bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi
Authors: Zhang Ning , Cai Guohong , Price Dana C. , Crouch Jo Anne , Gladieux Pierre , Hillman Bradley , Khang Chang Hyun , LeBrun Marc-Henri , Lee Yong-Hwan , Luo Jing , Qiu Huan , Veltri Daniel , Wisecaver Jennifer H. , Zhu Jie , Bhattacharya Debashish 
Published: April 2018

AbstractThe rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.
Pretreatment rate of decay in forced vital capacity predicts long-term response to pirfenidone in patients with idiopathic pulmonary fibrosis
Authors: Biondini Davide , Balestro Elisabetta , Lacedonia Donato , Cerri Stefania , Milaneschi Rosanna , Luppi Fabrizio , Cocconcelli Elisabetta , Bazzan Erica , Clini Enrico , Foschino Barbaro Maria Pia , Gregori Dario , Cosio Manuel G , Saetta Marina , Spagnolo Paolo 
Published: April 2018

AbstractPirfenidone reduces functional decline in patients with Idiopathic Pulmonary Fibrosis (IPF). However, response to treatment is highly heterogeneous. We sought to evaluate whether response to pirfenidone is influenced by the pretreatment rate of forced vital capacity (FVC) decline. Fifty-six IPF patients were categorized as rapid (RP) or slow progressors (SP) based on whether their FVC decline in the year preceding pirfenidone treatment was > or ≤ 10% predicted. Following pirfenidone treatment patients were followed-up every 6 months and up to 24 months. In the entire population, pirfenidone reduced significantly FVC decline from 231 to 49 ml/year at 6 months (T6) (p = 0.003) and this effect was maintained at the 12-, 18- and 24-month time points (p value for trend n.s.). In RP, the reduction of FVC decline was evident at 6 months (36 vs 706 ml/year pretreatment; p = 0.002) and maintained, though to a lesser degree, at 12 (106 ml/year), 18 (176 ml/year) and 24 months (162 ml/year; p value for trend n.s). Among SP, the reduction in FVC decline was not significant at any of the time points analyzed. In conclusion, pirfenidone reduces FVC decline in IPF patients. However, its beneficial effect is more pronounced in patients with rapidly progressive disease.
piRNA-like small RNAs are responsible for the maternal-specific knockdown in the ascidian Ciona intestinalis Type A
Authors: Satoh Teruki , Iitsuka Takako , Shiraishi Akira , Hozumi Akiko , Satake Honoo , Sasakura Yasunori 
Published: April 2018

AbstractThe mRNAs stored in eggs are crucial for embryogenesis. To address functions of maternal mRNAs, we recently reported the novel method MASK (maternal mRNA-specific knockdown), which we used to specifically knockdown maternal transcripts in the ascidian Ciona intestinalis Type A. In MASK, the cis element of a maternal gene is fused with eGFP or Kaede reporter gene, and the cassette is introduced into Ciona genome by transposon-mediated transgenesis. In eggs of the transgenic lines, the maternal expression of the gene whose cis element is used for driving the reporter gene is suppressed. The zygotic expression of the gene is not suppressed, suggesting that the MASK method can distinguish between maternal and zygotic functions of a gene. Here we investigated the cis and trans factors responsible for MASK results. In the ovaries in which knockdown of a maternal gene occurs, a number of antisense small RNAs are expressed that are complementary to the sequence of the knocked-down genes. We suspect that these antisense small RNAs are the factor responsible for MASK results. The antisense small RNAs have several features that are seen in PIWI-interacting RNAs (piRNAs), suggesting that MASK is likely to use a piRNA-mediated mechanism to knock down maternal mRNAs.
A fast and cost-effective method for apolipoprotein E isotyping as an alternative to APOE genotyping for patient screening and stratification
Authors: Calero Olga , García-Albert Luis , Rodríguez-Martín Andrés , Veiga Sergio , Calero Miguel 
Published: April 2018

AbstractApolipoprotein E (apoE) is a 34 kDa glycoprotein involved in lipid metabolism. The human APOE gene encodes for three different apoE protein isoforms: E2, E3 and E4. The interest in apoE isoforms is high for epidemiological research, patient stratification and identification of those at increased risk for clinical trials and prevention. The isoform apoE4 is associated with increased risk for coronary heart and Alzheimer’s diseases. This paper describes a method for specifically detecting the apoE4 isoform from biological fluids by taking advantage of the capacity of apoE to bind “specifically” to polystyrene surfaces as capture and a specific anti-apoE4 monoclonal antibody as reporter. Our results indicate that the apoE-polystyrene binding interaction is highly stable, resistant to detergents and acid and basic washes. The methodology here described is accurate, easily implementable, fast and cost-effective. Although at present, our technique is unable to discriminate homozygous APOE ε4/ε4 from APOE ε3/ε4 and ε2/ε4 heterozygous, it opens new avenues for the development of inexpensive, yet effective, tests for the detection of apoE4 for patients’ stratification. Preliminary results indicated that this methodology is also adaptable into turbidimetric platforms, which make it a good candidate for clinical implementation through its translation to the clinical analysis routine.
MEMS based highly sensitive dual FET gas sensor using graphene decorated Pd-Ag alloy nanoparticles for H2 detection
Authors: Sharma Bharat , Kim Jung-Sik 
Published: April 2018

AbstractA low power, dual-gate field-effect transistor (FET) hydrogen gas sensor with graphene decorated Pd-Ag for hydrogen sensing applications was developed. The FET hydrogen sensor was integrated with a graphene-Pd-Ag-gate FET (GPA-FET) as hydrogen sensor coupled with Pt-gate FET as a reference sensor on a single sensor platform. The sensing gate electrode was modified with graphene by an e-spray technique followed by Pd-Ag DC/MF sputtering. Morphological and structural properties were studied by FESEM and Raman spectroscopy. FEM simulations were performed to confirm the uniform temperature control at the sensing gate electrode. The GPA-FET showed a high sensing response to hydrogen gas at the temperature of 25~254.5 °C. The as-proposed FET H2 sensor showed the fast response time and recovery time of 16 s, 14 s, respectively at the operating temperature of 245 °C. The variation in drain current was positively related with increased working temperature and hydrogen concentration. The proposed dual-gate FET gas sensor in this study has potential applications in various fields, such as electronic noses and automobiles, owing to its low-power consumption, easy integration, good thermal stability and enhanced hydrogen sensing properties.
Super-resolution for asymmetric resolution of FIB-SEM 3D imaging using AI with deep learning
Authors: Hagita Katsumi , Higuchi Takeshi , Jinnai Hiroshi 
Published: April 2018

AbstractScanning electron microscopy equipped with a focused ion beam (FIB-SEM) is a promising three-dimensional (3D) imaging technique for nano- and meso-scale morphologies. In FIB-SEM, the specimen surface is stripped by an ion beam and imaged by an SEM installed orthogonally to the FIB. The lateral resolution is governed by the SEM, while the depth resolution, i.e., the FIB milling direction, is determined by the thickness of the stripped thin layer. In most cases, the lateral resolution is superior to the depth resolution; hence, asymmetric resolution is generated in the 3D image. Here, we propose a new approach based on an image-processing or deep-learning-based method for super-resolution of 3D images with such asymmetric resolution, so as to restore the depth resolution to achieve symmetric resolution. The deep-learning-based method learns from high-resolution sub-images obtained via SEM and recovers low-resolution sub-images parallel to the FIB milling direction. The 3D morphologies of polymeric nano-composites are used as test images, which are subjected to the deep-learning-based method as well as conventional methods. We find that the former yields superior restoration, particularly as the asymmetric resolution is increased. Our super-resolution approach for images having asymmetric resolution enables observation time reduction.
Electrically Enhanced Self-Thermophoresis of Laser-Heated Janus Particles under a Rotating Electric Field
Authors: Chen Yu-Liang , Yang Cheng-Xiang , Jiang Hong-Ren 
Published: April 2018

AbstractThe motion of a laser-heated Janus particle is experimentally measured under a rotating electric field. Directionally circular motions of the Janus particle following or countering the direction of the rotating electric field are observed in the low-frequency region (from 1 to 6 kHz) depending on the direction of electrorotation. In the higher frequency region (>10 kHz), only pure electrorotation and electrothermal flow are observed. By measuring the dependence of the frequency, voltage, and laser heating power, we propose that the tangential component of circular motion is caused by electric field enhanced self-thermophoresis, which is proportional to the laser heating power and the electric field. This result indicates that thermophoresis could be modified by the induced zeta potential of the Janus particle tuned by the applied electric fields. By this mechanism, the intrinsic thermophoresis can be enhanced several times at a relatively low applied voltage (~3 Volt). Electrically tunable thermophoresis of a particle may bring new insights to thermophoresis phenomenon and also open a new direction for tunable active materials.
Effect of antibiotic use for acute bronchiolitis on new-onset asthma in children
Authors: Chen I.-Lun , Huang Hsin-Chun , Chang Yu-Han , Huang Hsin-Yi , Yeh Wei-Ju , Wu Ting-Yi , Suen Jau-Ling , Yang San-Nan , Hung Chih-Hsing 
Published: April 2018

AbstractEarly-life use of antibiotics is associated with asthma. We examined the effect of antibiotic use for early-life bronchiolitis on the development of new-onset asthma in children from Taiwan between 2005 and 2010. Data were from the National Health Insurance Research Database 2010, and diseases were coded using the International Classification of Disease (ICD). We classified the patients, all of whom had bronchiolitis, as having asthma or not having asthma. Asthma was diagnosed using ICD criteria and by use of an inhaled bronchodilator and/or corticosteroid twice in one year. We identified age at asthma onset, sex, residential area, history of atopy and NSAID use, age at first use of antibiotics, and the specific antibiotic, and adjusted for these factors using conditional logistic regression analysis. Among all individuals, there was a relationship between risk of new-onset asthma with use of a high dose of an antibiotic (adjusted odds ratio [aOR] = 3.33, 95% confidence interval [CI] = 2.67–4.15). Among the different antibiotics, macrolides (aOR = 2.87, 95% CI = 1.99–4.16), and azithromycin specifically (aOR = 3.45, 95% CI = 1.62–7.36), had the greatest effect of development of asthma.
Mechanical Tension Drives Elongational Growth of the Embryonic Gut
Authors: Chevalier Nicolas R. , de Witte Tinke-Marie , Cornelissen Annemiek J. M. , Dufour Sylvie , Proux-Gillardeaux Véronique , Asnacios Atef 
Published: April 2018

AbstractDuring embryonic development, most organs are in a state of mechanical compression because they grow in a confined and limited amount of space within the embryo’s body; the early gut is an exception because it physiologically herniates out of the coelom. We demonstrate here that physiological hernia is caused by a tensile force transmitted by the vitelline duct on the early gut loop at its attachment point at the umbilicus. We quantify this tensile force and show that applying tension for 48 h induces stress-dependent elongational growth of the embryonic gut in culture, with an average 90% length increase (max: 200%), 65% volume increase (max: 160%), 50% dry mass increase (max: 100%), and 165% cell number increase (max: 300%); this mechanical cue is required for organ growth as guts not subject to tension do not grow. We demonstrate that growth results from increased cell proliferation when tension is applied. These results outline the essential role played by mechanical forces in shaping and driving the proliferation of embryonic organs.
Application of interspecific Somatic Cell Nuclear Transfer (iSCNT) in sturgeons and an unexpectedly produced gynogenetic sterlet with homozygous quadruple haploid
Authors: Fatira Effrosyni , Havelka Miloš , Labbé Catherine , Depincé Alexandra , Iegorova Viktoriia , Pšenička Martin , Saito Taiju 
Published: April 2018

AbstractSomatic cell nuclear transfer (SCNT) is a very promising cloning technique for reconstruction of endangered animals. The aim of the present research is to implement the interspecific SCNT (iSCNT) technique to sturgeon; one fish family bearing some of the most critically endangered species. We transplanted single cells enzymatically isolated from a dissociated fin-fragment of the Russian sturgeon (Acipenser gueldenstaedtii) into non-enucleated eggs of the sterlet (Acipenser ruthenus), two species bearing different ploidy (4n and 2n, respectively). Up to 12% of the transplanted eggs underwent early development, and one feeding larva (0.5%) was successfully produced. Interestingly, although this transplant displayed tetraploidism (4n) as the donor species, the microsatellite and species-specific analysis showed recipient-exclusive homozygosis without any donor markers. Namely, with regards to this viable larva, host genome duplication occurred twice to form tetraploidism during its early development, probably due to iSCNT manipulation. The importance of this first attempt is to apply iSCNT in sturgeon species, establishing the crucial first steps by adjusting the cloning-methodology in sturgeon’s biology. Future improvements in sturgeon’s cloning are necessary for providing with great hope in sturgeon’s reproduction.
Intact interleukin-10 receptor signaling protects from hippocampal damage elicited by experimental neurotropic virus infection of SJL mice
Authors: Uhde Ann-Kathrin , Ciurkiewicz Malgorzata , Herder Vanessa , Khan Muhammad Akram , Hensel Niko , Claus Peter , Beckstette Michael , Teich René , Floess Stefan , Baumgärtner Wolfgang , Jung Klaus , Huehn Jochen , Beineke Andreas 
Published: April 2018

AbstractTheiler’s murine encephalomyelitis virus (TMEV) infection represents an experimental mouse model to study hippocampal damage induced by neurotropic viruses. IL-10 is a pleiotropic cytokine with profound anti-inflammatory properties, which critically controls immune homeostasis. In order to analyze IL-10R signaling following virus-induced polioencephalitis, SJL mice were intracerebrally infected with TMEV. RNA-based next generation sequencing revealed an up-regulation ofIl10,Il10rαand further genes involved in IL-10 downstream signaling, includingJak1,Socs3andStat3in the brain upon infection. Subsequent antibody-mediated blockade of IL-10R signaling led to enhanced hippocampal damage with neuronal loss and increased recruitment of CD3+T cells, CD45R+B cells and an up-regulation ofIl1αmRNA. Increased expression ofTgfβandFoxp3as well as accumulation of Foxp3+regulatory T cells and arginase-1+macrophages/microglia was detected in the hippocampus, representing a potential compensatory mechanism following disturbed IL-10R signaling. Additionally, an increased peripheralChi3l3expression was found in spleens of infected mice, which may embody reactive regulatory mechanisms for prevention of excessive immunopathology. The present study highlights the importance of IL-10R signaling for immune regulation and its neuroprotective properties in the context of an acute neurotropic virus infection.
Effects of noise on the internal resonance of a nonlinear oscillator
Authors: Zanette Damián H. 
Published: April 2018

AbstractWe numerically analyze the response to noise of a system formed by two coupled mechanical oscillators, one of them having Duffing and van der Pol nonlinearities, and being excited by a self–sustaining force proportional to its own velocity. This system models the internal resonance of two oscillation modes in a vibrating solid beam clamped at both ends. In applications to nano– and micromechanical devices, clamped–clamped beams are subjected to relatively large thermal and electronic noise, so that characterizing the fluctuations induced by these effects is an issue of both scientific and technological interest. We pay particular attention to the action of stochastic forces on the stability of internal–resonance motion, showing that resonant oscillations become more robust than other forms of periodic motion as the quality factor of the resonant mode increases. The dependence on other model parameters —in particular, on the coupling strength between the two oscillators— is also assessed.
Asymmetric wave transmission through one dimensional lattices with cubic-quintic nonlinearity
Authors: Wasay Muhammad Abdul 
Published: April 2018

AbstractOne dimensional lattice with an on-site cubic-quintic nonlinear response described by a cubic-quintic discrete nonlinear Schrödinger equation is tested for asymmetric wave propagation. The lattice is connected to linear side chains. Asymmetry is introduced by breaking the mirror symmetry of the lattice with respect to the center of the nonlinear region. Three cases corresponding to dimer, trimer and quadrimer are discussed with focus on the corresponding diode-like effect. Transmission coefficients are analytically calculated for left and right moving waves via backward transfer map. The different transmission coefficients for the left and right moving waves impinging the lattice give rise to a diode-like effect which is tested for different variations in asymmetry and site dependent coefficients. We show that there is a higher transmission for incoming waves with lower wavenumbers as compared to the waves with comparatively larger wavenumbers and a diode-like effect improves by increasing the nonlinear layers. We also show that in the context of transport through such lattices, the cooperation between cubic and quintic nonlinear response is not “additive”. Finally, we numerically analyse Gaussian wave packet dynamics impinging on the CQDNLS lattice for all three cases.
Safety of Low-calcium Dialysate and its Effects on Coronary Artery Calcification in Patients Undergoing Maintenance Hemodialysis
Authors: Wen Yang , Gan Hua , Li Zhengrong , Sun Ximin , Xiong Ying , Xia Yunfeng 
Published: April 2018

AbstractTo determine the safety of low-calcium-dialysate in patients undergoing maintenance hemodialysis (MHD) and its effects on coronary artery calcification (CAC) and analyze clinical risk factors for CAC. A total of 174 MHD patients were recruited and randomly divided into two groups: high-calcium dialysate (HCD, 1.5 mmol/L Ca2+) and low-calcium dialysate (LCD, 1.25 mmol/L Ca2+). Changes in CAC score (CACS) and cardiac function were evaluated using spiral computed tomography and echocardiography, respectively. Clinical and laboratory parameters were measured. Intra-dialysis adverse reactions were recorded and compared between the two groups. CACS was significantly lower in the LCD group than in the HCD group by the end of the study. Cardiac E/Amax was significantly higher in the LCD group than in the HCD group by the end of the study. There was no significant difference in the frequency of any intra-dialysis adverse reactions between the two groups during the study. LCD is helpful in maintaining cardiac diastolic function and postponing CAC progression. LCD does not increase intra-dialysis adverse reactions. Age may be the most important factor impacting CAC in MHD patients.
Time rescaling reproduces EEG behavior during transition from propofol anesthesia-induced unconsciousness to consciousness
Authors: Boussen S. , Spiegler A. , Benar C. , Carrère M. , Bartolomei F. , Metellus P. , Voituriez R. , Velly L. , Bruder N. , Trébuchon A. 
Published: April 2018

AbstractGeneral anesthesia (GA) is a reversible manipulation of consciousness whose mechanism is mysterious at the level of neural networks leaving space for several competing hypotheses. We recorded electrocorticography (ECoG) signals in patients who underwent intracranial monitoring during awake surgery for the treatment of cerebral tumors in functional areas of the brain. Therefore, we recorded the transition from unconsciousness to consciousness directly on the brain surface. Using frequency resolved interferometry; we studied the intermediate ECoG frequencies (4–40 Hz). In the theoretical study, we used a computational Jansen and Rit neuron model to simulate recovery of consciousness (ROC). During ROC, we found thatfincreased by a factor equal to 1.62 ± 0.09, andδfvaried by the same factor (1.61 ± 0.09) suggesting the existence of a scaling factor. We accelerated the time course of an unconscious EEG trace by an approximate factor 1.6 and we showed that the resulting EEG trace match the conscious state. Using the theoretical model, we successfully reproduced this behavior. We show that the recovery of consciousness corresponds to a transition in the frequency (f, δf) space, which is exactly reproduced by a simple time rescaling. These findings may perhaps be applied to other altered consciousness states.