bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-quasiparticle transport and resistivity saturation: a view from the large-N limit
Authors: Werman Yochai , Kivelson Steven A. , Berg Erez
Published: February 2017

The electron dynamics in metals are usually well described by the semiclassical approximation for long-lived quasiparticles. However, in some metals, the scattering rate of the electrons at elevated temperatures becomes comparable to the Fermi energy; then, this approximation breaks down, and the full quantum-mechanical nature of the electrons must be considered. In this work, we study a solvable, large-N electron–phonon model, which at high temperatures enters the non-quasiparticle regime. In this regime, the model exhibits “resistivity saturation” to a temperature-independent value of the order of the quantum of resistivity—the first analytically tractable model to do so. The saturation is not due to a fundamental limit on the electron lifetime, but rather to the appearance of a second conductivity channel. This is suggestive of the phenomenological “parallel resistor formula”, known to describe the resistivity of a variety of saturating metals.
Decreased expression of STING predicts poor prognosis in patients with gastric cancer
Authors: Song Shushu , Peng Peike , Tang Zhaoqing , Zhao Junjie , Wu Weicheng , Li Haojie , Shao Miaomiao , Li Lili , Yang Caiting , Duan Fangfang , Zhang Mingming , Zhang Jie , Wu Hao , Li Can , Wang Xuefei , Wang Hongshan , Ruan Yuanyuan , Gu Jianxin
Published: February 2017

STING (stimulator of interferon genes) has recently been found to play an important role in host defenses against virus and intracellular bacteria via the regulation of type-I IFN signaling and innate immunity. Chronic infection with Helicobacter pylori is identified as the strongest risk factor for gastric cancer. Thus, we aim to explore the function of STING signaling in the development of gastric cancer. Immunohistochemistry was used to detect STING expression in 217 gastric cancer patients who underwent surgical resection. STING protein expression was remarkably decreased in tumor tissues compared to non-tumor tissues, and low STING staining intensity was positively correlated with tumor size, tumor invasion depth, lymph mode metastasis, TNM stage, and reduced patients’ survival. Multivariate analysis identified STING as an independent prognostic factor, which could improve the predictive accuracy for overall survival when incorporated into TNM staging system. In vitro studies revealed that knock-down of STING promoted colony formation, viability, migration and invasion of gastric cancer cells, and also led to a defect in cytosolic DNA sensing. Besides, chronic H. pylori infection up-regulated STING expression and activated STING signaling in mice. In conclusion, STING was proposed as a novel independent prognostic factor and potential immunotherapeutic target for gastric cancer.
Three novel ANO5 missense mutations in Caucasian and Chinese families and sporadic cases with gnathodiaphyseal dysplasia
Authors: Jin Lingling , Liu Yi , Sun Fanyue , Collins Michael T. , Blackwell Keith , Woo Albert S. , Reichenberger Ernst J. , Hu Ying
Published: February 2017

Gnathodiaphyseal dysplasia (GDD; MIM#166260) is an autosomal dominant syndrome with characteristic cemento-osseous lesions of jawbones, bone fragility, and diaphyseal sclerosis of tubular bones. To date, only five mutations in the proposed calcium-activated chloride channel ANO5/TMEM16E gene have been identified. In this study, we describe two families and two singular patients with three new mutations. One Caucasian family with seven affected members exhibited frequent bone fractures and florid osseous dysplasia (p.Cys356Tyr), while one Chinese family with two affected members suffered from cementoma and purulent osteomyelitis (p.Cys360Tyr). In addition, two different novel mutations (p.Gly518Glu and p.Arg215Gly) were identified in sporadic patients without family history. In vitro studies overexpressing GDD mutations (p.Cys356Tyr and p.Cys360Tyr) showed significantly reduced ANO5 protein. It appears that all GDD mutations known so far locate in an extracellular domain following the first transmembrane domain or in the 4th putative transmembrane domain. Both wild-type and mutant ANO5 protein localize to the endoplasmic reticulum. After Ano5 gene knock-down with shRNA in MC3T3-E1 osteoblast precursors we saw elevated expression of osteoblast-related genes such as Col1a1, osteocalcin, osterix and Runx2 as well as increased mineral nodule formation in differentiating cells. Our data suggest that ANO5 plays a role in osteoblast differentiation.
DoGMP1 from Dendrobium officinale contributes to mannose content of water-soluble polysaccharides and plays a role in salt stress response
Authors: He Chunmei , Yu Zhenming , Teixeira da Silva Jaime A. , Zhang Jianxia , Liu Xuncheng , Wang Xiaojuan , Zhang Xinhua , Zeng Songjun , Wu Kunlin , Tan Jianwen , Ma Guohua , Luo Jianping , Duan Jun
Published: February 2017

GDP-mannose pyrophosphorylase (GMP) catalyzed the formation of GDP-mannose, which serves as a donor for the biosynthesis of mannose-containing polysaccharides. In this study, three GMP genes from Dendrobium officinale (i.e., DoGMPs) were cloned and analyzed. The putative 1000 bp upstream regulatory region of these DoGMPs was isolated and cis-elements were identified, which indicates their possible role in responses to abiotic stresses. The DoGMP1 protein was shown to be localized in the cytoplasm. To further study the function of the DoGMP1 gene, 35S:DoGMP1 transgenic A. thaliana plants with an enhanced expression level of DoGMP1 were generated. Transgenic plants were indistinguishable from wild-type (WT) plants in tissue culture or in soil. However, the mannose content of the extracted water-soluble polysaccharides increased 67%, 96% and 92% in transgenic lines #1, #2 and #3, respectively more than WT levels. Germination percentage of seeds from transgenic lines was higher than WT seeds and the growth of seedlings from transgenic lines was better than WT seedlings under salinity stress (150 mM NaCl). Our results provide genetic evidence for the involvement of GMP genes in the biosynthesis of mannose-containing polysaccharides and the mediation of GMP genes in the response to salt stress during seed germination and seedling growth.
A putative MYB35 ortholog is a candidate for the sex-determining genes in Asparagus officinalis
Authors: Tsugama Daisuke , Matsuyama Kohei , Ide Mayui , Hayashi Masato , Fujino Kaien , Masuda Kiyoshi
Published: February 2017

Asparagus officinalis (garden asparagus) is a dioecious perennial crop. For agricultural production of A. officinalis, male plants have advantages over female plants. The dioecism of A. officinalis is determined by the single dominant masculinizing M locus, which is involved in tapetal cell development in stamens, but thus far no specific M locus genes have been identified. We re-analyzed previously published RNA-Seq data for the A. officinalis transcriptome, cloned some genes, and discovered that a putative ortholog of MYB35, which is indispensable for tapetal cell development in Arabidopsis thaliana, is absent in the genome of female plants in A. officinalis. In a reverse transcription-PCR analysis, this gene (AoMYB35) exhibited strong expression in stamens in male flowers at an early developmental stage. In an in situ hybridization analysis, AoMYB35 mRNA was detected in tapetal cells in young male flowers. GFP-fused AoMYB35 was detected in the nucleus when expressed in onion epidermal cells. These results suggest that AoMYB35 is a male-specific gene encoding a putative transcription factor that acts in tapetal cells at an early stage of flower development in A. officinalis. Together, the results support the idea that AoMYB35 is a candidate for one of the M locus genes in A. officinalis.
Uncertainties in the Shuttle Radar Topography Mission (SRTM) Heights: Insights from the Indian Himalaya and Peninsula
Authors: Mukul Manas , Srivastava Vinee , Jade Sridevi , Mukul Malay
Published: February 2017

The Shuttle Radar Topography Mission (SRTM) Digital Terrain Elevation Data (DTED) are used with the consensus view that it has a minimum vertical accuracy of 16 m absolute error at 90% confidence (Root Mean Square Error (RMSE) of 9.73 m) world-wide. However, vertical accuracy of the data decreases with increase in slope and elevation due to presence of large outliers and voids. Therefore, studies using SRTM data “as is”, especially in regions like the Himalaya, are not statistically meaningful. New data from ~200 high-precision static Global Position System (GPS) Independent Check Points (ICPs) in the Himalaya and Peninsular India indicate that only 1-arc X-Band data are usable “as is” in the Himalaya as it has height accuracy of 9.18 m (RMSE). In contrast, recently released (2014–2015) “as-is” 1-arc and widely used 3-arc C-Band data have a height accuracy of RMSE 23.53 m and 47.24 m and need to be corrected before use. Outlier and void filtering improves the height accuracy to RMSE 8 m, 10.14 m, 14.38 m for 1-arc X and C-Band and 3-arc C-Band data respectively. Our study indicates that the C-Band 90 m and 30 m DEMs are well-aligned and without any significant horizontal offset implying that area and length computations using both the datasets have identical values.
Respiratory impedance is correlated with morphological changes in the lungs on three-dimensional CT in patients with COPD
Authors: Karayama Masato , Inui Naoki , Mori Kazutaka , Kono Masato , Hozumi Hironao , Suzuki Yuzo , Furuhashi Kazuki , Hashimoto Dai , Enomoto Noriyuki , Fujisawa Tomoyuki , Nakamura Yutaro , Watanabe Hiroshi , Suda Takafumi
Published: February 2017

The forced oscillation technique provides information concerning respiratory impedance, which comprises resistance and reactance of the respiratory system. However, its relationship with morphological changes of the lungs in chronic obstructive pulmonary disease (COPD) remains unclear. Respiratory impedance and spirometric data were evaluated in 98 patients with COPD and 49 reference subjects. Wall thickness (WT) and airway intraluminal area (Ai) of third- to sixth-generation bronchi, and percentage low-attenuation area with less than −950 HU (%LAA) of lungs were measured using three-dimensional computed tomography. COPD patients had higher respiratory impedance, decreased Ai, and increased %LAA compared with reference subjects. Indices of respiratory resistance and reactance and forced expiratory volume in 1 second (FEV1) were correlated with Ai, and the association between percent predicted FEV1 and Ai was predominant in distal bronchi. The difference in respiratory resistance between 5 Hz and 20 Hz (R5–R20) and FEV1/forced vital capacity ratio (FEV1/FVC) were correlated with WT. The %LAA was correlated with the FEV1/FVC ratio and respiratory reactance. Airway function measurements with the forced oscillation technique provide complementary information to spirometry in COPD.
Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters
Authors: Helbo Alexandra Søgaard , Lay Fides D. , Jones Peter A. , Liang Gangning , Grønbæk Kirsten
Published: February 2017

Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.
Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal
Authors: Shaban Mohamed , Ahmed Ashour M. , Abdel-Rahman Ehab , Hamdy Hany
Published: February 2017

Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm3) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application.
Structural insights into human angiogenin variants implicated in Parkinson’s disease and Amyotrophic Lateral Sclerosis
Authors: Bradshaw William J. , Rehman Saima , Pham Tram T. K. , Thiyagarajan Nethaji , Lee Rebecca L. , Subramanian Vasanta , Acharya K. Ravi
Published: February 2017

Mutations in Angiogenin (ANG), a member of the Ribonuclease A superfamily (also known as RNase 5) are known to be associated with Amyotrophic Lateral Sclerosis (ALS, motor neurone disease) (sporadic and familial) and Parkinson’s Disease (PD). In our previous studies we have shown that ANG is expressed in neurons during neuro-ectodermal differentiation, and that it has both neurotrophic and neuroprotective functions. In addition, in an extensive study on selective ANG-ALS variants we correlated the structural changes to the effects on neuronal survival and the ability to induce stress granules in neuronal cell lines. Furthermore, we have established that ANG-ALS variants which affect the structure of the catalytic site and either decrease or increase the RNase activity affect neuronal survival. Neuronal cell lines expressing the ANG-ALS variants also lack the ability to form stress granules. Here, we report a detailed experimental structural study on eleven new ANG-PD/ALS variants which will have implications in understanding the molecular basis underlying their role in PD and ALS.
Clay mineralogical and geochemical proxies of the East Asian summer monsoon evolution in the South China Sea during Late Quaternary
Authors: Chen Quan , Liu Zhifei , Kissel Catherine
Published: February 2017

The East Asian summer monsoon controls the climatic regime of an extended region through temperature and precipitation changes. As the East Asian summer monsoon is primarily driven by the northern hemisphere summer insolation, such meteorological variables are expected to significantly change on the orbital timescale, influencing the composition of terrestrial sediments in terms of both mineralogy and geochemistry. Here we present clay mineralogy and major element composition of Core MD12-3432 retrieved from the northern South China Sea, and we investigate their relationship with the East Asian summer monsoon evolution over the last 400 ka. The variability of smectite/(illite + chlorite) ratio presents a predominant precession periodicity, synchronous with the northern hemisphere summer insolation changes and therefore with that of the East Asian summer monsoon. Variations in K2O/Al2O3 are characterized by eccentricity cycles, increasing during interglacials when the East Asian summer monsoon is enhanced. Based on the knowledge of sediment provenances, we suggest that these two proxies in the South China Sea are linked to the East Asian summer monsoon evolution with different mechanisms, which are (1) contemporaneous chemical weathering intensity in Luzon for smectite/(illite + chlorite) ratio and (2) river denudation intensity for K2O/Al2O3 ratio of bulk sediment.
Cognitive impairment categorized in community-dwelling older adults with and without dementia using in-home sensors that recognise activities of daily living
Authors: Urwyler Prabitha , Stucki Reto , Rampa Luca , Müri René , Mosimann Urs P , Nef Tobias
Published: February 2017

Cognitive impairment due to dementia decreases functionality in Activities of Daily Living (ADL). Its assessment is useful to identify care needs, risks and monitor disease progression. This study investigates differences in ADL pattern-performance between dementia patients and healthy controls using unobtrusive sensors. Around 9,600 person-hours of activity data were collected from the home of ten dementia patients and ten healthy controls using a wireless-unobtrusive sensors and analysed to detect ADL. Recognised ADL were visualized using activity maps, the heterogeneity and accuracy to discriminate patients from healthy were analysed. Activity maps of dementia patients reveal unorganised behaviour patterns and heterogeneity differed significantly between the healthy and diseased. The discriminating accuracy increases with observation duration (0.95 for 20 days). Unobtrusive sensors quantify ADL-relevant behaviour, useful to uncover the effect of cognitive impairment, to quantify ADL-relevant changes in the course of dementia and to measure outcomes of anti-dementia treatments.
Prediction of biomarkers of oral squamous cell carcinoma using microarray technology
Authors: Li Guang , Li Xian , Yang Meng , Xu Lvzi , Deng Shixiong , Ran Longke
Published: February 2017

Microarray data is used to screen the genes of oral squamous cell carcinoma (OSCC). Microarray data of OSCC and normal tissues were downloaded from GEO database and analyzed with Benjamini-Hochberg (BH) method. Differentially expressed genes (DEGs) were then uploaded on DAVID database to process enrichment analysis. Target genes were finally chosen for verification experiment in vitro and in vivo. 78 DEGs were selected from 54676 genes, including 46 up- and 32 down- regulation. GO term showed that these genes were related to epidermal growth (biological processes), extracellular region (cellular components) and cytokines activity (molecular function). Protein network interaction demonstrated that OSCC was closely allied to the five key genes including CXCL10, IFI6, IFI27, ADAMTS2 and COL5A1, which was consistent with the RT-PCR data. High-expressed gene CXCL10 was chosen for further cell experiment, and the results indicated that CXCL10 can promote the proliferation, migration and invasion of normal cells and inhibited the cancer cells after si-RNA transfection. Moreover, it has been proven that CXCL10 was possibly related to the occurrence and development of OSCC. Understanding the regulation of OSCC expression will shed light on the screening of cancer biomarker.
Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor
Authors: Goto-Ito Sakurako , Yamagata Atsushi , Takahashi Tomio S. , Sato Yusuke , Fukai Shuya
Published: February 2017

Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3β to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3β, the DUF1767–OB-fold domains of TDRD3 and their complex at 3.44 Å, 1.62 Å and 3.6 Å resolutions, respectively. The toroidal-shaped catalytic domain of TOP3β binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3β. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIα (TOP3α)–RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3β to avoid the non-cognate interaction with TOP3α.
Impact of Including Peritumoral Edema in Radiotherapy Target Volume on Patterns of Failure in Glioblastoma following Temozolomide-based Chemoradiotherapy
Authors: Choi Seo Hee , Kim Jun Won , Chang Jee Suk , Cho Jae Ho , Kim Se Hoon , Chang Jong Hee , Suh Chang-Ok
Published: February 2017

We assessed the impact of including peritumoral edema in radiotherapy volumes on recurrence patterns among glioblastoma multiforme (GBM) patients treated with standard chemoradiotherapy (CRT). We analyzed 167 patients with histologically confirmed GBM who received temozolomide (TMZ)-based CRT between May 2006 and November 2012. The study cohort was divided into edema (+) (n = 130) and edema (−) (n = 37) groups, according to whether the entire peritumoral edema was included. At a median follow-up of 20 months (range, 2–99 months), 118 patients (71%) experienced progression/recurrence (infield: 69%; marginal: 26%; outfield: 16%; CSF seeding: 12%). The median overall survival and progression-free survival were 20 months and 15 months, respectively. The marginal failure rate was significantly greater in the edema (−) group (37% vs. 22%, p = 0.050). Among 33 patients who had a favorable prognosis (total resection and MGMT-methylation), the difference in the marginal failure rates was increased (40% vs. 14%, p = 0.138). Meanwhile, treatment of edema did not significantly increase the incidence of pseudoprogression/radiation necrosis (edema (−) 49% vs. (+) 37%, p = 0.253). Inclusion of peritumoral edema in the radiotherapy volume can reduce marginal failures following TMZ-based CRT without increasing pseudoprogression/radiation necrosis.
Nanocarbon condensation in detonation
Authors: Bastea Sorin
Published: February 2017

We analyze the definition of the Gibbs free energy of a nanoparticle in a reactive fluid environment, and propose an approach for predicting the size of carbon nanoparticles produced by the detonation of carbon-rich explosives that regards their condensation as a nucleation process and takes into account absolute entropy effects of the cluster population. The results are consistent with experimental observations and indicate that such entropy considerations are important for determining chemical equilibrium states in energetic materials that contain an excess of carbon. The analysis may be useful for other applications that deal with the nucleation of nanoparticles under reactive conditions.
Photodeposited Pd Nanoparticles with Disordered Structure for Phenylacetylene Semihydrogenation
Authors: Fan Qining , He Sha , Hao Lin , Liu Xin , Zhu Yue , Xu Sailong , Zhang Fazhi
Published: February 2017

Developing effective heterogeneous metal catalysts with high selectivity and satisfactory activity for chemoselective hydrogenation of alkyne to alkene is of great importance in the chemical industry. Herein, we report our efforts to fabricate TiO2-supported Pd catalysts by a photodeposition method at room temperature for phenylacetylene semihydrogenation to styrene. The resulting Pd/TiO2 catalyst, possessing smaller Pd ensembles with ambiguous lattice fringes and more low coordination Pd sites, exhibits higher styrene selectivity compared to two contrastive Pd/TiO2 samples with larger ensembles and well-organized crystal structure fabricated by deposition-precipitation or photodeposition with subsequent thermal treatment at 300 °C. The sample derived from photodeposition exhibits greatly slow styrene hydrogenation in kinetic evaluation because the disordered structure of Pd particles in photodeposited Pd/TiO2 may prevent the formation of β-hydride phases and probably produce more surface H atoms, which may favor high styrene selectivity.
Annexin-A5 organized in 2D-network at the plasmalemma eases human trophoblast fusion
Authors: Degrelle Severine A. , Gerbaud Pascale , Leconte Ludovic , Ferreira Fatima , Pidoux Guillaume
Published: February 2017

Only a limited number of human cells can fuse to form a multinucleated syncytium. Cell fusion occurs as part of the differentiation of some cell types, including myotubes in muscle and osteoclasts in remodeling bone. In the differentiation of the human placenta, mononuclear cytotrophoblasts aggregate and fuse to form endocrinologically active, non-proliferative, multinucleated syncytia. These syncytia allow the exchange of nutrients and gases between the maternal and fetal circulation. Alteration of syncytial formation during pregnancy affects fetal growth and the outcome of the pregnancy. Here, we demonstrate the role of annexin A5 (AnxA5) in syncytial formation by cellular delivery of recombinant AnxA5 and RNA interference. By a variety of co-immunoprecipitation, immunolocalization and proximity experiments, we show that a pool of AnxA5 organizes at the inner-leaflet of the plasma membrane in the vicinity of a molecular complex that includes E-Cadherin, α-Catenin and β-Catenin, three proteins previously shown to form adherens junctions implicated in cell fusion. A combination of knockdown and reconstitution experiments with AnxA5, with or without the ability to self-assemble in 2D-arrays, demonstrate that this AnxA5 2D-network mediates E-Cadherin mobility in the plasmalemma that triggers human trophoblasts aggregation and thereby cell fusion.
A critical role of platelet TGF-β release in podoplanin-mediated tumour invasion and metastasis
Authors: Takemoto Ai , Okitaka Mina , Takagi Satoshi , Takami Miho , Sato Shigeo , Nishio Makoto , Okumura Sakae , Fujita Naoya
Published: February 2017

The tumour microenvironment is critical for various characteristics of tumour malignancies. Platelets, as part of the tumour microenvironment, are associated with metastasis formation via increasing the rate of tumour embolus formation in microvasculature. However, the mechanisms underlying the ability of tumour cells to acquire invasiveness and extravasate into target organs at the site of embolization remain unclear. In this study, we reported that platelet aggregation-inducing factor podoplanin expressed on tumour cell surfaces were found to not only promote the formation of tumour-platelet aggregates via interaction with platelets, but also induced the epithelial-mesenchymal transition (EMT) of tumour cells by enhancing transforming growth factor-β (TGF-β) release from platelets. In vitro and in vivo analyses revealed that podoplanin-mediated EMT resulted in increased invasiveness and extravasation of tumour cells. Treatment of mice with a TGF-β-neutralizing antibody statistically suppressed podoplanin-mediated distant metastasis in vivo, suggesting that podoplanin promoted haematogenous metastasis in part by releasing TGF-β from platelets that was essential for EMT of tumour cells. Therefore, our findings suggested that blocking the TGF-β signalling pathway might be a promising strategy for suppressing podoplanin-mediated haematogenous metastasis in vivo.
Application of Machine-Learning Models to Predict Tacrolimus Stable Dose in Renal Transplant Recipients
Authors: Tang Jie , Liu Rong , Zhang Yue-Li , Liu Mou-Ze , Hu Yong-Fang , Shao Ming-Jie , Zhu Li-Jun , Xin Hua-Wen , Feng Gui-Wen , Shang Wen-Jun , Meng Xiang-Guang , Zhang Li-Rong , Ming Ying-Zi , Zhang Wei
Published: February 2017

Tacrolimus has a narrow therapeutic window and considerable variability in clinical use. Our goal was to compare the performance of multiple linear regression (MLR) and eight machine learning techniques in pharmacogenetic algorithm-based prediction of tacrolimus stable dose (TSD) in a large Chinese cohort. A total of 1,045 renal transplant patients were recruited, 80% of which were randomly selected as the “derivation cohort” to develop dose-prediction algorithm, while the remaining 20% constituted the “validation cohort” to test the final selected algorithm. MLR, artificial neural network (ANN), regression tree (RT), multivariate adaptive regression splines (MARS), boosted regression tree (BRT), support vector regression (SVR), random forest regression (RFR), lasso regression (LAR) and Bayesian additive regression trees (BART) were applied and their performances were compared in this work. Among all the machine learning models, RT performed best in both derivation [0.71 (0.67–0.76)] and validation cohorts [0.73 (0.63–0.82)]. In addition, the ideal rate of RT was 4% higher than that of MLR. To our knowledge, this is the first study to use machine learning models to predict TSD, which will further facilitate personalized medicine in tacrolimus administration in the future.
Ferroelectric symmetry-protected multibit memory cell
Authors: Baudry Laurent , Lukyanchuk Igor , Vinokur Valerii M.
Published: February 2017

The tunability of electrical polarization in ferroelectrics is instrumental to their applications in information-storage devices. The existing ferroelectric memory cells are based on the two-level storage capacity with the standard binary logics. However, the latter have reached its fundamental limitations. Here we propose ferroelectric multibit cells (FMBC) utilizing the ability of multiaxial ferroelectric materials to pin the polarization at a sequence of the multistable states. Employing the catastrophe theory principles we show that these states are symmetry-protected against the information loss and thus realize novel topologically-controlled access memory (TAM). Our findings enable developing a platform for the emergent many-valued non-Boolean information technology and target challenges posed by needs of quantum and neuromorphic computing.
Genotoxic Effects of Culture Media on Human Pluripotent Stem Cells
Authors: Prakash Bangalore Megha , Adhikarla Syama , Mukherjee Odity , Panicker Mitradas M.
Published: February 2017

Culture conditions play an important role in regulating the genomic integrity of Human Pluripotent Stem Cells (HPSCs). We report that HPSCs cultured in Essential 8 (E8) and mTeSR, two widely used media for feeder-free culturing of HPSCs, had many fold higher levels of ROS and higher mitochondrial potential than cells cultured in Knockout Serum Replacement containing media (KSR). HPSCs also exhibited increased levels of 8-hydroxyguanosine, phospho-histone-H2a.X and p53, as well as increased sensitivity to γ-irradiation in these two media. HPSCs in E8 and mTeSR had increased incidence of changes in their DNA sequence, indicating genotoxic stress, in addition to changes in nucleolar morphology and number. Addition of antioxidants to E8 and mTeSR provided only partial rescue. Our results suggest that it is essential to determine cellular ROS levels in addition to currently used criteria i.e. pluripotency markers, differentiation into all three germ layers and normal karyotype through multiple passages, in designing culture media.
CRISPR/Cas9-mediated gene manipulation to create single-amino-acid-substituted and floxed mice with a cloning-free method
Authors: Ma Xiaolong , Chen Chao , Veevers Jennifer , Zhou XinMin , Ross Robert S. , Feng Wei , Chen Ju
Published: February 2017

Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology is a powerful tool to manipulate the genome with extraordinary simplicity and speed. To generate genetically modified animals, CRISPR/Cas9-mediated genome editing is typically accomplished by microinjection of a mixture of Cas9 DNA/mRNA and single-guide RNA (sgRNA) into zygotes. However, sgRNAs used for this approach require manipulation via molecular cloning as well as in vitro transcription. Beyond these complexities, most mutants obtained with this traditional approach are genetically mosaic, yielding several types of cells with different genetic mutations. Recently, a growing body of studies has utilized commercially available Cas9 protein together with sgRNA and a targeting construct to introduce desired mutations. Here, we report a cloning-free method to target the mouse genome by pronuclear injection of a commercial Cas9 protein:crRNA:tracrRNA:single-strand oligodeoxynucleotide (ssODN) complex into mouse zygotes. As illustration of this method, we report the successful generation of global gene-knockout, single-amino-acid-substituted, as well as floxed mice that can be used for conditional gene-targeting. These models were produced with high efficiency to generate non-mosaic mutant mice with a high germline transmission rate.
Nitrate leaching in a winter wheat-summer maize rotation on a calcareous soil as affected by nitrogen and straw management
Authors: Huang Tao , Ju Xiaotang , Yang Hao
Published: February 2017

Nitrate leaching is one of the most important pathways of nitrogen (N) loss which leads to groundwater contamination or surface water eutrophication. Clarifying the rates, controlling factors and characteristics of nitrate leaching is the pre-requisite for proposing effective mitigation strategies. We investigated the effects of interactions among chemical N fertilizer, straw and manure applications on nitrogen leaching in an intensively managed calcareous Fluvo-aquic soil with winter wheat-summer maize cropping rotations on the North China Plain from October 2010 to September 2013 using ceramic suction cups and seepage water calculations based on a long-term field experiment. Annual nitrate leaching reached 38–60 kg N ha−1 from conventional N managements, but declined by 32–71% due to optimum N, compost manure or municipal waste treatments, respectively. Nitrate leaching concentrated in the summer maize season, and fewer leaching events with high amounts are the characteristics of nitrate leaching in this region. Overuse of chemical N fertilizers, high net mineralization and nitrification, together with predominance of rainfall in the summer season with light soil texture are the main controlling factors responsible for the high nitrate leaching loss in this soil-crop-climatic system.
Dynamical beam manipulation based on 2-bit digitally-controlled coding metasurface
Authors: Huang Cheng , Sun Bo , Pan Wenbo , Cui Jianhua , Wu Xiaoyu , Luo Xiangang
Published: February 2017

Recently, a concept of digital metamaterials has been proposed to manipulate field distribution through proper spatial mixtures of digital metamaterial bits. Here, we present a design of 2-bit digitally-controlled coding metasurface that can effectively modulate the scattered electromagnetic wave and realize different far-field beams. Each meta-atom of this metasurface integrates two pin diodes, and by tuning their operating states, the metasurface has four phase responses of 0, π/2, π, and 3π/2, corresponding to four basic digital elements “00”, “01”, “10”, and “11”, respectively. By designing the coding sequence of the above digital element array, the reflected beam can be arbitrarily controlled. The proposed 2-bit digital metasurface has been demonstrated to possess capability of achieving beam deflection, multi-beam and beam diffusion, and the dynamical switching of these different scattering patterns is completed by a programmable electric source.
A novel human artery model to assess the magnetic accumulation of SPIONs under flow conditions
Authors: Janikowska Agata , Matuszak Jasmin , Lyer Stefan , Schreiber Eveline , Unterweger Harald , Zaloga Jan , Groll Jürgen , Alexiou Christoph , Cicha Iwona
Published: February 2017

Magnetic targeting utilises the properties of superparamagnetic iron oxide nanoparticles (SPIONs) to accumulate particles in specified vasculature regions under an external magnetic field. As the behaviour of circulating particles varies depending on nanoparticle characteristics, magnetic field strength and flow dynamics, we established an improved ex vivo model in order to estimate the magnetic capture of SPIONs in physiological-like settings. We describe here a new, easy to handle ex vivo model of human umbilical artery. Using this model, the magnetic targeting of different types of SPIONs under various external magnetic field gradients and flow conditions was investigated by atomic emission spectroscopy and histology. Among tested particles, SPION-1 with lauric acid shell had the largest capacity to accumulate at the specific artery segment. SPION-2 (lauric acid/albumin-coated) were also successfully targeted, although the observed peak in the iron content under the tip of the magnet was smaller than for SPION-1. In contrast, we did not achieve magnetic accumulation of dextran-coated SPION-3. Taken together, the umbilical artery model constitutes a time- and cost-efficient, 3R-compliant tool to assess magnetic targeting of SPIONs under flow. Our results further imply the possibility of an efficient in vivo targeting of certain types of SPIONs to superficial arteries.
Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling
Authors: Velez Daniel Ortiz , Mack Hannah , Jupe Julietta , Hawker Sinead , Kulkarni Ninad , Hedayatnia Behnam , Zhang Yang , Lawrence Shelley , Fraley Stephanie I.
Published: February 2017

In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously. Clinically relevant concentrations of bacterial DNA molecules are separated by digitization across 20,000 reactions and amplified with universal primers targeting the bacterial 16S gene. Amplification is followed by HRM sequence fingerprinting in all reactions, simultaneously. The resulting bacteria-specific melt curves are identified by Support Vector Machine learning, and individual pathogen loads are quantified. The platform reduces reaction volumes by 99.995% and achieves a greater than 200-fold increase in dynamic range of detection compared to traditional PCR HRM approaches. Type I and II error rates are reduced by 99% and 100% respectively, compared to intercalating dye-based digital PCR (dPCR) methods. This technology could impact a number of quantitative profiling applications, especially infectious disease diagnostics.
Towards enhanced optical sensor performance: SEIRA and SERS with plasmonic nanostars
Authors: Bibikova O. , Haas J. , López-Lorente A. I. , Popov A. , Kinnunen M. , Meglinski I. , Mizaikoff B.
Published: February 2017

We report the development of plasmonic chip-based systems comprising self-assembled gold nanostars at silicon substrates that enable concomitantly enhanced Raman (surface enhanced Raman spectroscopy; SERS) and mid-infrared (surface enhanced infrared reflection or absorption spectroscopy; SEIRA) spectral signatures.
Performance of surface renewable pH electrodes based on RuO2–graphite–epoxy composites
Authors: Huang Shanluo , Jin Yan , Su Ziqi , Jin Qinghui , Zhao Jianlong
Published: February 2017

In this work, surface renewable pH electrodes comprising RuO2–graphite–epoxy composites were developed.
Nanoscale mapping of newly-synthesised phospholipid molecules in a biological cell using tip-enhanced Raman spectroscopy
Authors: Kumar Naresh , Drozdz Marek M. , Jiang Haibo , Santos Daniela M. , Vaux David J.
Published: February 2017

Non-destructive & label-free nanoscale mapping of newly-synthesised phospholipid molecules inside a biological cell is demonstrated using tip-enhanced Raman spectroscopy for the first time.
Controlling dark catalysis with quasi half-cycle terahertz pulses
Authors: Sá Jacinto , Fernandes Daniel L. A. , Pavliuk Mariia V. , Szlachetko Jakub
Published: February 2017

This study reports the changes in the platinum electronic structure induced by a strong electric field originated from quasi half-cycle THz pulses, which forces the C–O molecule to dissociate.
Complexes of MN2S2·Fe(η5-C5R5)(CO) as platform for exploring cooperative heterobimetallic effects in HER electrocatalysis
Authors: Ghosh Pokhraj , Quiroz Manuel , Wang Ning , Bhuvanesh Nattamai , Darensbourg Marcetta Y.
Published: February 2017

Comparative study of bimetallic complexes with electronic modulations emphasizes reduction-induced hemi-lability as the key step for electrocatalytic proton reduction.
A reduced graphene oxide/mixed-valence manganese oxide composite electrode for tailorable and surface mountable supercapacitors with high capacitance and super-long life
Authors: Wang Yang , Lai Wenhui , Wang Ni , Jiang Zhi , Wang Xuanyu , Zou Peichao , Lin Ziyin , Fan Hong Jin , Kang Feiyu , Wong Ching-Ping , Yang Cheng
Published: February 2017

The rGO/MnOx composite is compatible with the slurry dispensing process for electrode fabrication, and can exhibit super-long life property.
Negative effects of divalent mineral cations on the bioaccessibility of carotenoids from plant food matrices and related physical properties of gastro-intestinal fluids
Authors: Corte-Real Joana , Bertucci Marie , Soukoulis Christos , Desmarchelier Charles , Borel Patrick , Richling Elke , Hoffmann Lucien , Bohn Torsten
Published: February 2017

Proposed interaction of divalent cations, bile acids, and fatty acids in the intestine, resulting in precipitation and entrapment of carotenoids.
Oxidative annulations triggered by a simple Lewis acid: facile synthesis of benzofurans
Authors: Sreenivasulu Chinnabattigalla , Gopi Krishna Reddy A. , Satyanarayana G.
Published: February 2017

The first example of Lewis acid promoted efficient one-pot synthesis of benzofurans is presented.
Aerobic oxidation and EATA-based highly enantioselective synthesis of lamenallenic acid
Authors: Jiang Xingguo , Xue Yufeng , Ma Shengming
Published: February 2017

A highly enantioselective synthesis of (−)-lamenallenic acid utilizing the recently developed EATA reaction and aerobic oxidation reaction has been accomplished.
Intramolecular oxidative cyclodehydrogenation route for the synthesis of strap-like conjugated polymers
Authors: Yang Junwei , Huang Wei , Lin Tingting , Pan Xiaoyong , Zhu Haoyun , Huang Yuli , Wang Weizhi
Published: February 2017

Based on tetraphenylethene (TPE), a bottom-up solution-based synthesis of narrow strap-like polymers was successfully achieved by intramolecular oxidative cyclodehydrogenation.
Mechanochemically induced transformation of CoO(OH) into Co3O4 nanoparticles and their highly reversible Li storage characteristics
Authors: Park Jae-Wan , Park Cheol-Min
Published: February 2017

A simple synthetic method for the mechanochemically induced transformation of cobalt oxyhydroxides (CoO(OH)) into cobalt oxide (Co3O4) nanoparticles is developed and applied to Li-ion batteries.
Experimental investigation of upgrading of lignin-derived bio-oil component anisole catalyzed by carbon nanotube-supported molybdenum
Authors: Rahzani Behnam , Saidi Majid , Rahimpour Hamid Reza , Gates Bruce C. , Rahimpour Mohammad Reza
Published: February 2017

Molybdenum supported on carbon nanotubes (CNTs) was synthesized and evaluated as a catalyst for the catalytic hydroprocessing of anisole.
Polymerization of polyhedral oligomeric silsequioxane (POSS) with perfluoro-monomers and a kinetic study
Authors: Hao Jinmeng , Wei Yanfeng , Chen Bo , Mu Jianxin
Published: February 2017

The polymerization of diphenol polyhedral oligomeric silsequioxane (2OH-DDSQ) with a series of perfluoro-monomers was studied to obtain the optimized reaction for the preparation of POSS-containing fluorinated poly(arylene ether)s.
Morphology-controlled synthesis and electron field emission properties of ZnSe nanowalls
Authors: Xie Pei , Xue Shaolin , Wang Youya , Gao Zhiyong , Feng Hange , Li Lingwei , Wu Dajun , Wang Lianwei , Chu Paul K.
Published: February 2017

Novel ZnSe nanowalls on a Zn substrate with optimum morphology exhibit enhanced field emission performance.
Novel application of peptaibiotics derived from Trichoderma sp. for methanogenic suppression and enhanced power generation in microbial fuel cells
Authors: Ray Ghosh , Noori Md. T. , Ghangrekar M. M.
Published: February 2017

A major limitation to achieving higher power output from microbial fuel cells (MFC) is the competitive environment for substrate utilization offered by methanogenic archaea.
Highly stable and biocompatible W18O49@PEG-PCL hybrid nanospheres combining CT imaging and cancer photothermal therapy
Authors: Mu Jianning , Meng Xiaoyu , Chen Li , Lu Zhanbin , Mou Qinwei , Li Xiaoxue , Wang Suiqin , Yue Hongyun
Published: February 2017

In this study, we encapsulated W18O49 NPs with PEG-PCL NPs (W18O49@PEG-PCL NPs).
A general strategy for controllable synthesis of Ba3(MO4)2:Mn5+ (M = V, P) nanoparticles
Authors: Zhang Xiaowen , Li Yang , Hu Zhongliang , Chen Zhi , Qiu Jianrong
Published: February 2017

The second near-infrared window (NIR-II, 1000–1400 nm) is ideal for fluorescence imaging. We report a facile synthesis approach to prepare Mn5+ doped Ba3(MO4)2 (M = V, P) nanoparticles with emission in the NIR-II region for the first time.
Monte Carlo track chemistry simulations of the radiolysis of water induced by the recoil ions of the 10B(n,α)7Li nuclear reaction. 1. Calculation of the yields of primary species up to 350 °C
Authors: Islam Muhammad Mainul , Lertnaisat Phantira , Meesungnoen Jintana , Sanguanmith Sunuchakan , Jay-Gerin Jean-Paul , Katsumura Yosuke , Mukai Satoru , Umehara Ryuji , Shimizu Yuichi , Suzuki Masashi
Published: February 2017

Monte Carlo calculations were used to simulate the radiolysis of water by 10B(n,α)7Li recoil ions.
Fabrication of a 3D Teflon microdevice for energy free homogeneous liquid flow inside a long microchannel and its application to continuous-flow PCR
Authors: Trinh Kieu The Loan , Wu Wenming , Lee Nae Yoon
Published: February 2017

The 3D spiral PTFE microdevice was fabricated for performing continuous-flow PCR using a single heater and via semi-automated sample injection method.
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost
Authors: Smith J. S. , Isayev O. , Roitberg A. E.
Published: February 2017

We demonstrate how a deep neural network (NN) trained on a data set of quantum mechanical (QM) DFT calculated energies can learn an accurate and transferable atomistic potential for organic molecules containing H, C, N, and O atoms.
A novel flower-like architecture of FeCo@NC-functionalized ultra-thin carbon nanosheets as a highly efficient 3D bifunctional electrocatalyst for full water splitting
Authors: Li Mian , Liu Tingting , Bo Xiangjie , Zhou Ming , Guo Liping
Published: February 2017

A novel three-dimensional hierarchically meso/macroporous flower-like architecture of ultra-thin N-doped carbon nanosheets with fine FeCo@NC core–shell units dispersed on their surfaces can efficiently catalyze water splitting.
In situ O2-emission assisted synthesis of molybdenum carbide nanomaterials as an efficient electrocatalyst for hydrogen production in both acidic and alkaline media
Authors: Ji Lvlv , Wang Jianying , Guo Lixia , Chen Zuofeng
Published: February 2017

A unique in situ O2-emission assisted synthesis method was developed to prepare MoxC-based nanomaterials which exhibit outstanding HER catalytic performance.