bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau
Authors: Qiao Qin , Wang Qia , Han Xi , Guan Yanlong , Sun Hang , Zhong Yang , Huang Jinling , Zhang Ticao 
Published: February 2016

AbstractThe extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.
Microbial succession in response to pollutants in batch-enrichment culture
Authors: Jiao Shuo , Chen Weimin , Wang Entao , Wang Junman , Liu Zhenshan , Li Yining , Wei Gehong 
Published: February 2016

AbstractAs a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments.
Disorganization of white matter architecture in major depressive disorder: a meta-analysis of diffusion tensor imaging with tract-based spatial statistics
Authors: Chen Guangxiang , Hu Xinyu , Li Lei , Huang Xiaoqi , Lui Su , Kuang Weihong , Ai Hua , Bi Feng , Gu Zhongwei , Gong Qiyong 
Published: February 2016

AbstractWhite matter (WM) abnormalities have long been suspected in major depressive disorder (MDD). Tract-based spatial statistics (TBSS) studies have detected abnormalities in fractional anisotropy (FA) in MDD, but the available evidence has been inconsistent. We performed a quantitative meta-analysis of TBSS studies contrasting MDD patients with healthy control subjects (HCS). A total of 17 studies with 18 datasets that included 641 MDD patients and 581 HCS were identified. Anisotropic effect size-signed differential mapping (AES-SDM) meta-analysis was performed to assess FA alterations in MDD patients compared to HCS. FA reductions were identified in the genu of the corpus callosum (CC) extending to the body of the CC and left anterior limb of the internal capsule (ALIC) in MDD patients relative to HCS. Descriptive analysis of quartiles, sensitivity analysis and subgroup analysis further confirmed these findings. Meta-regression analysis revealed that individuals with more severe MDD were significantly more likely to have FA reductions in the genu of the CC. This study provides a thorough profile of WM abnormalities in MDD and evidence that interhemispheric connections and frontal-striatal-thalamic pathways are the most convergent circuits affected in MDD.
Magnetic properties of N-doped graphene with high Curie temperature
Authors: Miao Qinghua , Wang Lidong , Liu Zhaoyuan , Wei Bing , Xu Fubiao , Fei Weidong 
Published: February 2016

AbstractN-doped graphene with Curie temperature higher than room temperature is a good candidate for nanomagnetic applications. Here we report a kind of N-doped graphene that exhibits ferromagnetic property with high Curie temperature (>600 K). Four graphene samples were prepared through self-propagating high-temperature synthesis (SHS) and the doped nitrogen contents of in the samples were 0 at.%, 2.53 at.%, 9.21 at.% and 11.17 at.%. It has been found that the saturation magnetization and coercive field increase with the increasing of nitrogen contents in the samples. For the sample with the highest nitrogen content, the saturation magnetizations reach 0.282 emu/g at 10 K and 0.148 emu/g at 300 K; the coercive forces reach 544.2 Oe at 10 K and 168.8 Oe at 300 K. The drop of magnetic susceptibility at ~625 K for N-doped graphene is mainly caused by the decomposition of pyrrolic N and pydinic N. Our results suggest that SHS method is an effective and high-throughput method to produce N-doped graphene with high nitrogen concentration and that N-doped graphene produced by SHS method is promising to be a good candidate for nanomagnetic applications.
Growth temperature and genotype both play important roles in sorghum grain phenolic composition
Authors: Wu Gangcheng , Johnson Stuart K. , Bornman Janet F. , Bennett Sarita J. , Clarke Michael W. , Singh Vijaya , Fang Zhongxiang 
Published: February 2016

AbstractPolyphenols in sorghum grains are a source of dietary antioxidants. Polyphenols in six diverse sorghum genotypes grown under two day/night temperature regimes of optimal temperature (OT, 32/21 °C"Equation missing" and high temperature (HT, 38/21 °C) were investigated. A total of 23 phenolic compounds were positively or tentatively identified by HPLC-DAD-ESIMS. Compared with other pigmented types, the phenolic profile of white sorghum PI563516 was simpler, since fewer polyphenols were detected. Brown sorghum IS 8525 had the highest levels of caffeic and ferulic acid, but apigenin and luteolin were not detected. Free luteolinidin and apigeninidin levels were lower under HT than OT across all genotypes (p ≤ 0.05), suggesting HT could have inhibited 3-deoxyanthocyanidins formation. These results provide new information on the effects of HT on specific polyphenols in various Australian sorghum genotypes, which might be used as a guide to grow high antioxidant sorghum grains under projected high temperature in the future.
Synthetic Capillaries to Control Microscopic Blood Flow
Authors: Sarveswaran K. , Kurz V. , Dong Z. , Tanaka T. , Penny S. , Timp G. 
Published: February 2016

AbstractCapillaries pervade human physiology. The mean intercapillary distance is only about 100 μm in human tissue, which indicates the extent of nutrient diffusion. In engineered tissue the lack of capillaries, along with the associated perfusion, is problematic because it leads to hypoxic stress and necrosis. However, a capillary is not easy to engineer due to its complex cytoarchitecture. Here, it is shown that it is possible to create in vitro, in about 30 min, a tubular microenvironment with an elastic modulus and porosity consistent with human tissue that functionally mimicks a bona fide capillary using “live cell lithography”(LCL) to control the type and position of cells on a composite hydrogel scaffold. Furthermore, it is established that these constructs support the forces associated with blood flow and produce nutrient gradients similar to those measured in vivo. With LCL, capillaries can be constructed with single cell precision—no other method for tissue engineering offers such precision. Since the time required for assembly scales with the number of cells, this method is likely to be adapted first to create minimal functional units of human tissue that constitute organs, consisting of a heterogeneous population of 100–1000 cells, organized hierarchically to express a predictable function.
Seasonal variation in harbour seal (Phoca vitulina) blubber cortisol - A novel indicator of physiological state?
Authors: Kershaw Joanna L. , Hall Ailsa J. 
Published: February 2016

AbstractCortisol is one of the main glucocorticoid hormones involved in both the mammalian stress response and in fat metabolism and energy regulation, making it of increasing interest as a biomarker for stress, health and overall physiological state. However, transient stress responses to animal handling and sampling may be important sources of measurement artefact when investigating circulating concentrations of this hormone in wildlife. Here, cortisol concentrations were measured in the plasma and, for the first time, in the blubber of live captured adult harbour seals (Phoca vitulina). Plasma cortisol concentrations were positively correlated with capture time, suggesting that they were largely driven by a stress response to the capture event. In contrast, blubber cortisol concentrations were shown not to be significantly affected by capture time and varied significantly by sex and by season, with higher concentrations during natural fasting periods of their life cycle, particularly during the moult. These results suggest that cortisol may play a key role in increased fat metabolism during highly energetically demanding periods and that blubber concentrations have the potential to be used as physiological state indicators in phocid seals.
Simultaneous knockdown of uPA and MMP9 can reduce breast cancer progression by increasing cell-cell adhesion and modulating EMT genes
Authors: Moirangthem Anuradha , Bondhopadhyay Banashree , Mukherjee Mala , Bandyopadhyay Arghya , Mukherjee Narendranath , Konar Karabi , Bhattacharya Shubham , Basu Anupam 
Published: February 2016

AbstractIn cancer progression, proteolytic enzymes like serine proteases and metalloproteinases degrade the basement membrane enabling the tumor cells to invade the adjacent tissues. Thus, invasion and metastasis are augmented by these enzymes. Simultaneous silencing of uPA and MMP9 in breast cancer cells decreased the wound healing, migratory, invasive and adhesive capacity of the cells. After simultaneous down regulation, cells were seen to be arrested in the cell cycle. There was a remarkable increase in the expression of cell to cell adhesion molecule E–cadherin, and decrease in Vimentin and Snail expression. In addition, there was a significant decrease in the expression of the stem cell marker Oct-4. In the breast tumor samples it has been observed that, tumors, expressing higher level of uPA and MMP9, express less amount of E–cadherin. It has also been observed that few tumors also show, Vimentin positive in the ductal epithelial area. Thus, our model can help for checking the aggressive tumor invasion by blocking of uPA and MMP9. Our present observations also give the concept of the presence of aggressive epithelial cells with mesenchymal nature in the tumor micro-environment, altering the expression of EMT genes.
One-step Multiplex Transgenesis via Sleeping Beauty Transposition in Cattle
Authors: Garrels Wiebke , Talluri Thirumala R. , Apfelbaum Ronja , Carratalá Yanet P. , Bosch Pablo , Pötzsch Kerstin , Grueso Esther , Ivics Zoltán , Kues Wilfried A. 
Published: February 2016

AbstractGenetically modified cattle are important for developing new biomedical models and for an improved understanding of the pathophysiology of zoonotic diseases. However, genome editing and genetic engineering based on somatic cell nuclear transfer suffer from a low overall efficiency. Here, we established a highly efficient one-step multiplex gene transfer system into the bovine genome.
The impact of inhibitory mechanisms in the inner retina on spatial tuning of RGCs
Authors: Huang Jin Y. , Protti Dario A. 
Published: February 2016

AbstractSpatial tuning properties of retinal ganglion cells (RGCs) are sharpened by lateral inhibition originating at both the outer and inner plexiform layers. Lateral inhibition in the retina contributes to local contrast enhancement and sharpens edges. In this study, we used dynamic clamp recordings to examine the contribution of inner plexiform inhibition, originating from spiking amacrine cells, to the spatial tuning of RGCs. This was achieved by injecting currents generated from physiologically recorded excitatory and inhibitory stimulus-evoked conductances, into different types of primate and mouse RGCs. We determined the effects of injections of size-dependent conductances in which presynaptic inhibition and/or direct inhibition onto RGCs were partly removed by blocking the activity of spiking amacrine cells. We found that inhibition originating from spiking amacrine cells onto bipolar cell terminals and onto RGCs, work together to sharpen the spatial tuning of RGCs. Furthermore, direct inhibition is crucial for preventing spike generation at stimulus offset. These results reveal how inhibitory mechanisms in the inner plexiform layer contribute to determining size tuning and provide specificity to stimulus polarity.
Highly Stable Nanocontainer of APTES-Anchored Layered Titanate Nanosheet for Reliable Protection/Recovery of Nucleic Acid
Authors: Kim Tae Woo , Kim In Young , Park Dae-Hwan , Choy Jin-Ho , Hwang Seong-Ju 
Published: February 2016

AbstractA universal technology for the encapsulative protection of unstable anionic species by highly stable layered metal oxide has been developed via the surface modification of a metal oxide nanosheet. The surface anchoring of (3-aminopropyl)triethoxysilane (APTES) on exfoliated titanate nanosheet yields a novel cationic metal oxide nanosheet, which can be universally used for the hybridization with various biological and inorganic anions. The encapsulation of deoxyribonucleic acid (DNA) in the cationic APTES-anchored titanate lattice makes possible the reliable long-term protection of DNA against enzymatic, chemical, and UV−vis light corrosions. The encapsulated DNA can be easily released from the titanate lattice via sonication, underscoring the functionality of the cationic APTES-anchored titanate nanosheet as a stable nanocontainer for DNA. The APTES-anchored titanate nanosheet can be also used as an efficient CO2 adsorbent and a versatile host material for various inorganic anions like polyoxometalates, leading to the synthesis of novel intercalative nanohybrids with unexplored properties and useful functionalities.
Quantum state transfer and controlled-phase gate on one-dimensional superconducting resonators assisted by a quantum bus
Authors: Hua Ming , Tao Ming-Jie , Deng Fu-Guo 
Published: February 2016

AbstractWe propose a quantum processor for the scalable quantum computation on microwave photons in distant one-dimensional superconducting resonators. It is composed of a common resonator R acting as a quantum bus and some distant resonators rj coupled to the bus in different positions assisted by superconducting quantum interferometer devices (SQUID), different from previous processors. R is coupled to one transmon qutrit and the coupling strengths between rj and R can be fully tuned by the external flux through the SQUID. To show the processor can be used to achieve universal quantum computation effectively, we present a scheme to complete the high-fidelity quantum state transfer between two distant microwave-photon resonators and another one for the high-fidelity controlled-phase gate on them. By using the technique for catching and releasing the microwave photons from resonators, our processor may play an important role in quantum communication as well.
Molecular orbital analysis of the hydrogen bonded water dimer
Authors: Wang Bo , Jiang Wanrun , Dai Xin , Gao Yang , Wang Zhigang , Zhang Rui-Qin 
Published: February 2016

AbstractAs an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems.
Oxidized plasma albumin promotes platelet-endothelial crosstalk and endothelial tissue factor expression
Authors: Pasterk Lisa , Lemesch Sandra , Leber Bettina , Trieb Markus , Curcic Sanja , Stadlbauer Vanessa , Schuligoi Rufina , Schicho Rudolf , Heinemann Akos , Marsche Gunther 
Published: February 2016

AbstractPlasma advanced oxidation protein products (AOPPs), a class of pro-inflammatory pathogenic mediators, accumulate in subjects with chronic kidney disease. Whether AOPPs contribute to coagulation abnormalities, which are frequently seen in uremic patients, is unknown. Here we report that AOPPs activate platelets via a CD36-mediated signaling pathway. Activation of signaling pathways by AOPP-platelet interaction resulted in the expression of several platelet activation markers and rapidly induced the expression of CD40 ligand, triggering platelet adhesion to endothelial cells and promoting endothelial tissue factor expression. AOPPs and serum tissue factor levels were considerably increased in end stage renal disease patients on hemodialysis and a significant correlation of AOPPs and serum tissue factor was found. Interestingly, serum levels of AOPPs and tissue factor were substantially lower in stable kidney transplant patients when compared with hemodialysis patients. Given that CD36 is known to transduce the effects of oxidized lipids into platelet hyperactivity, our findings reveal previously unknown pro-thrombotic activities of oxidized plasma albumin via a CD36 dependent pathway.
The fusion protein SS18-SSX1 employs core Wnt pathway transcription factors to induce a partial Wnt signature in synovial sarcoma
Authors: Cironi Luisa , Petricevic Tanja , Fernandes Vieira Victor , Provero Paolo , Fusco Carlo , Cornaz Sandrine , Fregni Giulia , Letovanec Igor , Aguet Michel , Stamenkovic Ivan 
Published: February 2016

AbstractExpression of the SS18/SYT-SSX fusion protein is believed to underlie the pathogenesis of synovial sarcoma (SS). Recent evidence suggests that deregulation of the Wnt pathway may play an important role in SS but the mechanisms whereby SS18-SSX might affect Wnt signaling remain to be elucidated. Here, we show that SS18/SSX tightly regulates the elevated expression of the key Wnt target AXIN2 in primary SS. SS18-SSX is shown to interact with TCF/LEF, TLE and HDAC but not β-catenin in vivo and to induce Wnt target gene expression by forming a complex containing promoter-bound TCF/LEF and HDAC but lacking β-catenin. Our observations provide a tumor-specific mechanistic basis for Wnt target gene induction in SS that can occur in the absence of Wnt ligand stimulation.
Strength gradient enhances fatigue resistance of steels
Authors: Ma Zhiwei , Liu Jiabin , Wang Gang , Wang Hongtao , Wei Yujie , Gao Huajian 
Published: February 2016

AbstractSteels are heavily used in infrastructure and the transportation industry, and enhancing their fatigue resistance is a major challenge in materials engineering. In this study, by introducing a gradient microstructure into 304 austenitic steel, which is one of the most widely used types of stainless steel, we show that a strength gradient substantially enhances the fatigue life of the material. Pre-notched samples with negative strength gradients in front of the notch’s tip endure many more fatigue cycles than do samples with positive strength gradients during the crack initiation stage, and samples with either type of gradient perform better than do gradient-free samples with the same average yield strength. However, as a crack grows, samples with positive strength gradients exhibit better resistance to fatigue crack propagation than do samples with negative gradients or no gradient. This study demonstrates a simple and promising strategy for using gradient structures to enhance the fatigue resistance of materials and complements related studies of strength and ductility.
High Throughput Profiling of Molecular Shapes in Crystals
Authors: Spackman Peter R. , Thomas Sajesh P. , Jayatilaka Dylan 
Published: February 2016

AbstractMolecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design.