bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of novel FP-based probes for live-cell imaging of nitric oxide dynamics
Authors: Eroglu Emrah , Gottschalk Benjamin , Charoensin Suphachai , Blass Sandra , Bischof Helmut , Rost Rene , Madreiter-Sokolowski Corina T. , Pelzmann Brigitte , Bernhart Eva , Sattler Wolfgang , Hallström Seth , Malinski Tadeusz , Waldeck-Weiermair Markus , Graier Wolfgang F. , Malli Roland 
Published: February 2016

AbstractNitric oxide ("Equation missing") is a free radical with a wide range of biological effects, but practically impossible to visualize in single cells. Here we report the development of novel multicoloured fluorescent quenching-based "Equation missing" probes by fusing a bacteria-derived "Equation missing"-binding domain close to distinct fluorescent protein variants. These genetically encoded "Equation missing" probes, referred to as geNOps, provide a selective, specific and real-time read-out of cellular "Equation missing" dynamics and, hence, open a new era of "Equation missing" bioimaging. The combination of geNOps with a Ca2+ sensor allowed us to visualize "Equation missing" and Ca2+ signals simultaneously in single endothelial cells. Moreover, targeting of the "Equation missing" probes was used to detect "Equation missing" signals within mitochondria. The geNOps are useful new tools to further investigate and understand the complex patterns of "Equation missing" signalling on the single (sub)cellular level.
Sustained hole inversion layer in a wide-bandgap metal-oxide semiconductor with enhanced tunnel current
Authors: Shoute Gem , Afshar Amir , Muneshwar Triratna , Cadien Kenneth , Barlage Douglas 
Published: February 2016

AbstractWide-bandgap, metal-oxide thin-film transistors have been limited to low-power, n-type electronic applications because of the unipolar nature of these devices. Variations from the n-type field-effect transistor architecture have not been widely investigated as a result of the lack of available p-type wide-bandgap inorganic semiconductors. Here, we present a wide-bandgap metal-oxide n-type semiconductor that is able to sustain a strong p-type inversion layer using a high-dielectric-constant barrier dielectric when sourced with a heterogeneous p-type material. A demonstration of the utility of the inversion layer was also investigated and utilized as the controlling element in a unique tunnelling junction transistor. The resulting electrical performance of this prototype device exhibited among the highest reported current, power and transconductance densities. Further utilization of the p-type inversion layer is critical to unlocking the previously unexplored capability of metal-oxide thin-film transistors, such applications with next-generation display switches, sensors, radio frequency circuits and power converters.
High resolution Physio-chemical Tissue Analysis: Towards Non-invasive In Vivo Biopsy
Authors: Xu Guan , Meng Zhuo-xian , Lin Jian-die , Deng Cheri X. , Carson Paul L. , Fowlkes J. Brian , Tao Chao , Liu Xiaojun , Wang Xueding 
Published: February 2016

AbstractConventional gold standard histopathologic diagnosis requires information of both high resolution structural and chemical changes in tissue. Providing optical information at ultrasonic resolution, photoacoustic (PA) technique could provide highly sensitive and highly accurate tissue characterization noninvasively in the authentic in vivo environment, offering a replacement for histopathology. A two-dimensional (2D) physio-chemical spectrogram (PCS) combining micrometer to centimeter morphology and chemical composition simultaneously can be generated for each biological sample with PA measurements at multiple optical wavelengths. This spectrogram presents a unique 2D “physio-chemical signature” for any specific type of tissue. Comprehensive analysis of PCS, termed PA physio-chemical analysis (PAPCA), can lead to very rich diagnostic information, including the contents of all relevant molecular and chemical components along with their corresponding histological microfeatures, comparable to those accessible by conventional histology. PAPCA could contribute to the diagnosis of many diseases involving diffusive patterns such as fatty liver.
Dual-functionalized liposomal delivery system for solid tumors based on RGD and a pH-responsive antimicrobial peptide
Authors: Zhang Qianyu , Lu Libao , Zhang Li , Shi Kairong , Cun Xingli , Yang Yuting , Liu Yayuan , Gao Huile , He Qin 
Published: February 2016

Abstract[D]-H6L9, as a pH-responsive anti-microbial peptide (AMP), has been evidenced by us to be an excellent choice in tumor microenvironment-responsive delivery as it could render liposomes responsive to the acidified tumor microenvironment. However, [D]-H6L9-modified liposomes could not actively target to tumor area. Therefore, integrin αvβ3-targeted peptide RGD was co-modified with [D]-H6L9 onto liposomes [(R + D)-Lip] for improved tumor delivery efficiency. Under pH 6.3, (R + D)-Lip could be taken up by C26 cells and C26 tumor spheroids (integrin αvβ3-positive) with significantly improved efficiency compared with other groups, which was contributed by both RGD and [D]-H6L9, while RGD did not increase the cellular uptake performance on MCF-7 cells (integrin αvβ3-negative). Results showed that RGD could decrease cellular uptake of (R + D)-Lip while [D]-H6L9 could increase it, implying the role of both RGD and [D]-H6L9 in cellular internalization of (R + D)-Lip. On the other hand, (R + D)-Lip could escape the entrapment of lysosomes. PTX-loaded (R + D)-Lip could further increase the cellular toxicity against C26 cells compared with liposomes modified only with RGD and [D]-H6L9 respectively and achieve remarkable tumor inhibition effect on C26 tumor models.
A Common Variant in CLDN14 is Associated with Primary Biliary Cirrhosis and Bone Mineral Density
Authors: Tang Ruqi , Wei Yiran , Li Zhiqiang , Chen Haoyan , Miao Qi , Bian Zhaolian , Zhang Haiyan , Wang Qixia , Wang Zhaoyue , Lian Min , Yang Fan , Jiang Xiang , Yang Yue , Li Enling , Seldin Michael F. , Gershwin M. Eric , Liao Wilson , Shi Yongyong , Ma Xiong 
Published: February 2016

AbstractPrimary biliary cirrhosis (PBC), a chronic autoimmune liver disease, has been associated with increased incidence of osteoporosis. Intriguingly, two PBC susceptibility loci identified through genome-wide association studies are also involved in bone mineral density (BMD). These observations led us to investigate the genetic variants shared between PBC and BMD. We evaluated 72 genome-wide significant BMD SNPs for association with PBC using two European GWAS data sets (n = 8392), with replication of significant findings in a Chinese cohort (685 cases, 1152 controls). Our analysis identified a novel variant in the intron of the CLDN14 gene (rs170183, Pfdr = 0.015) after multiple testing correction. The three associated variants were followed-up in the Chinese cohort; one SNP rs170183 demonstrated consistent evidence of association in diverse ethnic populations (Pcombined = 2.43 × 10−5). Notably, expression quantitative trait loci (eQTL) data revealed that rs170183 was correlated with a decline in CLDN14 expression in both lymphoblastoid cell lines and T cells (Padj = 0.003 and 0.016, respectively). In conclusion, our study identified a novel PBC susceptibility variant that has been shown to be strongly associated with BMD, highlighting the potential of pleiotropy to improve gene discovery.
Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain
Authors: Rajakumara Eerappa , Nakarakanti Naveen Kumar , Nivya M. Angel , Satish Mutyala 
Published: February 2016

Abstract5-Methylcytosine (5 mC) is associated with epigenetic gene silencing in mammals and plants. 5 mC is consecutively oxidized to 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by ten-eleven translocation enzymes. We performed binding and structural studies to investigate the molecular basis of the recognition of the 5 mC oxidation derivatives in the context of a CG sequence by the SET- and RING-associated domain (SRA) of the SUVH5 protein (SUVH5 SRA). Using calorimetric measurements, we demonstrate that the SRA domain binds to the hydroxymethylated CG (5hmCG) DNA duplex in a similar manner to methylated CG (5mCG). Interestingly, the SUVH5 SRA domain exhibits weaker affinity towards carboxylated CG (5caCG) and formylated CG (5fCG). We report the 2.6 Å resolution crystal structure of the SUVH5 SRA domain in a complex with fully hydroxymethyl-CG and demonstrate a dual flip-out mechanism, whereby the symmetrical 5hmCs are simultaneously extruded from the partner strands of the DNA duplex and are positioned within the binding pockets of individual SRA domains. The hydroxyl group of 5hmC establishes both intra- and intermolecular interactions in the binding pocket. Collectively, we show that SUVH5 SRA recognizes 5hmC in a similar manner to 5 mC, but exhibits weaker affinity towards 5 hmC oxidation derivatives.
Thermoreversible (Ionic-Liquid-Based) Aqueous Biphasic Systems
Authors: Passos Helena , Luís Andreia , Coutinho João A. P. , Freire Mara G. 
Published: February 2016

AbstractThe ability to induce reversible phase transitions between homogeneous solutions and biphasic liquid-liquid systems, at pre-defined and suitable operating temperatures, is of crucial relevance in the design of separation processes. Ionic-liquid-based aqueous biphasic systems (IL-based ABS) have demonstrated superior performance as alternative extraction platforms and their thermoreversible behaviour is here disclosed by the use of protic ILs. The applicability of the temperature-induced phase switching is further demonstrated with the complete extraction of two value-added proteins, achieved in a single-step. It is shown that these temperature-induced mono(bi)phasic systems are significantly more versatile than classical liquid-liquid systems which are constrained by their critical temperatures. IL-based ABS allow to work in a wide range of temperatures and compositions which can be tailored to fit the requirements of a given separation process.
Growing Embossed Nanostructures of Polymer Brushes on Wet-Etched Silicon Templated via Block Copolymers
Authors: Lu Xiaobin , Yan Qin , Ma Yinzhou , Guo Xin , Xiao Shou-Jun 
Published: February 2016

AbstractBlock copolymer nanolithography has attracted enormous interest in chip technologies, such as integrated silicon chips and biochips, due to its large-scale and mass production of uniform patterns. We further modified this technology to grow embossed nanodots, nanorods and nanofingerprints of polymer brushes on silicon from their corresponding wet-etched nanostructures covered with pendent SiHx (X = 1–3) species. Atomic force microscopy (AFM) was used to image the topomorphologies and multiple transmission-reflection infrared spectroscopy (MTR-IR) was used to monitor the surface molecular films in each step for the sequential stepwise reactions. In addition, two layers of polymethacrylic acid (PMAA) brush nanodots were observed, which were attributed to the circumferential convergence growth and the diffusion-limited growth of the polymer brushes. The pH response of PMAA nanodots in the same region was investigated by AFM from pH 3.0 to 9.0.
Massive and massless Dirac fermions in Pb1−xSnxTe topological crystalline insulator probed by magneto-optical absorption
Authors: Assaf B.A. , Phuphachong T. , Volobuev V.V. , Inhofer A. , Bauer G. , Springholz G. , de Vaulchier L.A. , Guldner Y. 
Published: February 2016

AbstractDirac fermions in condensed matter physics hold great promise for novel fundamental physics, quantum devices and data storage applications. IV-VI semiconductors, in the inverted regime, have been recently shown to exhibit massless topological surface Dirac fermions protected by crystalline symmetry, as well as massive bulk Dirac fermions. Under a strong magnetic field (B), both surface and bulk states are quantized into Landau levels that disperse as B1/2 and are thus difficult to distinguish. In this work, magneto-optical absorption is used to probe the Landau levels of high mobility Bi-doped Pb0.54Sn0.46Te topological crystalline insulator (111)-oriented films. The high mobility achieved in these thin film structures allows us to probe and distinguish the Landau levels of both surface and bulk Dirac fermions and extract valuable quantitative information about their physical properties. This work paves the way for future magnetooptical and electronic transport experiments aimed at manipulating the band topology of such materials.
Tensile Characterization of Single-Walled Carbon Nanotubes with Helical Structural Defects
Authors: Jhon Young I. , Kim Chulki , Seo Minah , Cho Woon Jo , Lee Seok , Jhon Young Min 
Published: February 2016

AbstractRecently, evidence was presented that certain single-walled carbon nanotubes (SWNTs) possess helical defective traces, exhibiting distinct cleaved lines, yet their mechanical characterization remains a challenge. On the basis of the spiral growth model of SWNTs, here we present atomic details of helical defects and investigate how the tensile behaviors of SWNTs change with their presence using molecular dynamics simulations. SWNTs have exhibited substantially lower tensile strength and strain than theoretical results obtained from a seamless tubular structure, whose physical origin cannot be explained either by any known SWNT defects so far. We find that this long-lasting puzzle could be explained by assuming helical defects in SWNTs, exhibiting excellent agreement with experimental observation. The mechanism of this tensile process is elucidated by analyzing atomic stress distribution and evolution and the effects of the chirality and diameter of SWNTs on this phenomenon are examined based on linear elastic fracture mechanics. This work contributes significantly to our understanding of the growth mechanism, defect hierarchies and mechanical properties of SWNTs.
Reciprocal regulation of autism-related genes MeCP2 and PTEN via microRNAs
Authors: Lyu Jing-Wen , Yuan Bo , Cheng Tian-Lin , Qiu Zi-Long , Zhou Wen-Hao 
Published: February 2016

AbstractMeCP2 encodes a methyl-CpG-binding protein that plays a critical role in repressing gene expression, mutations of which lead to Rett syndrome and autism. PTEN is a critical tumor suppressor gene that is frequently mutated in human cancers and autism spectrum disorders. Various studies have shown that both MeCP2 and PTEN proteins play important roles in brain development. Here we find that MeCP2 and PTEN reciprocally regulate expression of each other via microRNAs. Knockdown of MeCP2 leads to upregulation of microRNA-137, which in turn represses expression of PTEN, thus PTEN would be down-regulated when MeCP2 is knockdown. Furthermore, we find that deletion of PTEN leads to phosphorylation of Serine 133 of CREB, then increases the expression of microRNA-132. miR-132 inhibits the expression of MeCP2 by targeting on the 3′UTR of MeCP2 mRNA. Our work shows that two critical disorders-related gene MeCP2 and PTEN reciprocally regulate expression of each other by distinct mechanisms, suggesting that rare mutations in various disorders may lead to dysregulation of other critical genes and yield unexpected consequences.
A microbial transformation using Bacillus subtilis B7-S to produce natural vanillin from ferulic acid
Authors: Chen Peng , Yan Lei , Wu Zhengrong , Li Suyue , Bai Zhongtian , Yan Xiaojuan , Wang Ningbo , Liang Ning , Li Hongyu 
Published: February 2016

AbstractBacillus subtilis strain B7-S screened from18 strains is an aerobic, endospore-forming, model organism of Gram-positive bacteria which is capable to form vanillin during ferulic acid bioconversion. The bioconversion of ferulic acid to vanillin by Bacillus subtilis B7-S (B. subtilis B7-S) was investigated. Based on our results, the optimum bioconversion conditions for the production of vanillin by B. subtilis B7-S can be summarized as follows: temperature 35 °C; initial pH 9.0; inoculum volume 5%; ferulic acid concentration 0.6 g/L; volume of culture medium 20%; and shaking speed 200 r/min. Under these conditions, several repeated small-scale batch experiments showed that the maximum conversion efficiency was 63.30% after 3 h of bioconversion. The vanillin products were confirmed by spectral data achieved from UV–vis, inductively coupled plasma atomic emission spectroscope (ICP-AES) and Fourier transform infrared spectrometer (FT-IR) spectra. Scanning electron microscopy (SEM) and transmission electron spectroscopy (TEM) results confirmed that the cell surface of B. subtilis plays a role in the induction of ferulic acid tolerance. These results demonstrate that B. subtilis B7-S has the potential for use in vanillin production through bioconversion of ferulic acid.
Decreased B and T lymphocyte attenuator in Behcet’s disease may trigger abnormal Th17 and Th1 immune responses
Authors: Ye Zi , Deng Bolin , Wang Chaokui , Zhang Dike , Kijlstra Aize , Yang Peizeng 
Published: February 2016

AbstractBehcet’s disease (BD) is a chronic, systemic and recurrent inflammatory disease associated with hyperactive Th17 and Th1 immune responses. Recent studies have shown that B and T lymphocyte attenuator (BTLA) negatively regulates the immune response. In this study, we investigated whether BTLA activation could be exploited to inhibit the development of abnormal immune responses in BD patients. BTLA expression in PBMCs and CD4+ T cells was significantly decreased in active BD patients. Decreased BTLA level was associated with increased Th17 and Th1 responses. Activation of BTLA inhibited the abnormal Th17 and Th1 responses and IL-22 expression in both patients and controls. Addition of an agonistic anti-BTLA antibody remarkably inhibited DC-induced Th17 and Th1 cell responses, resulted in decreased production of the Th17 and Th1-related cytokines IL-1beta, IL-6, IL-23 and IL-12p70 and reduced CD40 expression in DCs. In conclusion, decreased BTLA expression in ocular BD may lead to inappropriate control of the Th17 and Th1 immune responses and DC functions. Therefore, BTLA may be involved in the development and recurrence of this disease. Agonistic agents of BTLA may represent a potential therapeutic approach for the treatment of BD and other inflammatory diseases mediated by abnormal Th17 and Th1 immune responses.
Depletion of the LINC complex disrupts cytoskeleton dynamics and meiotic resumption in mouse oocytes
Authors: Luo Yibo , Lee In-Won , Jo Yu-Jin , Namgoong Suk , Kim Nam-Hyung 
Published: February 2016

AbstractThe SUN (Sad-1/UNC-84) and KASH (Klarsicht/ANC-1/Syne/homology) proteins constitute the linker of nucleoskeleton and cytoskeleton (LINC) complex on the nuclear envelope. To date, the SUN1/KASH5 complex is known to function as meiotic-specific factors. In this study, gene-silencing methods were used to explore the roles of SUN1 and KASH5 in mouse oocytes after prophase. SUN1 was detected throughout the nucleus; however, KASH5 was dispersed through the cell. After germinal vesicle breakdown (GVBD), SUN1 and KASH5 migrated during spindle formation and localized to the spindle poles at the MII stage. Most oocytes were arrested at the germinal vesicle (GV) stage after depletion of either SUN1 or KASH5. The DNA damage response was triggered in SUN1-depleted oocytes and thus gave rise to the G2/M checkpoint protein, p-CHK1. Oocytes that underwent GVBD had relatively small and abnormal spindles and lower levels of cytoplasm F-actin mesh. Immunofluorescence results also indicated the dislocation of pericentrin and P150Glued after SUN1 or KASH5 depletion. Furthermore, KASH5 localized exclusively near the oocyte cortex after SUN1 depletion, but SUN1 localization was unaffected in KASH5-depleted oocytes. Taken together, the results suggest that SUN1 and KASH5 are essential factors in the regulation of meiotic resumption and spindle formation.
Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes
Authors: Li Angsheng , Yin Xianchen , Pan Yicheng 
Published: February 2016

AbstractIn this study, we propose a method for constructing cell sample networks from gene expression profiles and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns and identifies remarkable cells that form singleton submodules.
Preparation and Characterization of Immobilized Lipase from Pseudomonas Cepacia onto Magnetic Cellulose Nanocrystals
Authors: Cao Shi-Lin , Huang Yu-Mei , Li Xue-Hui , Xu Pei , Wu Hong , Li Ning , Lou Wen-Yong , Zong Min-Hua 
Published: February 2016

AbstractMagnetic cellulose nanocrystals (MCNCs) were prepared and used as an enzyme support for immobilization of Pseudomonas cepacialipase (PCL). PCL was successfully immobilized onto MCNCs (PCL@MCNC) by a precipitation-cross-linking method. The resulting PCL@MCNC with a nanoscale size had high enzyme loading (82.2 mg enzyme/g) and activity recovery (95.9%). Compared with free PCL, PCL@MCNC exhibited significantly enhanced stability and solvent tolerance, due to the increase of enzyme structure rigidity. The observable optimum pH and temperature for PCL@MCNC were higher than those of free PCL. PCL@MCNC manifested relatively higher enzyme-substrate affinity and catalytic efficiency. Moreover, PCL@MCNC was capable of effectively catalyzing asymmetric hydrolysis of ketoprofenethyl ester with high yield of 43.4% and product e.e. of 83.5%. Besides, immobilization allowed PCL@MCNC reuse for at least 6 consecutive cycles retaining over 66% of its initial activity. PCL@MCNC was readily recycled by magnetic forces. Remarkably, the as-prepared nanobiocatalyst PCL@MCNC is promising for biocatalysis.
Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition
Authors: Thorpe Chavaunne T. , Peffers Mandy J. , Simpson Deborah , Halliwell Elizabeth , Screen Hazel R. C. , Clegg Peter D. 
Published: February 2016

AbstractTendon is a simple aligned fibre composite, consisting of collagen-rich fascicles surrounded by a softer interfascicular matrix (IFM). The composition and interactions between these material phases are fundamental in ensuring tissue mechanics meet functional requirements. However the IFM is poorly defined, therefore tendon structure-function relationships are incompletely understood. We hypothesised that the IFM has a more complex proteome, with faster turnover than the fascicular matrix (FM). Using laser-capture microdissection and mass spectrometry, we demonstrate that the IFM contains more proteins and that many proteins show differential abundance between matrix phases. The IFM contained more protein fragments (neopeptides), indicating greater matrix degradation in this compartment, which may act to maintain healthy tendon structure. Protein abundance did not alter with ageing, but neopeptide numbers decreased in the aged IFM, indicating decreased turnover which may contribute to age-related tendon injury. These data provide important insights into how differences in tendon composition and turnover contribute to tendon structure-function relationships and the effects of ageing.