitian topology, the natural description for quantum systems open to the environment. This change of paradigm allows one to understand topological transitions and the emergence of zero modes in more general systems than can be described by band topology. This is achieved by studying exceptional point bifurcations in the complex spectrum of the system’s non-Hermitian Hamiltonian. Within this broader topological classification, Majoranas from both conventional band topology and a large subset of Andreev levels at zero energy are in fact topologically equivalent, which explains why they cannot be distinguished.
Multiple scattering theory of non-Hermitian sonic second-order topological insulators
Authors: Rosendo López María , Zhang Zhiwang , Torrent Daniel , Christensen Johan 
Published: October 2019

AbstractTopological phases of sound enable unconventional confinement of acoustic energy at the corners in higher-order topological insulators. These unique states which go beyond the conventional bulk-boundary correspondence have recently been extended to non-Hermitian wave physics comprising finite crystal structures including loss and gain units. We use a multiple scattering theory to calculate these topologically trapped complex states that agree very well to finite element predictions. Moreover, our semi-numerical tool allows us to compute the spectral dependence of corner states in the presence of defects, illustrating the limits of the topological resilience of these confined non-Hermitian acoustic states.