bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex disease and phenotype mapping in the domestic dog
Authors: Hayward Jessica J. , Castelhano Marta G. , Oliveira Kyle C. , Corey Elizabeth , Balkman Cheryl , Baxter Tara L. , Casal Margret L. , Center Sharon A. , Fang Meiying , Garrison Susan J. , Kalla Sara E. , Korniliev Pavel , Kotlikoff Michael I. , Moise N. S. , Shannon Laura M. , Simpson Kenneth W. , Sutter Nathan B. , Todhunter Rory J. , Boyko Adam R. 
Published: January 2016

AbstractThe domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies.
Msp40 effector of root-knot nematode manipulates plant immunity to facilitate parasitism
Authors: Niu Junhai , Liu Pei , Liu Qian , Chen Changlong , Guo Quanxin , Yin Junmei , Yang Guangsui , Jian Heng 
Published: January 2016

AbstractRoot-knot nematodes (RKNs) are obligate biotrophic parasites that invade plant roots and engage in prolonged and intimate relationships with their hosts. Nematode secretions, some of which have immunosuppressing activity, play essential roles in successful parasitism; however, their mechanisms of action remain largely unknown. Here, we show that the RKN-specific geneMiMsp40, cloned fromMeloidogyne incognita, is expressed exclusively in subventral oesophageal gland cells and is strongly upregulated during early parasitic stages.Arabidopsisplants overexpressingMiMsp40were more susceptible to nematode infection than were wild type plants. Conversely, the host-derivedMiMsp40RNAi suppressed nematode parasitism and/or reproduction. Moreover, overexpression ofMiMsp40in plants suppressed the deposition of callose and the expression of marker genes for bacterial elicitor elf18-triggered immunity. Transient expression ofMiMsp40prevented Bax-triggered defence-related programmed cell death. Co-agroinfiltration assays indicated that MiMsp40 also suppressed macroscopic cell death triggered by MAPK cascades or by the ETI cognate elicitors R3a/Avr3a. Together, these results demonstrate that MiMsp40 is a novelMeloidogyne-specific effector that is injected into plant cells by early parasitic stages of the nematode and that plays a role in suppressing PTI and/or ETI signals to facilitate RKN parasitism.
Functional mutagenesis screens reveal the ‘cap structure’ formation in disulfide-bridge free TASK channels
Authors: Goldstein Matthias , Rinné Susanne , Kiper Aytug K. , Ramírez David , Netter Michael F. , Bustos Daniel , Ortiz-Bonnin Beatriz , González Wendy , Decher Niels 
Published: January 2016

AbstractTwo-pore-domain potassium (K2P) channels have a large extracellular cap structure formed by two M1-P1 linkers, containing a cysteine for dimerization. However, this cysteine is not present in the TASK-1/3/5 subfamily. The functional role of the cap is poorly understood and it remained unclear whether K2P channels assemble in the domain-swapped orientation or not. Functional alanine-mutagenesis screens of TASK-1 and TRAAK were used to build an in silico model of the TASK-1 cap. According to our data the cap structure of disulfide-bridge free TASK channels is similar to that of other K2P channels and is most likely assembled in the domain-swapped orientation. As the conserved cysteine is not essential for functional expression of all K2P channels tested, we propose that hydrophobic residues at the inner leaflets of the cap domains can interact with each other and that this way of stabilizing the cap is most likely conserved among K2P channels.
A Two-Photon Fluorescent Probe for Lysosomal Thiols in Live Cells and Tissues
Authors: Fan Jiangli , Han Zhichao , Kang Yao , Peng Xiaojun 
Published: January 2016

AbstractLysosome-specific fluorescent probes are exclusive to elucidate the functions of lysosomal thiols. Moreover, two-photon microscopy offers advantages of less phototoxicity, better three dimensional spatial localization, deeper penetration depth and lower self-absorption. However, such fluorescent probes for thiols are still rare. In this work, an efficient two-photon fluorophore 1,8-naphthalimide-based probe conjugating a 2,4-dinitrobenzenesulfonyl chloride and morpholine was designed and synthesized, which exhibited high selectivity and sensitivity towards lysosomal thiols by turn-on fluorescence method quantitatively and was successfully applied to the imaging of thiols in live cells and tissues by two-photon microscopy.
Hypoxia-inducible miR-210 contributes to preeclampsia via targeting thrombospondin type I domain containing 7A
Authors: Luo Rongcan , Wang Yongqing , Xu Peng , Cao Guangming , Zhao Yangyu , Shao Xuan , Li Yu-xia , Chang Cheng , Peng Chun , Wang Yan-ling 
Published: January 2016

AbstractPreeclampsia, a relatively common pregnancy disorder, is a major contributor to maternal mortality and morbidity worldwide. An elevation in microRNA-210 (miR-210) expression in the placenta has been reported to be associated with preeclampsia. Our bioinformatic analysis showed that thrombospondin type I domain containing 7A (THSD7A) is a predicted target for miR-210. The aim of this study was to determine whether miR-210 is involved in preeclampsia through its targeting of THSD7A in human placental trophoblasts. In preeclamptic placental tissues, THSD7A levels were significantly downregulated and were inversely correlated with the levels of miR-210. THSD7A was validated as a direct target of miR-210 using quantitative real time PCR (qRT-PCR), Western blotting and dual luciferase assays in HTR8/SVneo cells. Transwell insert invasion assays showed that THSD7A mediated the invasion-inhibitory effect of miR-210 in HTR8/SVneo cells. Interestingly, hypoxia markedly increased miR-210 expression while suppressing THSD7A expression in a time-dependent manner in HTR8/SVneo cells. This study provides novel data on the function of THSD7A in human placental cells and extends our knowledge of how miR-210 is involved in the development of the preeclampsia.
Hydrophilic Mineral Coating of Membrane Substrate for Reducing Internal Concentration Polarization (ICP) in Forward Osmosis
Authors: Liu Qing , Li Jingguo , Zhou Zhengzhong , Xie Jianping , Lee Jim Yang 
Published: January 2016

AbstractInternal concentration polarization (ICP) is a major issue in forward osmosis (FO) as it can significantly reduce the water flux in FO operations. It is known that a hydrophilic substrate and a smaller membrane structure parameter (S) are effective against ICP. This paper reports the development of a thin film composite (TFC) FO membrane with a hydrophilic mineral (CaCO3)-coated polyethersulfone (PES)-based substrate. The CaCO3 coating was applied continuously and uniformly on the membrane pore surfaces throughout the TFC substrate. Due to the intrinsic hydrophilicity of the CaCO3 coating, the substrate hydrophilicity was significantly increased and the membrane S parameter was reduced to as low as the current best of cellulose-based membranes but without the mechanical fragility of the latter. As a result, the ICP of the TFC-FO membrane could be significantly reduced to yield a remarkable increase in water flux without the loss of membrane selectivity.
Ringing phenomenon based whispering-gallery-mode sensing
Authors: Ye Ming-Yong , Shen Mei-Xia , Lin Xiu-Min 
Published: January 2016

AbstractHighly sensitive sensing is one of the most important applications of whispering-gallery-mode (WGM) microresonators, which is usually accomplished through a tunable continuous-wave laser sweeping over a whispering-gallery mode with the help of a fiber taper in a relative slow speed. It is known that if a tunable continuous-wave laser sweeps over a high quality whispering-gallery mode in a fast speed, a ringing phenomenon will be observed. The ringing phenomenon in WGM microresonators is mainly used to measure the Q factors and mode-coupling strengths. Here we experimentally demonstrate that the WGM sensing can be achieved based on the ringing phenomenon. This kind of sensing is accomplished in a much shorter time and is immune to the noise caused by the laser wavelength drift.
Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks
Authors: Wang Yiheng , Liu Tong , Xu Dong , Shi Huidong , Zhang Chaoyang , Mo Yin-Yuan , Wang Zheng 
Published: January 2016

AbstractThe hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdAs) software named “DeepMethyl” to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures with different configurations of hidden layer(s) and amount of pre-training data and compared the performance of deep networks relative to support vector machines (SVMs). Using the methylation states of sequentially neighboring regions as one of the learning features, an SdA achieved a blind test accuracy of 89.7% for GM12878 and 88.6% for K562. When the methylation states of sequentially neighboring regions are unknown, the accuracies are 84.82% for GM12878 and 72.01% for K562. We also analyzed the contribution of genome topological features inferred from Hi-C. DeepMethyl can be accessed at http://dna.cs.usm.edu/deepmethyl/.
Methadone-induced Damage to White Matter Integrity in Methadone Maintenance Patients: A Longitudinal Self-control DTI Study
Authors: Li Wei , Li Qiang , Wang Yarong , Zhu Jia , Ye Jianjun , Yan Xuejiao , Li Yongbin , Chen Jiajie , Liu Jierong , Li Zhe , Wang Wei , Liu Yijun 
Published: January 2016

AbstractMethadone maintenance treatment (MMT) can induce impairments in brain function and structure, despite its clinical effectiveness. However, the effect of chronic MMT on brain white matter (WM) is not fully known. Thirty-three MMT patients underwent diffusion tensor imaging (DTI) twice – at the start of the study (Scan1) and one year later (Scan2). Tract-based spatial statistics were used to investigate changes in fractional anisotropy (FA), axial diffusivity (AD) and radial diffusivity (RD) between the two scans. The correlations between DTI indices and methadone consumption and neuropsychological status were analysed. We found significantly decreased FA, decreased AD and increased RD in Scan2 in extensive WM regions; overlapping regions were found in the left posterior limb and the retrolenticular part of internal capsule, superior and posterior corona radiata, bilateral external capsule and the right superior longitudinal fasciculus. In addition, the change of FA in the overlapping regions was positively correlated with the accumulated dosage of methadone use, the RD value in Scan2 and non-planning impulsiveness (NPI) measured at follow-up. The results suggest that methadone has damaging effects on WM integrity. The dose-dependent pattern and characteristics of the impairment may suggest new strategies for MMT.
Magnetism and exchange interaction of small rare-earth clusters; Tb as a representative
Authors: Peters Lars , Ghosh Saurabh , Sanyal Biplab , van Dijk Chris , Bowlan John , de Heer Walt , Delin Anna , Di Marco Igor , Eriksson Olle , Katsnelson Mikhail I. , Johansson Börje , Kirilyuk Andrei 
Published: January 2016

AbstractHere we follow, both experimentally and theoretically, the development of magnetism in Tb clusters from the atomic limit, adding one atom at a time. The exchange interaction is, surprisingly, observed to drastically increase compared to that of bulk and to exhibit irregular oscillations as a function of the interatomic distance. From electronic structure theory we find that the theoretical magnetic moments oscillate with cluster size in exact agreement with experimental data. Unlike the bulk, the oscillation is not caused by the RKKY mechanism. Instead, the inter-atomic exchange is shown to be driven by a competition between wave-function overlap of the 5dshell and the on-site exchange interaction, which leads to a competition between ferromagnetic double-exchange and antiferromagnetic super-exchange. This understanding opens up new ways to tune the magnetic properties of rare-earth based magnets with nano-sized building blocks.
Microbubble-mediated ultrasound promotes accumulation of bone marrow mesenchymal stem cell to the prostate for treating chronic bacterial prostatitis in rats
Authors: Yi Shanhong , Han Guangwei , Shang Yonggang , Liu Chengcheng , Cui Dong , Yu Shuangjiang , Liao Bin , Ao Xiang , Li Guangzhi , Li Longkun 
Published: January 2016

AbstractChronic bacterial prostatitis (CBP) is an intractable disease. Although bone marrow mesenchymal stem cells (BMMSCs) are able to regulate inflammation in CBP, the effect of microbubble-mediated ultrasound- induced accumulation of BMMSCs on CBP remains unclear. To address this gap, a model of CBP was established in SD rats, which were then treated with BMMSCs alone (BMMSC group), BMMSCs with ultrasound (ultrasound group), BMMSCs with microbubble-mediated ultrasound (MMUS group) and compared with a healthy control group. A therapeutic-ultrasound apparatus was used to treat the prostate in the presence of circulating microbubbles and BMMSCs. The BMMSC distribution was assessed with in vivo imaging and the prostate structure with light microscopy. Real-time quantitative RT-PCR, ELISA and immunohistochemistry were used to assess the expressions of TNF-α and IL-1β. More BMMSCs were found in the prostate in the MMUS group than in the CBP, ultrasound and BMMSC groups. Inflammatory cell infiltration, fibrous tissue hyperplasia and tumor-like epithelial proliferation were significantly reduced in the MMUS group, as were the mRNA and protein expressions of TNF-α and IL-1β. Microbubble-mediated ultrasound-induced accumulation of BMMSCs can inhibit inflammation and decrease TNF-α and IL-1β expressions in the prostate of CBP rats, suggesting that this method may be therapeutic for CPB.
Three-dimensional skeleton networks of graphene wrapped polyaniline nanofibers: an excellent structure for high-performance flexible solid-state supercapacitors
Authors: Hu Nantao , Zhang Liling , Yang Chao , Zhao Jian , Yang Zhi , Wei Hao , Liao Hanbin , Feng Zhenxing , Fisher Adrian , Zhang Yafei , Xu Zhichuan J. 
Published: January 2016

AbstractThin, robust, lightweight and flexible supercapacitors (SCs) have aroused growing attentions nowadays due to the rapid development of flexible electronics. Graphene-polyaniline (PANI) hybrids are attractive candidates for high performance SCs. In order to utilize them in real devices, it is necessary to improve the capacitance and the structure stability of PANI. Here we report a hierarchical three-dimensional structure, in which all of PANI nanofibers (NFs) are tightly wrapped inside reduced graphene oxide (rGO) nanosheet skeletons, for high-performance flexible SCs. The as-fabricated film electrodes with this unique structure showed a highest gravimetric specific capacitance of 921 F/g and volumetric capacitance of 391 F/cm3. The assembled solid-state SCs gave a high specific capacitance of 211 F/g (1 A/g), a high area capacitance of 0.9 F/cm2 and a competitive volumetric capacitance of 25.6 F/cm3. The SCs also exhibited outstanding rate capability (~75% retention at 20 A/g) as well as excellent cycling stability (100% retention at 10 A/g for 2000 cycles). Additionally, no structural failure and loss of performance were observed under the bending state. This structure design paves a new avenue for engineering rGO/PANI or other similar hybrids for high performance flexible energy storage devices.
All-optical central-frequency-programmable and bandwidth-tailorable radar
Authors: Zou Weiwen , Zhang Hao , Long Xin , Zhang Siteng , Cui Yuanjun , Chen Jianping 
Published: January 2016

AbstractRadar has been widely used for military, security and rescue purposes and modern radar should be reconfigurable at multi-bands and have programmable central frequencies and considerable bandwidth agility. Microwave photonics or photonics-assisted radio-frequency technology is a unique solution to providing such capabilities. Here, we demonstrate an all-optical central-frequency-programmable and bandwidth-tailorable radar architecture that provides a coherent system and utilizes one mode-locked laser for both signal generation and reception. Heterodyning of two individually filtered optical pulses that are pre-chirped via wavelength-to-time mapping generates a wideband linearly chirped radar signal. The working bands can be flexibly tailored with the desired bandwidth at a user-preferred carrier frequency. Radar echoes are first modulated onto the pre-chirped optical pulse, which is also used for signal generation and then stretched in time or compressed in frequency several fold based on the time-stretch principle. Thus, digitization is facilitated without loss of detection ability. We believe that our results demonstrate an innovative radar architecture with an ultra-high-range resolution.
Mechanism of substrate recognition by the novel Botulinum Neurotoxin subtype F5
Authors: Guo Jiubiao , Chan Edward Wai Chi , Chen Sheng 
Published: January 2016

AbstractBotulinum Neurotoxins (BoNTs) are the causative agents of botulism, which act by potently inhibiting the neurotransmitter release in motor neurons. Seven serotypes of BoNTs designated as BoNT/A-G have been identified. Recently, two novel types of Botulinum neurotoxins, which cleave a novel scissile bond, L54-E55, of VAMP-2 have been reported including BoNT/F subtype F5 and serotype H. However, little has been known on how these BoNTs recognize their substrates. The present study addressed for the first time the unique substrate recognition mechanism of LC/F5. Our data indicated that the optimal peptide required for efficient LC/F5 substrate cleavage is VAMP-2 (20–65). Interestingly, the overall mode of substrate recognition adopted by LC/F5 was similar to LC/F1, except that its recognition sites were shifted one helix toward the N-terminus of VAMP-2 when compared to that of LC/F1. The composition of LC/F5 pockets were found to have changed accordingly to facilitate specific recognition of these new sites of VAMP-2, including the P2′, P1′, P2, P3, B3, B2 and B1 sites. The study provides direct evidence of the evolutionary adaption of BoNT to recognize its substrate which is useful for effective antitoxin and inhibitor development.
Achromatic flat optical components via compensation between structure and material dispersions
Authors: Li Yang , Li Xiong , Pu Mingbo , Zhao Zeyu , Ma Xiaoliang , Wang Yanqin , Luo Xiangang 
Published: January 2016

AbstractChromatism causes great quality degradation of the imaging system, especially for diffraction imaging. The most commonly method to overcome chromatism is refractive/diffractive hybrid optical system which, however, sacrifices the light weight and integration property of diffraction elements. A method through compensation between the structure dispersion and material dispersion is proposed to overcome the chromatism in flat integrated optical components. This method is demonstrated by making use of silver nano-slits waveguides to supply structure dispersion of surface plasmon polaritons (SPP) in metal-insulator-metal (MIM) waveguide to compensate the material dispersion of metal. A broadband deflector and lens are designed to prove the achromatic property of this method. The method demonstrated here may serve as a solution of broadband light manipulation in flat integrated optical systems.
Characterization of a double-CRD-mutated Gal-8 recombinant protein that retains co-stimulatory activity on antigen-specific T-cell response
Authors: Schroeder Matías Nicolás , Tribulatti María Virginia , Carabelli Julieta , André-Leroux Gwenaëlle , Caramelo Julio Javier , Cattaneo Valentina , Campetella Oscar 
Published: January 2016

Galectins (Gals) constitute a family of mammalian lectins with affinity for β-galactosides, characterized by the presence of conserved CRDs (carbohydrate-recognition domains). We have found previously that Gal-8, from the tandem-repeat group with two linked CRDs, exerts two separate actions on CD4+ T-cells: antigen-independent proliferation and, at lower concentration, antigen-specific co-stimulation. Whereas proliferation can be ascribed to the pro-inflammatory role of Gal-8, the co-stimulatory activity of borderline T-cell-specific responses allows the proposal of Gal-8 as an adjuvant in vaccination. To study the relevance of glycan–lectin interaction to these T-cell activities, we generated a double-mutated protein (Gal-8mut) by replacing canonical arginine residues on each CRD, so as to abolish sugar-binding capacity. As expected, Gal-8mut was unable to bind to lactosyl-Sepharose, confirming that lactose recognition was precluded; however, preservation of lectin activity was still evident since Gal-8mut displayed haemoagglutinatory effects and binding capacity to the T-cell surface. To search for glycan affinity, a glycan microarray analysis was conducted which revealed that Gal-8mut lost most low- and intermediate-, but retained high-, affinity interactions, mainly to polylactosamines and blood group antigens. These findings were supported further by molecular modelling. Regarding biological activity, Gal-8mut was unable to induce T-cell proliferation, but efficiently co-stimulated antigen-specific responses, both in vitro and in vivo. Therefore Gal-8mut represents a useful tool to dissect the specificities of lectin–glycan interactions underlying distinctive Gal-8 activities on T-cell biology. Moreover, given its distinguishing properties, Gal-8mut could be used to enhance borderline immune responses without the non-specific pro-inflammatory activity or other potential adverse effects.