bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellMethy: Identification of a focal concordantly methylated pattern of CpGs revealed wide differences between normal and cancer tissues
Authors: Wang Fang , Zhang Shaojun , Liu Hongbo , Wei Yanjun , Wang Yihan , Han Xiaole , Su Jianzhong , Zhang Dongwei , Xie Baodong , Zhang Yan 
Published: December 2015

AbstractDNA methylation patterns may serve as a key in determining cell phenotypes and functions. Adjacent CpG patterns may provide insight into methylation functional mechanisms. Some regions display different DNA methylation patterns between normal and cancer tissues, but the same average methylation level. Here, we developed a method (CellMethy) to infer a region in which all CpGs exhibit concordant methylation (CM) and to quantify the extent of CM in the region. Using simulation data, CellMethy showed high performance in discovering the concordant methylation patterns (AUC = 0.89). CellMethy was then applied to RRBS data including 11 normal tissues and 12 tumors. We found that the extent of CM exhibited wider differentials among tissues than did the average methylation levels from the CM regions, with 45% of CM regions occurring specifically in one tissue and mainly in tumors. Then, we identified CM regions through genome wide bisulfite sequencing (GWBS) data on breast cancer. Approximately 82% of CM regions revealed a significantly different extent of CM between cancer and normal tissues. CellMethy can accurately describe concordantly methylated regions and the results suggest that CM might also serve as a stable marker of cell sub-populations.
Nanoparticle-assisted optical tethering of endosomes reveals the cooperative function of dyneins in retrograde axonal transport
Authors: Chowdary Praveen D. , Che Daphne L. , Kaplan Luke , Chen Ou , Pu Kanyi , Bawendi Moungi , Cui Bianxiao 
Published: December 2015

AbstractDynein-dependent transport of organelles from the axon terminals to the cell bodies is essential to the survival and function of neurons. However, quantitative knowledge of dyneins on axonal organelles and their collective function during this long-distance transport is lacking because current technologies to do such measurements are not applicable to neurons. Here, we report a new method termed nanoparticle-assisted optical tethering of endosomes (NOTE) that made it possible to study the cooperative mechanics of dyneins on retrograde axonal endosomes in live neurons. In this method, the opposing force from an elastic tether causes the endosomes to gradually stall under load and detach with a recoil velocity proportional to the dynein forces. These recoil velocities reveal that the axonal endosomes, despite their small size, can recruit up to 7 dyneins that function as independent mechanical units stochastically sharing load, which is vital for robust retrograde axonal transport. This study shows that NOTE, which relies on controlled generation of reactive oxygen species, is a viable method to manipulate small cellular cargos that are beyond the reach of current technology.
Duration of Untreated Psychosis and Brain Function during Verbal Fluency Testing in First-Episode Schizophrenia: A Near-Infrared Spectroscopy Study
Authors: Chou Po-Han , Lin Wei-Hao , Lin Chih-Chien , Hou Po-Hsun , Li Wan-Rung , Hung Chia-Chun , Lin Ching-Po , Lan Tsuo-Hung , Chan Chin-Hong 
Published: December 2015

AbstractA longer duration of untreated psychosis (DUP) has been associated with poor clinical outcomes in patients with schizophrenia (SZ); however, it remains unclear whether this is due to neurotoxic effects of psychosis. The purpose of this study was to use near-infrared spectroscopy (NIRS) to investigate the influence of DUP on brain function using two verbal fluency tests (VFTs) in patients with first-episode SZ (FES). A total of 28 FES patients and 29 healthy controls (HC) underwent NIRS during VFTs. Group comparisons of cortical activity were made using two-tailed t-tests and the false discovery rate method. We then examined the associations between DUP and hemodynamic changes in each channel to identify any effects of DUP on brain cortical activity. During the letter VFT, the HC group exhibited significantly greater cortical activations over bilateral frontotemporal regions compared to FES patients. However, this distinction was not observed while performing a category version of the VFT. In addition, no associations between DUP and brain cortical activity were observed in the FES group during either VFT. In conclusion, we did not find an association between DUP and frontotemporal cortical activities. This might be because neurodevelopmental disturbances result in neurocognitive deficits long before psychotic symptoms onset.
Discovery of Anti-inflammatory Ingredients in Chinese Herbal Formula Kouyanqing Granule based on Relevance Analysis between Chemical Characters and Biological Effects
Authors: Liu Hong , Zheng Yan-fang , Li Chu-yuan , Zheng Yu-ying , Wang De-qin , Wu Zhong , Huang Lin , Wang Yong-gang , Li Pei-bo , Peng Wei , Su Wei-wei 
Published: December 2015

AbstractKouyanqing Granule (KYQG) is a traditional Chinese herbal formula composed of Flos lonicerae (FL), Radix scrophulariae (RS), Radix ophiopogonis (RO), Radix asparagi (RA) and Radix et rhizoma glycyrrhizae (RG). In contrast with the typical method of separating and then biologicalily testing the components individually, this study was designed to establish an approach in order to define the core bioactive ingredients of the anti-inflammatory effects of KYQG based on the relevance analysis between chemical characters and biological effects. Eleven KYQG samples with different ingredients were prepared by changing the ratios of the 5 herbs. Thirty-eight ingredients in KYQG were identified using Ultra-fast liquid chromatography-Diode array detector-Quadrupole-Time-of-flight-Tandem mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) technology. Human oral keratinocytes (HOK) were cultured for 24 hours with 5% of Cigarette smoke extract (CSE) to induce inflammation stress. Interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8) and tumour necrosis factor-α (TNF-α) were evaluated after treatment with the eleven KYQG samples. Grey relational analysis(GRA), Pearson’s correlations (PCC) and partial least-squares (PLS) were utilized to evaluate the contribution of each ingredient. The results indicated that KYQG significantly reduced interleukin-1β, interleukin-6, interleukin-8 and tumour necrosis factor-α levels, in which lysine, γ-aminobutyric acid, chelidonic acid, tyrosine, harpagide, neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, isoquercitrin, luteolin-7-o-glucoside, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, angoroside C, harpagoside, cinnamic acid and ruscogenin play a vital role.
FgMon1, a guanine nucleotide exchange factor of FgRab7, is important for vacuole fusion, autophagy and plant infection in Fusarium graminearum
Authors: Li Ying , Li Bing , Liu Luping , Chen Huaigu , Zhang Haifeng , Zheng Xiaobo , Zhang Zhengguang 
Published: December 2015

AbstractThe Ccz1-Mon1 protein complex, the guanine nucleotide exchange factor (GEF) of the late endosomal Rab7 homolog Ypt7, is required for the late step of multiple vacuole delivery pathways, such as cytoplasm-to-vacuole targeting (Cvt) pathway and autophagy processes. Here, we identified and characterized the yeast Mon1 homolog in Fusarium graminearum, named FgMon1. FgMON1 encodes a trafficking protein and is well conserved in filamentous fungi. Targeted gene deletion showed that the ∆Fgmon1 mutant was defective in vegetative growth, asexual/sexual development, conidial germination and morphology, plant infection and deoxynivalenol production. Cytological examination revealed that the ∆Fgmon1 mutant was also defective in vacuole fusion and autophagy and delayed in endocytosis. Yeast two hybrid and in vitro GST-pull down assays approved that FgMon1 physically interacts with a Rab GTPase FgRab7 which is also important for the development, infection, membrane fusion and autophagy in F. graminearum. FgMon1 likely acts as a GEF of FgRab7 and constitutively activated FgRab7 was able to rescue the defects of the ∆Fgmon1 mutant. In summary, our study provides evidences that FgMon1 and FgRab7 are critical components that modulate vesicle trafficking, endocytosis and autophagy and thereby affect the development, plant infection and DON production of F. graminearum.
CRISPR/Cas9-mediated knockout of factors in non-homologous end joining pathway enhances gene targeting in silkworm cells
Authors: Zhu Li , Mon Hiroaki , Xu Jian , Lee Jae Man , Kusakabe Takahiro 
Published: December 2015

AbstractGene targeting can be achieved by precise genetic modifications through homology-directed repair (HDR) after DNA breaks introduced by genome editing tools such as CRISPR/Cas9 system. The most common form of HDR is homologous recombination (HR). Binding to the DNA breaks by HR factors is thought to compete with non-homologous end joining (NHEJ), an alternative DNA repair pathway. Here, we knocked out the factors in NHEJ by CRISPR/Cas9 system in silkworm cells, so that increased the activities of HR up to 7-fold. Also efficient HR-mediated genome editing events occurred between the chromosomal BmTUDOR-SN gene and donor DNA sequences with an EGFP gene in the middle of two homologous arms for the target gene. Utilizing the NHEJ-deficient silkworm cells, we found that homologous arms as short as 100 bp in donor DNA could be designed to perform precise genome editing. These studies should greatly accelerate investigations into genome editing of silkworm.
Ballistic Thermal Transport in Carbyne and Cumulene with Micron-Scale Spectral Acoustic Phonon Mean Free Path
Authors: Wang Mingchao , Lin Shangchao 
Published: December 2015

AbstractThe elastic modulus of carbyne, a one-dimensional carbon chain, was recently predicted to be much higher than graphene. Inspired by this discovery and the fundamental correlation between elastic modulus and thermal conductivity, we investigate the intrinsic thermal transport in two carbon allotropes: carbyne and cumulene. Using molecular dynamics simulations, we discover that thermal conductivities of carbyne and cumulene at the quantum-corrected room temperature can exceed 54 and 148 kW/m/K, respectively, much higher than that for graphene. Such conductivity is attributed to high phonon energies and group velocities, as well as reduced scattering from non-overlapped acoustic and optical phonon modes. The prolonged spectral acoustic phonon lifetime of 30–110 ps and mean free path of 0.5–2.5 μm exceed those for graphene and allow ballistic phonon transport along micron-length carbon chains. Tensile extensions can enhance the thermal conductivity of carbyne due to the increased phonon density of states in the acoustic modes and the increased phonon lifetime from phonon bandgap opening. These findings provide fundamental insights into phonon transport and band structure engineering through tensile deformation in low-dimensional materials and will inspire studies on carbyne, cumulene and boron nitride chains for their practical deployments in nano-devices.
Serum Metabolomics to Identify the Liver Disease-Specific Biomarkers for the Progression of Hepatitis to Hepatocellular Carcinoma
Authors: Gao Rong , Cheng Jianhua , Fan Chunlei , Shi Xiaofeng , Cao Yuan , Sun Bo , Ding Huiguo , Hu Chengjin , Dong Fangting , Yan Xianzhong 
Published: December 2015

AbstractHepatocellular carcinoma (HCC) is a common malignancy that has region specific etiologies. Unfortunately, 85% of cases of HCC are diagnosed at an advanced stage. Reliable biomarkers for the early diagnosis of HCC are urgently required to reduced mortality and therapeutic expenditure. We established a non-targeted gas chromatography–time of flight–mass spectrometry (GC-TOFMS) metabolomics method in conjunction with Random Forests (RF) analysis based on 201 serum samples from healthy controls (NC), hepatitis B virus (HBV), liver cirrhosis (LC) and HCC patients to explore the metabolic characteristics in the progression of hepatocellular carcinogenesis. Ultimately, 15 metabolites were identified intimately associated with the process. Phenylalanine, malic acid and 5-methoxytryptamine for HBV vs. NC, palmitic acid for LC vs. HBV and asparagine and β-glutamate for HCC vs. LC were screened as the liver disease-specific potential biomarkers with an excellent discriminant performance. All the metabolic perturbations in these liver diseases are associated with pathways for energy metabolism, macromolecular synthesis and maintaining the redox balance to protect tumor cells from oxidative stress.
NMR structure and function of Helicoverpa armigera sterol carrier protein-2, an important insecticidal target from the cotton bollworm
Authors: Ma Haihao , Ma Yuemin , Liu Xuehui , Dyer David H. , Xu Pingyong , Liu Kaiyu , Lan Que , Hong Huazhu , Peng Jianxin , Peng Rong 
Published: December 2015

AbstractThe cotton bollworm, Helicoverpa armigera, has developed strong resistance to many insecticides. Sterol Carrier Protein-2 (SCP-2) is an important non-specific lipid transfer protein in insects and appears to be a potential new target. In order to elucidate the structure and function of Helicoverpa armigera SCP-2 (HaSCP-2), NMR spectroscopy, docking simulations, mutagenesis and bioassays were performed. HaSCP-2 composed of five α-helices and four stranded β-sheets. The folds of α-helices and β-sheets interacted together to form a hydrophobic cavity with putative entrance and exit openings, which served as a tunnel for accommodating and transporting of lipids. Several sterols and fatty acids could interact with HaSCP-2 via important hydrophobic sites, which could be potential targets for insecticides. Mutagenesis experiments indicated Y51, F53, F89, F110, I117 and Q131 may be the key functional sites. HaSCP-2 showed high cholesterol binding activity and SCP-2 inhibitors (SCPIs) could inhibit the biological activity of HaSCP-2. SCPI-treated larvae at young stage showed a significant decrease of cholesterol uptake in vivo. Our study describes for the first time a NMR structure of SCP-2 in lepidopteran H. armigera and reveals its important function in cholesterol uptake, which facilitates the screening of effective insecticides targeting the insect cholesterol metabolism.
The Effect of Irreversible Electroporation on the Femur: Experimental Study in a Rabbit Model
Authors: Song Yue , Zheng Jingjing , Yan Mingwei , Ding Weidong , Xu Kui , Fan Qingyu , Li Zhao 
Published: December 2015

AbstractIrreversible electroporation (IRE) is a novel ablation method that has been tested in humans with lung, prostate, kidney, liver, lymph node and presacral cancers. As a new non-thermal treatment, the use of IRE to ablate tumors in the musculoskeletal system might reduce the incidence of fractures. We aimed to determine the ablation threshold of cortical bone and to evaluate the medium- and long-term healing process and mechanical properties of the femur in a rabbit model post-IRE ablation. The ablation threshold of cortical bone was between 1090 V/cm and 1310 V/cm (120 pulses). IRE-ablated femurs displayed no detectable fracture but did exhibit signs of recovery, including osteoblast regeneration, angiogenesis and bone remodeling. In the ablation area, revascularization appeared at 4 weeks post-IRE. Osteogenic activity peaked 8 weeks post-IRE and remained high at 12 weeks. The mechanical strength decreased briefly 4 weeks post-IRE but returned to normal levels within 8 weeks. Our experiment revealed that IRE ablation preserved the structural integrity of the bone cortex and the ablated bone was able to regenerate rapidly. IRE may hold unique promise forin situbone tissue ablation because rapid revascularization and active osteogenesis in the IRE ablation area are possible.
Ionic Liquid Directed Mesoporous Carbon Nanoflakes as an Effiencient Electrode material
Authors: Kong Lirong , Chen Wei 
Published: December 2015

AbstractSupercapacitors are considered to be the most promising approach to meet the pressing requirements for energy storage devices. The electrode materials for supercapacitors have close relationship with their electrochemical properties and thus become the key point to improve their energy storage efficiency. Herein, by using poly (vinylidene fluoride-co-hexafluoropropylene) and ionic liquid as the dual templates, polyacrylonitrile as the carbon precursor, a flake-like carbon material was prepared by a direct carbonization method. In this method, poly (vinylidene fluoride-co-hexafluoropropylene) worked as the separator for the formation of isolated carbon flakes while aggregated ionic liquid worked as the pore template. The obtained carbon flakes exhibited a specific capacitance of 170 F/g at 0.1 A/g, a high energy density of 12.2 Wh/kg and a high power density of 5 kW/kg at the current of 10 A/g. It also maintained a high capacitance retention capability with almost no declination after 500 charge-discharge cycles. The ionic liquid directed method developed here also provided a new idea for the preparation of hierarchically porous carbon nanomaterials.
Switchable directional scattering of electromagnetic radiation with subwavelength asymmetric silicon dimers
Authors: Albella Pablo , Shibanuma Toshihiko , Maier Stefan A. 
Published: December 2015

AbstractHigh refractive index dielectric nanoparticles show high promise as a complementary nanophotonics platform due to compared with plasmonic nanostructures low absorption losses and the co-existence of magnetic and electric resonances. Here we explore their use as resonantly enhanced directional scatterers. We theoretically demonstrate that an asymmetric dimer of silicon nanoparticles shows tuneable directional scattering depending on the frequency of excitation. This is due to the interference between electric and magnetic dipoles excited in each nanoparticle, enabling directional control of the scattered light. Interestingly, this control can be achieved regardless of the polarization direction with respect to the dimer axis; however, difference in the polarization can shift the wavelengths at which the directional scattering is achieved. We also explore the application of such an asymmetric nanoantenna as a tuneable routing element in a nanometer scale, suggesting applications in optical nanocircuitry.
Modeling the toxicity of chemical pesticides in multiple test species using local and global QSTR approaches
Authors: Basant Nikita , Gupta Shikha , Singh Kunwar P. 
Published: December 2015

Abstract
The safety assessment processes require the toxicity data of chemicals in multiple test species and thus, emphasize the need for computational methods capable of toxicity prediction in multiple test species. Pesticides are designed toxic substances and find extensive applications worldwide. In this study, we have established local and global QSTR (quantitative structure–toxicity relationship) and ISC QSAAR (interspecies correlation quantitative structure activity–activity relationship) models for predicting the toxicities of pesticides in multiple aquatic test species using the toxicity data in crustacean (Daphnia magna, Americamysis bahia, Gammarus fasciatus, and Penaeus duorarum) and fish (Oncorhynchus mykiss and Lepomis macrochirus) species in accordance with the OECD guidelines. The ensemble learning based QSTR models (decision tree forest, DTF and decision tree boost, DTB) were constructed and validated using several statistical coefficients derived on the test data. In all the QSTR and QSAAR models, Log P was an important predictor. The constructed local, global and interspecies QSAAR models yielded high correlations (R2) of &gt;0.941; &gt;0.943 and &gt;0.826, respectively between the measured and model predicted endpoint toxicity values in the test data. The performances of the local and global QSTR models were comparable. Furthermore, the chemical applicability domains of these QSTR/QSAAR models were determined using the leverage and standardization approaches. The results suggest for the appropriateness of the developed QSTR/QSAAR models to reliably predict the aquatic toxicity of structurally diverse pesticides in multiple test species and can be used for the screening and prioritization of new pesticides.
3D printing technique for the development of non‐planar electromagnetic bandgap structures for antenna applications
Authors: Jun S. , Sanz‐Izquierdo B. , Parker E.A. 
Published: December 2015

The use of 3D printing for the development of non‐planar electromagnetic bandgap (EBG) structures for antenna applications is proposed. A coplanar waveguide (CPW) fed antenna is tested on a non‐planar EBG substrate, fabricated using additive manufacturing techniques. Inexpensive fuse filament fabrication is used as the fabrication process. Silver‐loaded conducting ink is employed for the metallic components of the EBG. The CPW antenna on the non‐planar EBG structure has a satisfactory reflection coefficient at 2.45 GHz, which is suitable for Bluetooth/WLAN communications. The radiation patterns have reduced back lobes and improved gain compared with the antenna in free space.
Optical pulse generation by polarisation modulation and fibre dispersion
Authors: Zhang Fangzheng , Gao Bindong , Pan Shilong 
Published: December 2015

Optical pulse generation based on polarisation modulation and fibre dispersion is proposed that has the ability of generating multiform optical pulse trains by applying a single electro‐optic modulator and a low frequency driving signal. In the experiment, using a 10 GHz RF source, the generation of a 20 GHz time and polarisation interleaved optical pulse train, a 10 GHz single‐polarisation pulse train and a 20 GHz single‐polarisation pulse train is demonstrated. By using differential group delay in a polarisation maintaining fibre to realise time‐division‐multiplexing, the repetition rate of the pulse train can be further increased. Based on this principle, the generation of a 40 GHz time and polarisation interleaved optical pulse train, and a 40 GHz single‐polarisation pulse train is successfully implemented.
Wideband tissue‐equivalent liquid for multiband specific absorption rate measurements (850 MHz–2.5 GHz)
Authors: Mouthaan R. , Loader B. 
Published: December 2015

A tissue‐equivalent liquid has been developed that yields permittivity and conductivity values within ±10% of the IEEE 1528, IEC 62209 and FCC OET65‐C target ‘head’ values between 850 MHz and 2.5 GHz. The formulation of the new tissue‐equivalent liquid is presented along with measurements of the dielectric properties, thermal properties and density.
Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding
Authors: Zhao Yusheng , Li Zuo , Liu Guozheng , Jiang Yong , Maurer Hans Peter , Würschum Tobias , Mock Hans-Peter , Matros Andrea , Ebmeyer Erhard , Schachschneider Ralf , Kazman Ebrahim , Schacht Johannes , Gowda Manje , Longin C. Friedrich H. , Reif Jochen C. 
Published: December 2015

Significance
Selfing species wheat are bred as pure-line varieties with stagnating yield growths. In contrast, selection gain in maize is high, owing to massive investment sustained by hybrid seed sales, coupled with an efficient exploitation of hybrid vigor. We have developed a three-step strategy for establishing a heterotic pattern, which was one of the central unsolved challenges for initiating hybrid breeding programs. The benefits of our approach are demonstrated using data for wheat, but the strategy is relevant for several autogamous crops. Our three-step approach facilitates identification of a heterotic pattern, and thus may contribute to meeting the global challenge of increasing demand for food, feed, and fuel.