bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the DNA damage response to SFOM-0046, a new small-molecule drug inducing DNA double-strand breaks
Authors: Pauty Joris , Côté Marie-France , Rodrigue Amélie , Velic Denis , Masson Jean-Yves , Fortin Sébastien 
Published: March 2016

Abstract2-Ethylphenyl 4-(3-ethylureido)benzenesulfonate (SFOM-0046) is a novel anticancer agent that arrests cell cycle in S-phase and causes DNA replication stress leading to the phosphorylation of H2AX into γ-H2AX. First, using the M21, HT29, HT-1080 and HeLa cell lines, we confirmed that S-phase cell cycle arrest and γ-H2AX foci induction by SFOM-0046 is a general mechanism occurring in diverse cancer cell lines. In addition to γ-H2AX, SFOM-0046 activates preferentially ATR-Chk1 in M21 and HT29 cells while both ATR-Chk1 and ATM-Chk2 pathways are activated in HCT116 cells. Co-localization of SFOM-0046-induced 53BP1 foci with γ-H2AX foci validates that the DNA damage generated corresponds to double-strand-breaks (DSBs). Consistent with an S-phase arrest, SFOM-0046 treatment induces RAD51 foci formation but not DNA-PKcs foci, confirming that homologous recombination is the major DSB repair pathway targeted by the drug. Furthermore, using isogenic HCT116 p53+/+ and HCT116 p53−/− cells, we showed that p53 plays a key role in the survival mechanism to SFOM-0046. Finally, SFOM-0046 exhibits a dose-dependent antitumor activity on human fibrosarcoma HT-1080 tumours grafted onto chick chorioallantoic membranes without showing embryo toxicity even at high doses. Altogether, our results highlight SFOM-0046 as a very promising drug that induces a replication stress response.
Novel Signal-Amplified Fenitrothion Electrochemical Assay, Based on Glassy Carbon Electrode Modified with Dispersed Graphene Oxide
Authors: Wang Limin , Dong Jinbo , Wang Yulong , Cheng Qi , Yang Mingming , Cai Jia , Liu Fengquan 
Published: March 2016

AbstractA novel signal-amplified electrochemical assay for the determination of fenitrothion was developed, based on the redox behaviour of organophosphorus pesticides on a glassy carbon working electrode. The electrode was modified using graphene oxide dispersion. The electrochemical response of fenitrothion at the modified electrode was investigated using cyclic voltammetry, current-time curves, and square-wave voltammetry. Experimental parameters, namely the accumulation conditions, pH value, and volume of dispersed material, were optimised. Under the optimum conditions, a good linear relationship was obtained between the oxidation peak current and the fenitrothion concentration. The linear range was 1–400 ng·mL−1, with a detection limit of 0.1 ng·mL−1 (signal-to-nose ratio = 3). The high sensitivity of the sensor was demonstrated by determining fenitrothion in pakchoi samples.
Structural and electronic properties of graphene nanoflakes on Au(111) and Ag(111)
Authors: Tesch Julia , Leicht Philipp , Blumenschein Felix , Gragnaniello Luca , Fonin Mikhail , Marsoner Steinkasserer Lukas Eugen , Paulus Beate , Voloshina Elena , Dedkov Yuriy 
Published: March 2016

AbstractWe investigate the electronic properties of graphene nanoflakes on Ag(111) and Au(111) surfaces by means of scanning tunneling microscopy and spectroscopy as well as density functional theory calculations. Quasiparticle interference mapping allows for the clear distinction of substrate-derived contributions in scattering and those originating from graphene nanoflakes. Our analysis shows that the parabolic dispersion of Au(111) and Ag(111) surface states remains unchanged with the band minimum shifted to higher energies for the regions of the metal surface covered by graphene, reflecting a rather weak interaction between graphene and the metal surface. The analysis of graphene-related scattering on single nanoflakes yields a linear dispersion relation E(k), with a slight p-doping for graphene/Au(111) and a larger n-doping for graphene/Ag(111). The obtained experimental data (doping level, band dispersions around EF and Fermi velocity) are very well reproduced within DFT-D2/D3 approaches, which provide a detailed insight into the site-specific interaction between graphene and the underlying substrate.
Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis
Authors: Puniya Bhanwar Lal , Kulshreshtha Deepika , Mittal Inna , Mobeen Ahmed , Ramachandran Srinivasan 
Published: March 2016

AbstractRobustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness.
Electrochemical fecal pellet sensor for simultaneous real-time ex vivo detection of colonic serotonin signalling and motility
Authors: Morris Rachel , Fagan-Murphy Aidan , MacEachern Sarah J. , Covill Derek , Patel Bhavik Anil 
Published: March 2016

AbstractVarious investigations have focused on understanding the relationship between mucosal serotonin (5-HT) and colonic motility, however contradictory studies have questioned the importance of this intestinal transmitter. Here we described the fabrication and use of a fecal pellet electrochemical sensor that can be used to simultaneously detect the release of luminal 5-HT and colonic motility. Fecal pellet sensor devices were fabricated using carbon nanotube composite electrodes that were housed in 3D printed components in order to generate a device that had shape and size that mimicked a natural fecal pellet. Devices were fabricated where varying regions of the pellet contained the electrode. Devices showed that they were stable and sensitive forex vivodetection of 5-HT and no differences in the fecal pellet velocity was observed when compared to natural fecal pellets. The onset of mucosal 5-HT was observed prior to the movement of the fecal pellet. The release of mucosal 5-HT occurred oral to the fecal pellet and was linked to the contraction of the bowel wall that drove pellet propulsion. Taken, together these findings provide new insights into the role of mucosal 5-HT and suggest that the transmitter acts as a key initiator of fecal pellet propulsion.
Neurological complications and risk factors of cardiopulmonary failure of EV-A71-related hand, foot and mouth disease
Authors: Long Lili , Xu Lin , Xiao Zhenghui , Hu Shixiong , Luo Ruping , Wang Hua , Lu Xiulan , Xu Zhiyue , Yao Xu , Zhou Luo , Long Hongyu , Gong Jiaoe , Song Yanmin , Zhao Li , Luo Kaiwei , Zhang Mengqi , Feng Li , Yang Liming , Sheng Xiaoqi , Fan Xuegong , Xiao Bo 
Published: March 2016

AbstractFrom 2010 to 2012, large outbreaks of EV-A71-related- hand foot and mouth disease (HFMD) occurred annually in China. Some cases had neurological complications and were closely associated with fatal cardiopulmonary collapse, but not all children with central nervous system (CNS) involvement demonstrated a poor prognosis. To identify which patients and which neurological complications are more likely to progress to cardiopulmonary failure, we retrospectively studied 1,125 paediatric inpatients diagnosed with EV-A71-related HFMD in Hunan province, including 1,017 cases with CNS involvement. These patients were divided into cardiopulmonary failure (976 people) group and group without cardiopulmonary failure (149 people). A logistic regression analysis was used to compare the clinical symptoms, laboratory test results and neurological complications between these two groups. The most significant risk factors included young age, fever duration ≥3 days, coma, limb weakness, drowsiness and ANS involvement. Patients with brainstem encephalitis and more CNS-involved regions were more likely to progress to cardiopulmonary failure. These findings can help front-line clinicians rapidly and accurately determine patient prognosis, thus rationally distributing the limited medical resources and implementing interventions as early as possible.
Electrically tunable terahertz metamaterials with embedded large-area transparent thin-film transistor arrays
Authors: Xu Wei-Zong , Ren Fang-Fang , Ye Jiandong , Lu Hai , Liang Lanju , Huang Xiaoming , Liu Mingkai , Shadrivov Ilya V. , Powell David A. , Yu Guang , Jin Biaobing , Zhang Rong , Zheng Youdou , Tan Hark Hoe , Jagadish Chennupati 
Published: March 2016

AbstractEngineering metamaterials with tunable resonances are of great importance for improving the functionality and flexibility of terahertz (THz) systems. An ongoing challenge in THz science and technology is to create large-area active metamaterials as building blocks to enable efficient and precise control of THz signals. Here, an active metamaterial device based on enhancement-mode transparent amorphous oxide thin-film transistor arrays for THz modulation is demonstrated. Analytical modelling based on full-wave techniques and multipole theory exhibits excellent consistent with the experimental observations and reveals that the intrinsic resonance mode at 0.75 THz is dominated by an electric response. The resonant behavior can be effectively tuned by controlling the channel conductivity through an external bias. Such metal/oxide thin-film transistor based controllable metamaterials are energy saving, low cost, large area and ready for mass-production, which are expected to be widely used in future THz imaging, sensing, communications and other applications.
Unraveling the formation mechanism of graphitic nitrogen-doping in thermally treated graphene with ammonia
Authors: Li Xiao-Fei , Lian Ke-Yan , Liu Lingling , Wu Yingchao , Qiu Qi , Jiang Jun , Deng Mingsen , Luo Yi 
Published: March 2016

AbstractNitrogen-doped graphene (N-graphene) has attractive properties that has been widely studied over the years. However, its possible formation process still remains unclear. Here, we propose a highly feasible formation mechanism of the graphitic-N doing in thermally treated graphene with ammonia by performing ab initio molecular dynamic simulations at experimental conditions. Results show that among the commonly native point defects in graphene, only the single vacancy 5–9 and divacancy 555–777 have the desirable electronic structures to trap N-containing groups and to mediate the subsequent dehydrogenation processes. The local structure of the defective graphene in combining with the thermodynamic and kinetic effect plays a crucial role in dominating the complex atomic rearrangement to form graphitic-N which heals the corresponding defect perfectly. The importance of the symmetry, the localized force field, the interaction of multiple trapped N-containing groups, as well as the catalytic effect of the temporarily formed bridge-N are emphasized and the predicted doping configuration agrees well with the experimental observation. Hence, the revealed mechanism will be helpful for realizing the targeted synthesis of N-graphene with reduced defects and desired properties.
Selection of urinary sediment miRNAs as specific biomarkers of IgA nephropathy
Authors: Duan Zhi-Yu , Cai Guang-yan , Bu Ru , Lu Yang , Hou Kai , Chen Xiang-Mei 
Published: March 2016

AbstractThe miRNAs in urinary sediment are easy to obtain, which provides a new approach to searching for non-invasive biomarkers of IgA nephropathy (IgAN). Compared with normal controls (n = 3), 214 different miRNAs in the urinary sediment of IgAN (n = 9) were found by miRNA chip assay. By quantitative PCR analysis, miR-25-3p, miR-144-3p and miR-486-5p were confirmed to be significantly higher in IgAN (n = 93) than in the normal group (n = 82) or disease control (n = 40). These three miRNAs had good specificity and sensitivity for the diagnosis of IgAN by receiver operating characteristic curve analysis, in which the AUC value of miR-486-5p was the largest at 0.935. Urinary sediment miR-25-3p, miR-144-3p and miR-486-5p were demonstrated to be mainly derived from urinary erythrocytes, which were separated by CD235a magnetic beads. The increased expression of urinary erythrocyte miRNAs in IgAN patients was not associated with those in the blood erythrocytes. In addition, urinary supernatant microvesicles of miR-144-3p and miR-486-5p in the IgAN group were also significantly increased. This study showed that the miR-25-3p, miR-144-3p and miR-486-5p in urinary sediment were mainly derived from urinary erythrocytes, which could be non-invasive candidate biomarkers for IgA nephropathy.
Integrated dual-mode 3 dB power coupler based on tapered directional coupler
Authors: Luo Yuchan , Yu Yu , Ye Mengyuan , Sun Chunlei , Zhang Xinliang 
Published: March 2016

AbstractA dual-mode 3 dB power coupler based on silicon-on-insulator platform for mode division multiplexing system is proposed and demonstrated. The device, which consists of a tapered directional coupler and two output bend waveguides, has a 50:50 coupling ratio around the wavelength of 1550 nm for both fundamental and first order transverse magnetic (TM0 and TM1) modes. Based on asymmetrical tapered structure, a short common coupling length of ~15.2 μm for both modes is realized by optimizing the width of the tapered waveguide. The measured insertion loss for both modes is less than 0.7 dB. The crosstalks are about −14.3 dB for TM0 mode and −18.1 dB for TM1 mode.
Role of metabolic modulator Bet-CA in altering mitochondrial hyperpolarization to suppress cancer associated angiogenesis and metastasis
Authors: Saha Suchandrima , Ghosh Monisankar , Dutta Samir Kumar 
Published: March 2016

AbstractSolid tumors characteristically reflect a metabolic switching from glucose oxidation to glycolysis that plays a fundamental role in angiogenesis and metastasis to facilitate aggressive tumor outcomes. Hyperpolarized mitochondrial membrane potential is a manifestation of malignant cells that compromise the intrinsic pathways of apoptosis and confer a suitable niche to promote the cancer associated hallmark traits. We have previously reported that co-drug Bet-CA selectively targets cancer cells by inducing metabolic catastrophe without a manifest in toxicity. Here we report that the same molecule at a relatively lower concentration deregulates the cardinal phenotypes associated with angiogenesis and metastasis. In mice syngeneic 4T1 breast cancer model, Bet-CA exhibited effective abrogation of angiogenesis and concomitantly obliterated lung metastasis consistent with altered mitochondrial bioenergetics. Furthermore, Bet-CA significantly lowered vascular endothelial growth factor (VEGF) levels and obviated matrix metalloproteases (MMP-2/9) production directly to the criterion where abrogation of autocrine VEGF/VEGFR2 signalling loop was documented. In vitro studies anticipatedly documented the role of Bet-CA in inhibiting actin remodeling, lamellipodia formation and cell membrane ruffling to constitutively suppress cell motility and invasion. Results comprehensively postulate that Bet-CA, a mitochondria targeting metabolic modulator may serve as an excellent candidate for combating angiogenesis and metastasis.
Highly selective fluorescent chemosensor for detection of Fe3+ based on Fe3O4@ZnO
Authors: Li Jingshuai , Wang Qi , Guo Zhankui , Ma Hongmin , Zhang Yong , Wang Bing , Bin Du , Wei Qin 
Published: March 2016

AbstractThe combination of fluorescent nanoparticles and specific molecular probes appears to be a promising strategy for developing fluorescent nanoprobes. In this work, L-cysteine (L-Cys) capped Fe3O4@ZnO core-shell nanoparticles were synthesized for the highly selective detection of Fe3+. The proposed nanoprobe shows excellent fluorescent property and high selectivity for Fe3+ due to the binding affinity of L-Cys with Fe3+. The binding of Fe3+ to the nanoprobe induces an apparent decrease of the fluorescence. Thus a highly selective fluorescent chemosensor for Fe3+ was proposed based on Fe3O4@ZnO nanoprobe. The magnetism of the nanoprobe enables the facile separation of bound Fe3+ from the sample solution with an external magnetic field, which effectively reduces the interference of matrix. The detection limit was 3 nmol L−1 with a rapid response time of less than 1 min. The proposed method was applied to detect Fe3+ in both serum and wastewater samples with acceptable performance. All above features indicated that the proposed fluorescent probe as sensing platform held great potential in applications of biological and analytical field.
Identification of three LRR-RKs involved in perception of root meristem growth factor in
Arabidopsis
Authors: Shinohara Hidefumi , Mori Ayaka , Yasue Naoko , Sumida Kumiko , Matsubayashi Yoshikatsu 
Published: March 2016

Significance
There is a growing awareness that receptor kinases (RKs) regulate various aspects of plant development in response to perception of specific ligands, but the highly redundant nature of this family's members often makes it difficult to identify their ligands by a conventional mutant screening approach. To sidestep gene redundancy problems, here we used a combination of a custom-made RK expression library and exhaustive photoaffinity labeling and identified three RKs that directly interact with root meristem growth factor (RGF), a peptide hormone regulating root meristem development. The receptor triple mutant was insensitive to externally applied RGF peptide and displayed a short root phenotype accompanied by a considerable decrease in meristematic cell number, representing a previously unidentified ligand–receptor system in plants.
XIBD: software for inferring pairwise identity by descent on the X chromosome
Authors: Henden Lyndal , Wakeham David , Bahlo Melanie 
Published: March 2016

AbstractSummary: XIBD performs pairwise relatedness mapping on the X chromosome using dense single nucleotide polymorphism (SNP) data from either SNP chips or next generation sequencing data. It correctly accounts for the difference in chromosomal numbers between males and females and estimates global relatedness as well as regions of the genome that are identical by descent (IBD). XIBD also generates novel graphical summaries of all pairwise IBD tracts for a cohort making it very useful for disease locus mapping.Availability and implementation: XIBD is written in R/Rcpp and executed from shell scripts that are freely available from http://bioinf.wehi.edu.au/software/XIBD along with accompanying reference datasets.Contact: henden.l@wehi.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data
Authors: Christinat Yann , Pawłowski Rafał , Krek Wilhelm 
Published: March 2016

Abstract
Motivation: Alternative splicing represents a prime mechanism of post-transcriptional gene regulation whose misregulation is associated with a broad range of human diseases. Despite the vast availability of transcriptome data from different cell types and diseases, bioinformatics-based surveys of alternative splicing patterns remain a major challenge due to limited availability of analytical tools that combine high accuracy and rapidity.
Results: We describe here a novel junction-centric method, jSplice, that enables de novo extraction of alternative splicing events from RNA-sequencing data with high accuracy, reliability and speed. Application to clear cell renal carcinoma (ccRCC) cell lines and 65 ccRCC patients revealed experimentally validatable alternative splicing changes and signatures able to prognosticate ccRCC outcome. In the aggregate, our results propose jSplice as a key analytic tool for the derivation of cell context-dependent alternative splicing patterns from large-scale RNA-sequencing datasets.
Availability and implementation: jSplice is a standalone Python application freely available at http://www.mhs.biol.ethz.ch/research/krek/jsplice.
Contact: wilhelm.krek@biol.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks
Authors: Pang Chao , van Enckevort David , de Haan Mark , Kelpin Fleur , Jetten Jonathan , Hendriksen Dennis , de Boer Tommy , Charbon Bart , Winder Erwin , van der Velde K. Joeri , Doiron Dany , Fortier Isabel , Hillege Hans , Swertz Morris A. 
Published: March 2016

Abstract
Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration.
Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data.
Availability and Implementation: Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect.
Contact: m.a.swertz@rug.nl
Supplementary information: Supplementary data are available at Bioinformatics online.