bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase
Authors: Klein Tobias , Vajpai Navratna , Phillips Jonathan J. , Davies Gareth , Holdgate Geoffrey A. , Phillips Chris , Tucker Julie A. , Norman Richard A. , Scott Andrew D. , Higazi Daniel R. , Lowe David , Thompson Gary S. , Breeze Alexander L. 
Published: July 2015

AbstractProtein tyrosine kinases differ widely in their propensity to undergo rearrangements of the N-terminal Asp–Phe–Gly (DFG) motif of the activation loop, with some, including FGFR1 kinase, appearing refractory to this so-called ‘DFG flip’. Recent inhibitor-bound structures have unexpectedly revealed FGFR1 for the first time in a ‘DFG-out’ state. Here we use conformationally selective inhibitors as chemical probes for interrogation of the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our detailed structural and biophysical insights identify contributions from altered dynamics in distal elements, including the αH helix, towards the outstanding stability of the DFG-out complex with the inhibitor ponatinib. We conclude that the αC-β4 loop and ‘molecular brake’ regions together impose a high energy barrier for this conformational rearrangement, and that this may have significance for maintaining autoinhibition in the non-phosphorylated basal state of FGFR1.
Transmission of genital human papillomavirus infection in couples: a population-based cohort study in rural China
Authors: Liu Mengfei , He Zhonghu , Zhang Chanyuan , Liu Fangfang , Liu Ying , Li Jingjing , Xu Zhongyao , Wang Qiyan , Hang Dong , Shen Na , Pan Yaqi , Guo Chuanhai , Cai Hong , Ke Yang 
Published: July 2015

AbstractHPV transmission dynamics have rarely been studied in the general population, especially in China. We followed the genital HPV infection status of both partners in 874 couples aged 25-65 years from rural China for up to 7 bi-annual visits during 2009-2013. The positive HPV concordance and transmission rate for partners in a couple were evaluated and relevant risk factors were assessed. The concordance of any, oncogenic and non-oncogenic HPV was 15.52%, 16.18% and 10.41%, respectively. Male-to-female transmission rate was 7.11, 12.13 and 4.77/1000 person months for any, oncogenic and non-oncogenic HPV respectively. The female-to-male transmission rate was 5.56, 2.37 and 17.01/1000 person months for any, oncogenic and non-oncogenic HPV respectively. The risk of male-to-female transmission was significantly higher than that of female-to-male transmission for oncogenic types. However, for non-oncogenic types, the risk of male-to-female transmission was significantly lower than that of female-to-male transmission. Younger couples, persistent infection with HPV, higher numbers of sexual partners and higher frequency of sexual intercourse were positively associated with HPV transmission in couples. Our results indicate that men in rural China play a more important role than men in western populations as a source of cervical oncogenic HPV infection in women.
Theoretical analysis of hot electron dynamics in nanorods
Authors: Kumarasinghe Chathurangi S. , Premaratne Malin , Bao Qiaoliang , Agrawal Govind P. 
Published: July 2015

AbstractLocalised surface plasmons create a non-equilibrium high-energy electron gas in nanostructures that can be injected into other media in energy harvesting applications. Here, we derive the rate of this localised-surface-plasmon mediated generation of hot electrons in nanorods and the rate of injecting them into other media by considering quantum mechanical motion of the electron gas. Specifically, we use the single-electron wave function of a particle in a cylindrical potential well and the electric field enhancement factor of an elongated ellipsoid to derive the energy distribution of electrons after plasmon excitation. We compare the performance of nanorods with equivolume nanoparticles of other shapes such as nanospheres and nanopallets and report that nanorods exhibit significantly better performance over a broad spectrum. We present a comprehensive theoretical analysis of how different parameters contribute to efficiency of hot-electron harvesting in nanorods and reveal that increasing the aspect ratio can increase the hot-electron generation and injection, but the volume shows an inverse dependency when efficiency per unit volume is considered. Further, the electron thermalisation time shows much less influence on the injection rate. Our derivations and results provide the much needed theoretical insight for optimization of hot-electron harvesting process in highly adaptable metallic nanorods.
Epstein-Barr virus positive diffuse large B-cell lymphoma predict poor outcome, regardless of the age
Authors: Lu Ting-Xun , Liang Jin-Hua , Miao Yi , Fan Lei , Wang Li , Qu Xiao-Yan , Cao Lei , Gong Qi-Xing , Wang Zhen , Zhang Zhi-Hong , Xu Wei , Li Jian-Yong 
Published: July 2015

AbstractEpstein-Barr virus (EBV) positive diffuse large B-cell lymphoma (DLBCL) of the elderly is defined as patients older than 50 years alone. However, recent studies showed young patients with sound immune status could also be affected. In this study, we investigated the clinical features and outcomes of patients with EBV positive DLBCL in the different age groups using different EBER cut-off values. The prevalence of EBV positive DLBCL was 14.0% (35/250) and 10.4% (26/250) for EBER cut-off of 20% and 50%, respectively. With both EBER cut-off values, patients with EBV DLBCL shared many unfavorable prognostic characteristics, regardless of age. EBV positive patients, both in the elderly and young groups, showed significantly worse overall survival and progression-free survival than negative cases. Moreover, no significant differences of outcomes were identified between different age groups with EBV positive DLBCL. In conclusion, EBV positive DLBCL patients, regardless of age, shared similar poor prognostic features and showed worse outcome than negative cases. We suggest that the age criterion of EBV positive DLBCL of the elderly and possibly the name itself, be modified in future.
Fluorescence Polarization Switching from a Single Silicon Vacancy Colour Centre in Diamond
Authors: Liu Yan , Chen Gengxu , Rong Youying , McGuinness Liam Paul , Jelezko Fedor , Tamura Syuto , Tanii Takashi , Teraji Tokuyuki , Onoda Shinobu , Ohshima Takeshi , Isoya Junichi , Shinada Takahiro , Wu E , Zeng Heping 
Published: July 2015

AbstractSingle-photon emitters with stable and uniform photoluminescence properties are important for quantum technology. However, in many cases, colour centres in diamond exhibit spectral diffusion and photoluminescence intensity fluctuation. It is therefore essential to investigate the dynamics of colour centres at the single defect level in order to enable the on-demand manipulation and improved applications in quantum technology. Here we report the polarization switching, intensity jumps and spectral shifting observed on a negatively charged single silicon-vacancy colour centre in diamond. The observed phenomena elucidate the single emitter dynamics induced by photoionization of nearby electron donors in the diamond.
Independent Emergence of the Cosmopolitan Asian Chikungunya Virus, Philippines 2012
Authors: Tan Kim-Kee , Sy Ava Kristy D. , Tandoc Amado O. , Khoo Jing-Jing , Sulaiman Syuhaida , Chang Li-Yen , AbuBakar Sazaly 
Published: July 2015

AbstractOutbreaks involving the Asian genotype Chikungunya virus (CHIKV) caused over one million infections in the Americas recently. The outbreak was preceded by a major nationwide outbreak in the Philippines. We examined the phylogenetic and phylogeographic relationships of representative CHIKV isolates obtained from the 2012 Philippines outbreak with other CHIKV isolates collected globally. Asian CHIKV isolated from the Philippines, China, Micronesia and Caribbean regions were found closely related, herein denoted as Cosmopolitan Asian CHIKV (CACV). Three adaptive amino acid substitutions in nsP3 (D483N), E1 (P397L) and E3 (Q19R) were identified among CACV. Acquisition of the nsP3-483N mutation in Compostela Valley followed by E1-397L/E3-19R in Laguna preceded the nationwide spread in the Philippines. The China isolates possessed two of the amino acid substitutions, nsP3-D483N and E1-P397L whereas the Micronesian and Caribbean CHIKV inherited all the three amino acid substitutions. The unique amino acid substitutions observed among the isolates suggest multiple independent virus dissemination events. The possible biological importance of the specific genetic signatures associated with the rapid global of the virus is not known and warrant future in-depth study and epidemiological follow-up. Molecular evidence, however, supports the Philippines outbreak as the possible origin of the CACV.
Small Dielectric Spheres with High Refractive Index as New Multifunctional Elements for Optical Devices
Authors: Tribelsky Michael I. , Geffrin Jean-Michel , Litman Amelie , Eyraud Christelle , Moreno Fernando 
Published: July 2015

AbstractThe future of ultra-fast optical communication systems is inevitably connected with progress in optical circuits and nanoantennas. One of the key points of this progress is the creation of elementary components of optical devices with scattering diagrams tailored for redirecting the incident light in a desired manner. Here we demonstrate theoretically and experimentally that a small, simple, spatially homogeneous dielectric subwavelength sphere with a high refractive index and low losses (as some semiconductors in the visible or near infrared region) exhibits properties allowing to utilize it as a new multifunctional element for the mentioned devices. This can be achieved by taking advantage of the coherent effects between dipolar and multipolar modes, which produce anomalous scattering effects. The effects open a new way to control the directionality of the scattered light. The directional tuning can be obtained in a practical way just by a change in the frequency of the incident wave, and/or by a well-chosen diameter of the sphere. Dielectric nanoparticles with the required optical properties in the VIS-NIR may be now readily fabricated. These particles could be an efficient alternative to the widely discussed scattering units with a more complicated design.
Path-programmable water droplet manipulations on an adhesion controlled superhydrophobic surface
Authors: Seo Jungmok , Lee Seoung-Ki , Lee Jaehong , Seung Lee Jung , Kwon Hyukho , Cho Seung-Woo , Ahn Jong-Hyun , Lee Taeyoon 
Published: July 2015

AbstractHere, we developed a novel and facile method to control the local water adhesion force of a thin and stretchable superhydrophobic polydimethylsiloxane (PDMS) substrate with micro-pillar arrays that allows the individual manipulation of droplet motions including moving, merging and mixing. When a vacuum pressure was applied below the PDMS substrate, a local dimple structure was formed and the water adhesion force of structure was significantly changed owing to the dynamically varied pillar density. With the help of the lowered water adhesion force and the slope angle of the formed dimple structure, the motion of individual water droplets could be precisely controlled, which facilitated the creation of a droplet-based microfluidic platform capable of a programmable manipulation of droplets. We showed that the platform could be used in newer and emerging microfluidic operations such as surface-enhanced Raman spectroscopy with extremely high sensing capability (10−15 M) and in vitro small interfering RNA transfection with enhanced transfection efficiency of ~80%.
A route to possible civil engineering materials: the case of high-pressure phases of lime
Authors: Bouibes A. , Zaoui A. 
Published: July 2015

AbstractLime system has a chemical composition CaO, which is known as thermodynamically stable. The purpose here is to explore further possible phases under pressure, by means of variable-compositionab initioevolutionary algorithm. The present investigation shows surprisingly new stable compounds of lime. At ambient pressure we predict, in addition to CaO, CaO2as new thermodynamically stable compound. The latter goes through two phases transition from C2/c space group structure to Pna21 at 1.5 GPa and Pna21 space group structure to I4/mcm at 23.4 GPa. Under increasing pressure, further compounds such as CaO3become the most stable and stabilize in P-421m space group structure above 65 GPa. For the necessary knowledge of the new predicted compounds, we have computed their mechanical and electronic properties in order to show and to explain the main reasons leading to the structural changes.
Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
Authors: Graw Stefan , Meier Richard , Minn Kay , Bloomer Clark , Godwin Andrew K. , Fridley Brooke , Vlad Anda , Beyerlein Peter , Chien Jeremy 
Published: July 2015

AbstractCurrent genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.
A Comprehensive Inter-Tissue Crosstalk Analysis Underlying Progression and Control of Obesity and Diabetes
Authors: Samdani Pawan , Singhal Meet , Sinha Neeraj , Tripathi Parul , Sharma Sachin , Tikoo Kamiya , Rao Kanury V. S. , Kumar Dhiraj 
Published: July 2015

AbstractObesity is a metabolic state associated with excess of positive energy balance. While adipose tissues are considered the major contributor for complications associated with obesity, they influence a variety of tissues and inflict significant metabolic and inflammatory alterations. Unfortunately, the communication network between different cell-types responsible for such systemic alterations has been largely unexplored. Here we study the inter-tissue crosstalk during progression and cure of obesity using multi-tissue gene expression data generated through microarray analysis. We used gene expression data sets from 10 different tissues from mice fed on high-fat-high-sugar diet (HFHSD) at various stages of disease development and applied a novel analysis algorithm to deduce the tissue crosstalk. We unravel a comprehensive network of inter-tissue crosstalk that emerges during progression of obesity leading to inflammation and insulin resistance. Many of the crosstalk involved interactions between well-known modulators of obesity and associated pathology like inflammation. We then used similar datasets from mice that in addition to HFHSD were also administered with a herbal concoction known to circumvent the effects of HFHSD in the diet induced model of obesity in mice. We propose, the analysis presented here could be applied to understand systemic details of several chronic diseases.
Localization-based full-field microscopy: how to attain super-resolved images
Authors: Son Taehwang , Lee Wonju , Kim Donghyun 
Published: July 2015

AbstractIn this study, we have investigated localization-based microscopy to achieve full-field super-resolution. For localized sampling, we have considered combs consisting of unit pulses and near-fields localized by surface nanoapertures. Achievable images after reconstruction were assessed in terms of peak signal-to-noise ratio (PSNR). It was found that spatial switching of individual pulses may be needed to break the diffraction limit. Among the parameters, the resolution was largely determined by sampling period while the effect of width of a sampling pulse on PSNR was relatively limited. For the range of sampling parameters that we considered, the highest resolution achievable is estimated to be 70 nm, which can further be enhanced by optimizing the localization parameters.
Chemoprevention of Colonic Aberrant Crypt Foci by Novel Schiff Based Dichlorido(4-Methoxy-2-{[2-(Piperazin-4-Ium-1-Yl)Ethyl]Iminomethyl}Phenolate)Cd Complex in Azoxymethane-Induced Colorectal Cancer in Rats
Authors: Hajrezaie Maryam , Shams Keivan , Moghadamtousi Soheil Zorofchian , Karimian Hamed , Hassandarvish Pouya , Emtyazjoo Mozhgan , Zahedifard Maryam , Majid Nazia Abdul , Ali Hapipah Mohd , Abdulla Mahmood Ameen 
Published: July 2015

AbstractSchiff-based complexes as a source of cancer chemotherapeutic compounds have been subjected to the variety of anticancer studies. The in-vitro analysis confirmed the CdCl2(C14H21N3O2) complex possess cytotoxicity and apoptosis induction properties in colon cancer cells, so lead to investigate the inhibitory efficiency of the compound on colonic aberrant crypt foci (ACF). Five groups of adult male rats were used in this study: Vehicle, cancer control, positive control groups and the groups treated with 25 and 50 mg/kg of complex for 10 weeks. The rats in vehicle group were injected subcutaneously with 15 mg/kg of sterile normal saline once a week for 2 weeks and orally administered with 5% Tween-20 (5 ml/kg) for 10 weeks, other groups were injected subcutaneously with 15 mg/kg azoxymethane once a week for 2 weeks. The rats in positive groups were injected intra-peritoneally with 35 mg/kg 5-Flourouracil four times in a month. Administration of the complex suppressed total colonic ACF formation up to 73.4% (P < 0.05). The results also showed that treatment with the complex significantly reduced the level of malondialdehyde while increasing superoxide dismutase and catalase activities. Furthermore, the down-regulation of PCNA and Bcl2 and the up-regulation of Bax was confirmed by immunohistochemical staining.
One-dimensional porous nanofibers of Co3O4 on the carbon matrix from human hair with superior lithium ion storage performance
Authors: Tan Yanli , Gao Qiuming , Yang Chunxiao , Yang Kai , Tian Weiqian , Zhu Lihua 
Published: July 2015

AbstractOne-dimensional (1D) hierarchical porous nanofibers of Co3O4 possessing of (220) facets on the carbon matrix from human hair (H2@Co3O4) with 20–30 nm in width and 3–5 μm in length are prepared by a facile solvothermal and calcination approach. The well crystallized small Co3O4 particles with the diameter of about 8–12 nm were closely aggregated together in the nanofibers. Electrochemical analyses show that the first discharge capacity of H2@Co3O4 electrode is 1368 mAh g−1 at the current density of 0.1 A g−1 based on the total mass of composite. A high reversible capacity of 916 mAh g −1 was obtained over 100 cycles at 0.1 A g−1, presenting a good cycling stability. When cycled at a high current density of 1 and 2 A g−1, the specific capacity of 659 and 573 mAh g−1 could be still achieved, respectively, indicating a superior power capability.
Integrated genomic approaches identify major pathways and upstream regulators in late onset Alzheimer’s disease
Authors: Li Xinzhong , Long Jintao , He Taigang , Belshaw Robert , Scott James 
Published: July 2015

AbstractPrevious studies have evaluated gene expression in Alzheimer’s disease (AD) brains to identify mechanistic processes, but have been limited by the size of the datasets studied. Here we have implemented a novel meta-analysis approach to identify differentially expressed genes (DEGs) in published datasets comprising 450 late onset AD (LOAD) brains and 212 controls. We found 3124 DEGs, many of which were highly correlated with Braak stage and cerebral atrophy. Pathway Analysis revealed the most perturbed pathways to be (a) nitric oxide and reactive oxygen species in macrophages (NOROS), (b) NFkB and (c) mitochondrial dysfunction. NOROS was also up-regulated and mitochondrial dysfunction down-regulated, in healthy ageing subjects. Upstream regulator analysis predicted the TLR4 ligands, STAT3 and NFKBIA, for activated pathways and RICTOR for mitochondrial genes. Protein-protein interaction network analysis emphasised the role of NFKB; identified a key interaction of CLU with complement; and linked TYROBP, TREM2 and DOK3 to modulation of LPS signalling through TLR4 and to phosphatidylinositol metabolism. We suggest that NEUROD6, ZCCHC17, PPEF1 and MANBAL are potentially implicated in LOAD, with predicted links to calcium signalling and protein mannosylation. Our study demonstrates a highly injurious combination of TLR4-mediated NFKB signalling, NOROS inflammatory pathway activation and mitochondrial dysfunction in LOAD.
A Novel Bio-carrier Fabricated Using 3D Printing Technique for Wastewater Treatment
Authors: Dong Yang , Fan Shu-Qian , Shen Yu , Yang Ji-Xiang , Yan Peng , Chen You-Peng , Li Jing , Guo Jin-Song , Duan Xuan-Ming , Fang Fang , Liu Shao-Yang 
Published: July 2015

AbstractThe structure of bio-carriers is one of the key operational characteristics of a biofilm reactor. The goal of this study is to develop a series of novel fullerene-type bio-carriers using the three-dimensional printing (3DP) technique. 3DP can fabricate bio-carriers with more specialized structures compared with traditional fabrication processes. In this research, three types of fullerene-type bio-carriers were fabricated using the 3DP technique and then compared with bio-carrier K3 (from AnoxKaldnes) in the areas of physicochemical properties and biofilm growth. Images acquired by 3D profiling and SEM indicated that the surface roughness of the 3DP bio-carrier was greater than that of K3. Furthermore, contact angle data indicated that the 3DP bio-carriers were more hydrophilic than K3. The biofilm on the 3DP bio-carriers exhibited higher microbial activity and stronger adhesion ability. These findings were attributed to excellent mass transfer of the substrate (and oxygen) between the vapour-liquid-solid tri-phase system and to the surface characteristics. It is concluded that the novel 3DP fullerene-type bio-carriers are ideal carriers for biofilm adherence and growth.
Application of Chan-Lam cross coupling for the synthesis of N-heterocyclic carbene precursors bearing strong electron donating or withdrawing groups
Authors: Huang Liliang , He Chengxiang , Sun Zhihua 
Published: July 2015

AbstractChan-Lam cross coupling allowed efficient synthesis of N,N’-disubstituted ortho-phenylene diamines bearing strong electron donating or withdrawing groups, such as nitro or methoxy groups, with moderate to high yields. These diamines can then be turned into N-heterocyclic carbene precursors after condensation with trimethyl orthoformate. The same strategy can also be utilized for the synthesis of N-monosubstituted aniline derivatives containing a functionalized ortho-aminomethyl group as intermediates for chiral 6-membered ring carbene precursors.