bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
Authors: Pradhan Barun , Cajuso Tatiana , Katainen Riku , Sulo Päivi , Tanskanen Tomas , Kilpivaara Outi , Pitkänen Esa , Aaltonen Lauri A. , Kauppi Liisa , Palin Kimmo 
Published: October 2017

AbstractLong interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3′ transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches. We developed a long-distance inverse PCR (LDI-PCR) based approach to monitor the mobility of active L1 elements based on their 3′ transduction activity. LDI-PCR requires no prior knowledge of the insertion target region. By applying LDI-PCR in conjunction with Nanopore sequencing (Oxford Nanopore Technologies) on one L1 reported to be particularly active in human cancer genomes, we detected 14 out of 15 3′ transductions previously identified by whole genome sequencing in two different colorectal tumour samples. In addition we discovered 25 novel highly subclonal insertions. Furthermore, the long sequencing reads produced by LDI-PCR/Nanopore sequencing enabled the identification of both the 5′ and 3′ junctions and revealed detailed insertion sequence information.
Butyrate and propionate inhibit antigen-specific CD8+ T cell activation by suppressing IL-12 production by antigen-presenting cells
Authors: Nastasi Claudia , Fredholm Simon , Willerslev-Olsen Andreas , Hansen Morten , Bonefeld Charlotte Menné , Geisler Carsten , Andersen Mads Hald , Ødum Niels , Woetmann Anders 
Published: October 2017

AbstractShort chain fatty acids (SCFAs), such as acetate, butyrate and propionate, are products of microbial macronutrients fermentation that distribute systemically and are believed to modulate host immune responses. Recent data have indicated that certain SCFAs, such as butyrate and propionate, directly modulate human dendritic cell (DC) function. Given the role of DCs in initiating and shaping the adaptive immune response, we now explore how SCFAs affect the activation of antigen-specific CD8+T cells stimulated with autologous, MART1 peptide-pulsed DC. We show that butyrate reduces the frequency of peptide-specific CD8+T cells and, together with propionate, inhibit the activity of those cells. On the contrary, acetate does not affect them. Importantly, butyrate and propionate inhibit the production of IL-12 and IL-23 in the DCs and exogenous IL-12 fully restores the activation of the MART-1-specific CD8+T cells, whereas IL-23 has no effect. In conclusion, these results point to a pivotal role of butyrate and propionate in modulating CD8+T cell activation via the inhibition of IL-12 secretion from DCs. These findings reveal a novel mechanism whereby bacterial fermentation products may modulate CD8+T cell function with possible implications in anti-cancer immunotherapy.
Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline
Authors: Wang Yun , Tian Hao , Huang Fei , Long Wenmin , Zhang Qianpeng , Wang Jing , Zhu Ying , Wu Xiaogang , Chen Guanzhou , Zhao Liping , Bakken Lars R. , Frostegård Åsa , Zhang Xiaojun 
Published: November 2017

AbstractQuinoline is biodegradable under anaerobic conditions, but information about the degradation kinetics and the involved microorganisms is scarce. Here, the dynamics of a quinoline-degrading bacterial consortium were studied in anoxic batch cultures containing nitrate. The cultures removed 83.5% of the quinoline during the first 80 hours, which were dominated by denitrification, and then switched to methanogenesis when the nitrogen oxyanions were depleted. Time-resolved community analysis using pyrosequencing revealed that denitrifiying bacteria belonging to the genusThauerawere enriched during the denitrification stage from 12.2% to 38.8% and 50.1% relative abundance in DNA and cDNA libraries, respectively. This suggests that they are key organisms responsible for the initial attack on quinoline. Altogether, 13 different co-abundance groups (CAGs) containing 76 different phylotypes were involved, directly or indirectly, in quinoline degradation. The dynamics of these CAGs show that specific phylotypes were associated with different phases of the degradation. Members ofRhodococcusandDesulfobacterium, as well asRhodocyclaceae- andSyntrophobacteraceae-related phylotypes, utilized initial metabolites of the quinoline, while the resulting smaller molecules were used by secondary fermenters belonging toAnaerolineae. The concerted action by the different members of this consortium resulted in an almost complete anaerobic mineralization of the quinoline.
Passage-dependent accumulation of somatic mutations in mesenchymal stromal cells during in vitro culture revealed by whole genome sequencing
Authors: Kim Myungshin , Rhee Je-Keun , Choi Hayoung , Kwon Ahlm , Kim Jiyeon , Lee Gun Dong , Jekarl Dong Wook , Lee Seungok , Kim Yonggoo , Kim Tae-Min 
Published: October 2017

AbstractHuman mesenchymal stromal cells (MSCs) have served as a major cellular resource for cell-based immunomodulatory and regenerative therapies. However, genomic instability may accumulate during ex vivo expansion of MSCs, thereby increasing the potential of malignant transformation. Here, we performed whole genome sequencing of two peripheral blood-derived MSC lines (MSC1 and MSC2) at various passages (passage 1 [P1] to P9). The majority of single-nucleotide variations (SNVs) occurred in later passages; specifically, 90% and 70% of all SNVs in MSC1 and MSC2 were observed in P9 and P7/P9, respectively. These late-occurring SNVs were enriched with C > A transversions and were overrepresented in intronic regions compared to intergenic regions, suggesting that the mutational forces are not constant across the passages. Clonality analyses also distinguished early-occurring, subclonal SNVs from late-occurring, clonally fixed SNVs. In addition, MSCs were largely devoid of copy number alterations (CNAs) (i.e., 0–2 CNAs per passage), with one exception (MSC2-P3) harboring 29 passage-specific CNAs. Our findings suggest that the SNVs found to be abundant at later passages likely resulted from the accumulation of replication stress, which can be associated with proliferation activity. Thus, the genomic instability associated with proliferation records should be considered for clinical applications of MSCs.
Dynamic self-assembly and self-organized transport of magnetic micro-swimmers
Authors: Kokot Gašper , Kolmakov German V. , Aranson Igor S. , Snezhko Alexey 
Published: November 2017

AbstractWe demonstrate experimentally and in computer simulations that magnetic microfloaters can self-organize into various functional structures while energized by an external alternating (ac) magnetic field. The structures exhibit self-propelled motion and an ability to carry a cargo along a pre-defined path. The morphology of the self-assembled swimmers is controlled by the frequency and amplitude of the magnetic field.
The EphB6 receptor is overexpressed in pediatric T cell acute lymphoblastic leukemia and increases its sensitivity to doxorubicin treatment
Authors: El Zawily Amr , McEwen Emily , Toosi Behzad , Vizeacoumar Frederick S. , Freywald Tanya , Vizeacoumar Franco J. , Freywald Andrew 
Published: November 2017

AbstractWhile impressive improvements have been achieved in T-ALL therapy, current treatment approaches fail in approximately 25% of patients and these patients have limited treatment options. Another significant group of patients is being overtreated, which causes long-lasting side effects. Identification of molecules controlling drug resistance in T-ALL is crucial for treatment optimisation in both scenarios. We report here the EphB6 receptor is frequently overexpressed in T-ALL. Remarkably, our observations indicate that EphB6 acts in T-ALL cells to enhance sensitivity to a DNA-damaging drug, doxorubicin, as interruption of EphB6 activity interferes with the efficiency of doxorubicin-induced eradication of T-ALL cells in cell culture and in xenograft animals. This effect relies on the protection of Akt kinase signaling, while Akt inhibition combined with doxorubicin application produces synergistic effects on the elimination of EphB6-deficient T-ALL cells. These data imply that EphB6 suppresses T-ALL resistance by interfering with Akt activity. Our observations highlight a novel role for EphB6 in reducing drug resistance of T-ALL and suggest that doxorubicin treatment should produce better results if personalised based on EphB6 levels. If successfully verified in clinical studies, this approach should improve outcomes for T-ALL patients resistant to current therapies and for patients, who are being overtreated.
Using CRISPR-Cas9-mediated genome editing to generate C. difficile mutants defective in selenoproteins synthesis
Authors: McAllister Kathleen N. , Bouillaut Laurent , Kahn Jennifer N. , Self William T. , Sorg Joseph A. 
Published: November 2017

AbstractClostridium difficile is a significant concern as a nosocomial pathogen, and genetic tools are important when analyzing the physiology of such organisms so that the underlying physiology/pathogenesis of the organisms can be studied. Here, we used TargeTron to investigate the role of selenoproteins in C. difficile Stickland metabolism and found that a TargeTron insertion into selD, encoding the selenophosphate synthetase that is essential for the specific incorporation of selenium into selenoproteins, results in a significant growth defect and a global loss of selenium incorporation. However, because of potential polar effects of the TargeTron insertion, we developed a CRISPR-Cas9 mutagenesis system for C. difficile. This system rapidly and efficiently introduces site-specific mutations into the C. difficile genome (20–50% mutation frequency). The selD CRISPR deletion mutant had a growth defect in protein-rich medium and mimicked the phenotype of a generated TargeTron selD mutation. Our findings suggest that Stickland metabolism could be a target for future antibiotic therapies and that the CRISPR-Cas9 system can introduce rapid and efficient modifications into the C. difficile genome.
Breeding and study of two new photoperiod- and thermo-sensitive genic male sterile lines of polyploid rice (Oryza sativa L.)
Authors: Zhang Xianhua , Zuo Bo , Song Zhaojian , Wang Wei , He Yuchi , Liu Yuhua , Cai Detian 
Published: November 2017

AbstractMale sterile lines play an important role in the utilization of heterosis. To explore and exploit the heterosis of polyploid hybrid rice, two photoperiod- and thermo-sensitive genic male sterile lines of polyploid rice, PS006 and PS012, were bred via chromosome doubling, complex hybridization and self-breeding. The characteristics of these two lines, including the agronomic traits, growth, development, fertility transformation and combining ability, were investigated. Both lines had good agronomic characteristics and flowering habits, a high outcrossing rate, obvious fertility alterations and good combining abilities. Their hybrids showed strong heterosis and great potential for increasing rice productivity and quality. The new polyploid rice photoperiod- and thermo-sensitive genic male sterile lines will provide material for further research into polyploidy and hybrid vigour in rice and promote the exploitation of polyploid hybrid rice.
Metasurface electrode light emitting diodes with planar light control
Authors: Park Yeonsang , Kim Jineun , Cho Kyung-Sang , Kim Hyochul , Lee Min-kyung , Lee Jae-soong , Kim Un Jeong , Hwang Sung Woo , Brongersma Mark L. , Roh Young-Geun , Park Q-Han 
Published: November 2017

AbstractThe ability of metasurfaces to manipulate light at the subwavelength scale offers unprecedented functionalities for passive and active lasing devices. However, applications of metasurfaces to optical devices are rare due to fabrication difficulties. Here, we present quantum dot light emitting diodes (QDLEDs) with a metasurface-integrated metal electrode and demonstrate microscopically controlled LED emission. By incorporating slot-groove antennas into the metal electrode, we show that LED emission from randomly polarized QD sources can be polarized and directed at will. Utilizing the relation between polarization and emission direction, we also demonstrate microscopic LED beam splitting through the selective choice of polarization.
Resistance monitoring and cross-resistance role of CYP6CW1 between buprofezin and pymetrozine in field populations of Laodelphax striatellus (Fallén)
Authors: Zhang Yueliang , Han Yangchun , Liu Baosheng , Yang Qiong , Guo Huifang , Liu Zewen , Wang Lihua , Fang Jichao 
Published: November 2017

AbstractMonitoring resistance and investigating insecticide resistance mechanisms are necessary for controlling the small brown planthopper, Laodelphax striatellus. The susceptibility to four common insecticides of L. striatellus collected from Jiangsu, Anhui, Zhejiang and Jilin provinces of China in 2015 was monitored. The results showed that all field populations remained susceptible to chlorpyrifos and thiamethoxam with resistance ratios (RRs) of 2.3- to 9.5 and 1.6- to 3.3, respectively, while the insects had developed moderate pymetrozine resistance with RRs of 18.7 to 34.5. Resistance against buprofezin had developed to an alarmingly high level in three southeastern provinces of China with RRs of 108.8 to 156.1, but in Jilin it had an RR of only 26.6. Moreover, in line with both the buprofezin and pymetrozine resistance levels, we found LsCYP6CW1 to be over-expressed in all field L. striatellus populations, which indicated that it might be important for cross-resistance between buprofezin and pymetrozine. RNA interference (RNAi) ingestion resulted in the effective suppression of LsCYP6CW1 expression, and significantly increased susceptibility to both buprofezin and pymetrozine compared with the control, which further confirmed that overexpression of LsCYP6CW1 was involved in the cross-resistance to buprofezin and pymetrozine in field L. Striatellus populations.
Activation of G-protein-gated inwardly rectifying potassium (Kir3/GirK) channels rescues hippocampal functions in a mouse model of early amyloid-β pathology
Authors: Sánchez-Rodríguez Irene , Temprano-Carazo Sara , Nájera Alberto , Djebari Souhail , Yajeya Javier , Gruart Agnès , Delgado-García José M. , Jiménez-Díaz Lydia , Navarro-López Juan D. 
Published: November 2017

AbstractThe hippocampus plays a critical role in learning and memory. Its correct performance relies on excitatory/inhibitory synaptic transmission balance. In early stages of Alzheimer’s disease (AD), neuronal hyperexcitability leads to network dysfunction observed in cortical regions such as the hippocampus. G-protein-gated potassium (GirK) channels induce neurons to hyperpolarize, contribute to the resting membrane potential and could compensate any excesses of excitation. Here, we have studied the relationship between GirK channels and hippocampal function in a mouse model of early AD pathology. Intracerebroventricular injections of amyloid-β (Aβ1-42) peptide—which have a causal role in AD pathogenesis—were performed to evaluate CA3–CA1 hippocampal synapse functionality in behaving mice. Aβ increased the excitability of the CA3–CA1 synapse, impaired long-term potentiation (LTP) and hippocampal oscillatory activity, and induced deficits in novel object recognition (NOR) tests. Injection of ML297 alone, a selective GirK activator, was also translated in LTP and NOR deficits. However, increasing GirK activity rescued all hippocampal deficits induced by Aβ due to the restoration of excitability values in the CA3–CA1 synapse. Our results show a synaptic mechanism, through GirK channel modulation, for the prevention of the hyperexcitability that causally contributes to synaptic, network, and cognitive deficits found in early AD pathogenesis.
Tighter bound of quantum randomness certification for independent-devices scenario
Authors: Fei Xin-Wei , Yin Zhen-Qiang , Huang Wei , Xu Bing-Jie , Wang Shuang , Chen Wei , Han Yun-Guang , Guo Guang-Can , Han Zheng-Fu 
Published: November 2017

AbstractQuantum random number generation attracts considerable attention, since its randomness inherently originates in quantum mechanics, but not mathematical assumptions. Randomness certification, e.g. entropy estimation, becomes a key issue in the context of quantum random number generation protocol. We study a self-testing protocol based on dimension witness, with the assumption of independent devices. It addresses the random number extraction problem in a practical prepare-and-measure scenario with uncharacterized devices. However, the lower bound of min-entropy as a function of dimension witness is not tight in existing works. We present a tighter bound of analytic form, by introducing the Lagrangian multiplier method to closely analyze the optimization problem on average guessing probability. Through simulation, it turns out that a significantly higher random number generation rate can be achieved in practice.
One-step Synthesis of Ordered Pd@TiO2 Nanofibers Array Film as Outstanding NH3 Gas Sensor at Room Temperature
Authors: Wu Hongyuan , Huang Haitao , Zhou Jiao , Hong Dahai , Ikram Muhammad , Rehman Afrasiab Ur , Li Li , Shi Keying 
Published: November 2017

AbstractThe one dimensional (1D) ordered porous Pd@TiO2 nanofibers (NFs) array film have been fabricated via a facile one-step synthesis of the electrospinning approach. The Pd@TiO2 NFs (PTND3) contained Pd (2.0 wt %) and C, N element (16.2 wt %) display high dispersion of Pd nanoparticles (NPs) on TiO2 NFs. Adding Pd meshed with C, N element to TiO2 based NFs might contribute to generation of Lewis acid sites and Brønsted acid sites, which have been recently shown to enhance NH3 adsorption-desorption ability; Pd NPs could increase the quantity of adsorbed O2 on the surface of TiO2 based NFs, and accelerated the O2 molecule-ion conversion rate, enhanced the ability of electron transmission. The response time of PTND3 sensor towards 100 ppm NH3 is only 3 s at room temperature (RT). Meantime, the response and response time of the PTND3 to the NH3 is 1 and 14s even at the concentration of 100 ppb. Therefore, the ordered Pd@TiO2 NFs array NH3 sensor display great potential for practical applications.
Intravascular Optical Coherence Tomography for Characterization of Atherosclerosis with a 1.7 Micron Swept-Source Laser
Authors: Li Yan , Jing Joseph , Heidari Emon , Zhu Jiang , Qu Yueqiao , Chen Zhongping 
Published: October 2017

AbstractThe main cause of acute coronary events, such as thrombosis, is the rupture of atherosclerotic plaques. Typical intravascular optical coherence tomography (IVOCT) imaging systems that utilize a 1.3 μm swept source laser are often used for identifying fibrous cap thickness of plaques, yet cannot provide adequate depth penetration to resolve the size of the lipid pool. Here, we present a novel IVOCT system with a 1.7 μm center wavelength swept light source that can readily penetrate deeper into the tissue because of the longer wavelength and allows for better identification of plaques due to the lipid absorption spectrum at 1.7 μm. Using this system, we have imaged a human coronary artery to evaluate the performance of the novel OCT system and verified the results by hematoxylin and eosin (H&E) histology. The significantly improved imaging depth and better identification sensitivity suggest that the 1.7 μm OCT system holds great potential that can be further translated for in-vivo applications of atherosclerosis characterization.
Organic-inorganic hybrid electrochromic materials, polysilsesquioxanes containing triarylamine, changing color from colorless to blue
Authors: Wang Shuzhong , Cai Shuwei , Cai Wanan , Niu Haijun , Wang Cheng , Bai Xuduo , Wang Wen , Hou Yanjun 
Published: November 2017

AbstractFour kinds of soluble monomers, containing triarylamine (TAA) group with reactive siloxane group, were synthesized under mild conditions via the reaction between 3-(triethoxysilyl)propyl isocyanate (TEOSPIC) and four TAA derivatives, respectively. Then the corresponding colorless organic-inorganic hybrid materials (PSSOs) were derived from the hydrolytic condensation of the monomers. PSSOs revealed good solubility in polar solvents on account of the effect of propeller-like TAA unit as well as the auxo-action effect of the flexible chain within the monomers. The structural characteristics of these PSSOs were identified by 1H NMR, 29Si NMR, FT-IR spectroscopies and X-ray diffraction (XRD). The morphology, dynamic changes of the transmittance and current before and after electro-oxidizing reaction were studied, and didn’t show significant change suggesting good stability of the PSSOs. Meanwhile, these PSSOs performed high contrast of optical transmittance change up to 84% with the highest coloration efficiency to 241 cm2·C−1. Furthermore, electrofluorescent properties of PSSOs were investigated with high-contrast.
Task engagement and mental workload involved in variation and repetition of a motor skill
Authors: Lelis-Torres Natália , Ugrinowitsch Herbert , Apolinário-Souza Tércio , Benda Rodolfo N. , Lage Guilherme M. 
Published: November 2017

AbstractExplanatory hypotheses proposed in behavioral studies assumed that less repetitive practice schedules, such as random practice, seem to demand greater cognitive effort than more repetitive types of practice organization, such as constant. All of these hypotheses emphasize the enhanced demand to memory processes promoted by less repetitive practice schedules. In the present study, we investigated the cognitive effort involved in random and constant practice schedules with an electrophysiological approach. Twenty-one male participants practiced a sequential key-pressing task with two goals: learning the relative timing dimension and learning the absolute timing dimension. Sixty trials were performed in a constant practice schedule (only one absolute timing goal), and sixty trials were performed in random order (three absolute timing goals). Two electroencephalography based measures of cognitive states were used: (a) task engagement (sensory processing and attention resources) and (b) mental workload (working memory load). The results showed that random practice induced greater cognitive effort than constant practice when task engagement was analyzed. Throughout practice, both task engagement and mental workload decreased more in the constant practice condition than in the random practice condition. The increased demand for sensory processing observed in random practice opens a new exciting field of study in practice organization.