bluuebunny/crossref_metadata_2025_split huggingface dataset:
A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme
Authors: Paul Deepanjan , Sinha Ashis Narayan , Ray Arjun , Lal Megha , Nayak Subhashree , Sharma Anchal , Mehani Bharati , Mukherjee Debasish , Laddha Saurabh V. , Suri Ashish , Sarkar Chitra , Mukhopadhyay Arijit 
Published: May 2017

AbstractEditing in microRNAs, particularly in seed can significantly alter the choice of their target genes. We show that out of 13 different human tissues, different regions of brain showed higher adenosine to inosine (A-to-I) editing in mature miRNAs. These events were enriched in seed sequence (73.33%), which was not observed for cytosine to uracil (17.86%) editing. More than half of the edited miRNAs showed increased stability, 72.7% of which had ΔΔG values less than −6.0 Kcal/mole and for all of them the edited adenosines mis-paired with cytosines on the pre-miRNA structure. A seed-editing event in hsa-miR-411 (with A – C mismatch) lead to increased expression of the mature form compared to the unedited version in cell culture experiments. Further, small RNA sequencing of GBM patients identified significant miRNA hypoediting which correlated with downregulation of ADAR2 both in metadata and qRT-PCR based validation. Twenty-two significant (11 novel) A-to-I hypoediting events were identified in GBM samples. This study highlights the importance of specific sequence and structural requirements of pre-miRNA for editing along with a suggestive crucial role for ADAR2. Enrichment of A-to-I editing in seed sequence highlights this as an important layer for genomic regulation in health and disease, especially in human brain.
Atomic layer etching of graphene through controlled ion beam for graphene-based electronics
Authors: Kim Ki Seok , Ji You Jin , Nam Yeonsig , Kim Ki Hyun , Singh Eric , Lee Jin Yong , Yeom Geun Young 
Published: May 2017

AbstractThe electronic and optical properties of graphene are greatly dependent on the the number of layers. For the precise control of the graphene layers, atomic layer etching (ALE), a cyclic etching method achieved through chemical adsorption and physical desorption, can be the most powerful technique due to barely no damage and no contamination. In this study, we demonstrated the ALE process of graphene layers without noticeably damaging the graphene by using a controlled low energy oxygen (O2+/O+)-ion for chemical adsorption and a low energy Ar+-ion (11.2 eV) for physical desorption. In addition, using a trilayer graphene, mono- and bi-layer graphene could be successfully fabricated after one- and two-cycle ALE of the trilayer graphene, respectively. We believe that the ALE technique presented herein can be applicable to all layered materials such as graphene, black phosphorous and transition metal dichalcogenides which are important for next generation electronic devices.
Anti-proliferative Effects of Nucleotides on Gastric Cancer via a Novel P2Y6/SOCE/Ca2+/β-catenin Pathway
Authors: Wan Hanxing , Xie Rui , Xu Jiangyu , He Jialin , Tang Bo , Liu Qingqing , Wang Sumin , Guo Yanjun , Yang Xin , Dong Tobias Xiao , Carethers John M. , Yang Shiming , Dong Hui 
Published: May 2017

AbstractAlthough purinegic signaling is important in regulating gastric physiological functions, it is currently unknown for its role in gastric cancer (GC). We demonstrate for the first time that the expression of P2Y6 receptors was markedly down-regulated in human GC cells and primary GC tissues compared to normal tissues, while the expression of P2Y2 and P2Y4 receptors was up-regulated in GC cells. Moreover, the expression levels of P2Y6 receptors in GC tissues were correlated to tumor size, differentiation, metastasis to lymph nodes, and the survival rate of the patients with GC. Ncleotides activated P2Y6 receptors to raise cytosolic Ca2+ concentrations in GC cells through store-operated calcium entry (SOCE), and then mediated Ca2+-dependent inhibition of β-catenin and proliferation, eventually leading to GC suppression. Furthermore, UTP particularly blocked the G1/S transition of GC cells but did not induce apoptosis. Collectively, we conclude that nucleotides activate P2Y6 receptors to suppress GC growth through a novel SOCE/Ca2+/β-catenin-mediated anti-proliferation of GC cells, which is different from the canonical SOCE/Ca2+-induced apoptosis in other tumors.
Differences in selectivity to natural images in early visual areas (V1–V3)
Authors: Coggan David D. , Allen Luke A. , Farrar Oliver R. H. , Gouws Andre D. , Morland Antony B. , Baker Daniel H. , Andrews Timothy J. 
Published: May 2017

AbstractHigh-level regions of the ventral visual pathway respond more to intact objects compared to scrambled objects. The aim of this study was to determine if this selectivity for objects emerges at an earlier stage of processing. Visual areas (V1–V3) were defined for each participant using retinotopic mapping. Participants then viewed intact and scrambled images from different object categories (bottle, chair, face, house, shoe) while neural responses were measured using fMRI. Our rationale for using scrambled images is that they contain the same low-level properties as the intact objects, but lack the higher-order combinations of features that are characteristic of natural images. Neural responses were higher for scrambled than intact images in all regions. However, the difference between intact and scrambled images was smaller in V3 compared to V1 and V2. Next, we measured the spatial patterns of response to intact and scrambled images from different object categories. We found higher within-category compared to between category correlations for both intact and scrambled images demonstrating distinct patterns of response. Spatial patterns of response were more distinct for intact compared to scrambled images in V3, but not in V1 or V2. These findings demonstrate the emergence of selectivity to natural images in V3.
Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity
Authors: Pilkington Emily H. , Xing Yanting , Wang Bo , Kakinen Aleksandr , Wang Miaoyi , Davis Thomas P. , Ding Feng , Ke Pu Chun 
Published: May 2017

AbstractAggregation of islet amyloid polypeptide (IAPP), a peptide hormone co-synthesized and co-stored with insulin in pancreatic cells and also co-secreted to the circulation, is associated with beta-cell death in type-2 diabetes (T2D). In T2D patients IAPP is found aggregating in the extracellular space of the islets of Langerhans. Although the physiological environments of these intra- and extra-cellular compartments and vascular systems significantly differ, the presence of proteins is ubiquitous but the effects of protein binding on IAPP aggregation are largely unknown. Here we examined the binding of freshly-dissolved IAPP as well as pre-formed fibrils with two homologous proteins, namely cationic lysozyme (Lys) and anionic alpha-lactalbumin (aLac), both of which can be found in the circulation. Biophysical characterizations and a cell viability assay revealed distinct effects of Lys and aLac on IAPP amyloid aggregation, fibril remodelling and cytotoxicity, pointing to the role of protein “corona” in conferring the biological impact of amyloidogenic peptides. Systematic molecular dynamics simulations further provided molecular and structural details for the observed differential effects of proteins on IAPP amyloidosis. This study facilitates our understanding of the fate and transformation of IAPP in vivo, which are expected to have consequential bearings on IAPP glycemic control and T2D pathology.
Doping of metal–organic frameworks towards resistive sensing
Authors: Shiozawa Hidetsugu , Bayer Bernhard C. , Peterlik Herwig , Meyer Jannik C. , Lang Wolfgang , Pichler Thomas 
Published: May 2017

AbstractCoordination polymerization leads to various metal–organic frameworks (MOFs) with unique physical properties and chemical functionalities. One of the challenges towards their applications as porous materials is to make MOFs optimally conductive to be used as electronic components. Here, it is demonstrated that Co-MOF-74, a honeycomb nano–framework with one–dimensionally arranged cobalt atoms, advances its physical properties by accommodating tetracyanochinodimethan (TCNQ), an acceptor molecule. Strong intermolecular charge transfer reduces the optical band gap down to 1.5 eV of divalent TCNQ and enhances the electrical conduction, which allows the MOF to be utilized for resistive gas- and photo-sensing. The results provide insight into the electronic interactions in doped MOFs and pave the way for their electronic applications.
High-resolution bioelectrical imaging of Aβ-induced network dysfunction on CMOS-MEAs for neurotoxicity and rescue studies
Authors: Amin Hayder , Nieus Thierry , Lonardoni Davide , Maccione Alessandro , Berdondini Luca 
Published: May 2017

AbstractNeurotoxicity and the accumulation of extracellular amyloid-beta1–42 (Aβ) peptides are associated with the development of Alzheimer’s disease (AD) and correlate with neuronal activity and network dysfunctions, ultimately leading to cellular death. However, research on neurodegenerative diseases is hampered by the paucity of reliable readouts and experimental models to study such functional decline from an early onset and to test rescue strategies within networks at cellular resolution. To overcome this important obstacle, we demonstrate a simple yet powerful in vitro AD model based on a rat hippocampal cell culture system that exploits large-scale neuronal recordings from 4096-electrodes on CMOS-chips for electrophysiological quantifications. This model allows us to monitor network activity changes at the cellular level and to uniquely uncover the early activity-dependent deterioration induced by Aβ-neurotoxicity. We also demonstrate the potential of this in vitro model to test a plausible hypothesis underlying the Aβ-neurotoxicity and to assay potential therapeutic approaches. Specifically, by quantifying N-methyl D-aspartate (NMDA) concentration-dependent effects in comparison with low-concentration allogenic-Aβ, we confirm the role of extrasynaptic-NMDA receptors activation that may contribute to Aβ-neurotoxicity. Finally, we assess the potential rescue of neural stem cells (NSCs) and of two pharmacotherapies, memantine and saffron, for reversing Aβ-neurotoxicity and rescuing network-wide firing.
A novel, somatic, transforming mutation in the extracellular domain of Epidermal Growth Factor Receptor identified in myeloproliferative neoplasm
Authors: Casolari D. A. , Nguyen T. , Butcher C. M. , Iarossi D. G. , Hahn C. N. , Bray S. C. , Neufing P. , Parker W. T. , Feng J. , Maung K. Z. Y. , Wee A. , Vidovic L. , Kok C. H. , Bardy P. G. , Branford S. , Lewis I. D. , Lane S. W. , Scott H. S. , Ross D. M. , D’Andrea R. J. 
Published: May 2017

AbstractWe describe a novel ERBB1/EGFR somatic mutation (p. C329R; c.985 T > C) identified in a patient with JAK2V617F Polycythaemia Vera (PV). This substitution affects a conserved cysteine residue in EGFR domain 2 and leads to the formation of a ligand-independent covalent receptor dimer, associated with increased transforming potential. Aberrant signalling from the EGFRC329R receptor is cell type-dependent and in the TF1.8 erythroid cell line expression of this mutant suppresses EPO-induced differentiation. Clonal analysis shows that the dominant JAK2V617F-positive clone in this PV patient harbors EGFRC329R, thus this mutation may contribute to clonal expansion. Somatic mutations affecting other ERBB and related receptor tyrosine kinases are observed in myeloproliferative neoplasms (MPN), and we show elevated EGFR levels in MPN samples, consistent with previous reports. Thus activation of this group of receptors, via multiple mechanisms, may contribute to clonal growth and survival of the JAK2V617F disease clone in MPN.
Artefact-free Evaluation of Metal Enhanced Fluorescence in Silica Coated Gold Nanoparticles
Authors: Ribeiro Tânia , Baleizão Carlos , Farinha José Paulo S. 
Published: May 2017

AbstractMetal nanoparticles can either quench or enhance the emission of dyes in their vicinity, but the precise measurement and understanding of this effect is still hindered by experimental artifacts, especially for particles in colloidal dispersion. Here, we introduce a new methodology to correct the inner filter effect of the metal on the dye emission. To test the method, we developed new hybrid nanoparticles with a gold core and a silica shell of precise thickness (tuned from 7 to 13 nm), with a high quantum yield perylenediimide dye on the surface. This novel approach effectively avoids fluorescence quenching, allowing us to measure emission enhancements of 5 to 30 times, with no change on the dye fluorescence lifetime. Being able to measure the emission enhancement in dye-metal hybrid nanoparticles in dispersion, free from inner filter and quenching artifacts, offers excellent prospects to guide the development of more efficient fluorescent probes, sensors and photonic devices.
Seasonally lagged effects of climatic factors on malaria incidence in South Africa
Authors: Ikeda Takayoshi , Behera Swadhin K. , Morioka Yushi , Minakawa Noboru , Hashizume Masahiro , Tsuzuki Ataru , Maharaj Rajendra , Kruger Philip 
Published: May 2017

AbstractGlobally, malaria cases have drastically dropped in recent years. However, a high incidence of malaria remains in some sub-Saharan African countries. South Africa is mostly malaria-free, but northeastern provinces continue to experience seasonal outbreaks. Here we investigate the association between malaria incidence and spatio-temporal climate variations in Limpopo. First, dominant spatial patterns in malaria incidence anomalies were identified using self-organizing maps. Composite analysis found significant associations among incidence anomalies and climate patterns. A high incidence of malaria during the pre-peak season (Sep-Nov) was associated with the climate phenomenon La Niña and cool air temperatures over southern Africa. There was also high precipitation over neighbouring countries two to six months prior to malaria incidence. During the peak season (Dec-Feb), high incidence was associated with positive phase of Indian Ocean Subtropical Dipole. Warm temperatures and high precipitation in neighbouring countries were also observed two months prior to increased malaria incidence. This lagged association between regional climate and malaria incidence suggests that in areas at high risk for malaria, such as Limpopo, management plans should consider not only local climate patterns but those of neighbouring countries as well. These findings highlight the need to strengthen cross-border control of malaria to minimize its spread.
Opposite polarities of ENSO drive distinct patterns of coral bleaching potentials in the southeast Indian Ocean
Authors: Zhang Ningning , Feng Ming , Hendon Harry H. , Hobday Alistair J. , Zinke Jens 
Published: May 2017

AbstractEpisodic anomalously warm sea surface temperature (SST) extremes, or marine heatwaves (MHWs), amplify ocean warming effects and may lead to severe impacts on marine ecosystems. MHW-induced coral bleaching events have been observed frequently in recent decades in the southeast Indian Ocean (SEIO), a region traditionally regarded to have resilience to global warming. In this study, we assess the contribution of El Niño-Southern Oscillation (ENSO) to MHWs across the mostly understudied reefs in the SEIO. We find that in extended summer months, the MHWs at tropical and subtropical reefs (divided at ~20°S) are driven by opposite ENSO polarities: MHWs are more likely to occur at the tropical reefs during eastern Pacific El Niño, driven by enhanced solar radiation and weaker Australian Monsoon, some likely alleviated by positive Indian Ocean Dipole events, and at the subtropical reefs during central Pacific La Niña, mainly caused by increased horizontal heat transport, and in some cases reinforced by local air-sea interactions. Madden-Julian Oscillations (MJO) also modulate the MHW occurrences. Projected future increases in ENSO and MJO intensity with greenhouse warming will enhance thermal stress across the SEIO. Implementing forecasting systems of MHWs can be used to anticipate future coral bleaching patterns and prepare management responses.
Hydrologic Evaluation of TRMM Multisatellite Precipitation Analysis for Nanliu River Basin in Humid Southwestern China
Authors: Zhao Yinjun , Xie Qiongying , Lu Yuan , Hu Baoqing 
Published: May 2017

AbstractThe accuracy of Tropical Rainfall Measuring Mission (TRMM) multi-satellite precipitation analysis (TMPA) daily accumulated precipitation products (3B42RTV7 and 3B42V7) was evaluated for a small basin (the Nanliu river basin). A direct comparison was performed against gauge observations from a period of 9 years (2000–2009) at temporal and spatial scales. The results show that the temporal-spatial precipitation characteristics of the Nanliu river basin are highly consistent with 3B42V7 relative to 3B42RTV7, with higher correlation coefficient (CC) approximately 0.9 at all temporal scales except for the daily scale and a lower relative bias percentage. 3B42V7 slightly overestimates precipitation at all temporal scales except the yearly scale; it slightly underestimates the precipitation at the daily spatial scale. The results also reveal that the precision of TMPA products increases with longer time-aggregated data, and the detection capability of daily TMPA precipitation products are enhanced by augmentation with daily precipitation rates. In addition, daily TMPA products were input into the Xin’anjiang hydrologic model; the results show that 3B42V7-based simulated outputs were well in line with actual stream flow observations, with a high CC (0.90) and Nash-Sutcliffe efficiency coefficient (NSE, 0.79), and the results adequately captured the pattern of the observed flow curve.
Antigenicity of Bovine Pericardium Determined by a Novel Immunoproteomic Approach
Authors: Gates Katherine V. , Dalgliesh Ailsa J. , Griffiths Leigh G. 
Published: May 2017

AbstractDespite bovine pericardium (BP) being the primary biomaterial used in heart valve bioprostheses, recipient graft-specific immune responses remain a significant cause of graft failure. Consequently, tissue antigenicity remains the principal barrier for expanding use of such biomaterials in clinical practice. We hypothesize that our understanding of BP antigenicity can be improved by application of a combined affinity chromatography shotgun immunoproteomic approach to identify antigens that have previously been overlooked. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) analysis of affinity chromatography purified antigens resulted in identification of 133 antigens. Most importantly, antigens were identified from all subcellular locations, including 18 integral membrane protein antigens. Critically, isoforms of several protein families were found to be antigenic suggesting the possibility that shared epitope domains may exist. Furthermore, proteins associated with immune, coagulation, and inflammatory pathways were over-represented, suggesting that these biological processes play a key role in antigenicity. This study brings to light important determinants of antigenicity in a clinically relevant xenogeneic biomaterial (i.e. BP) and further validates a rapid, high-throughput method for immunoproteomic antigen identification.
Differential methylation is associated with non-syndromic cleft lip and palate and contributes to penetrance effects
Authors: Alvizi Lucas , Ke Xiayi , Brito Luciano Abreu , Seselgyte Rimante , Moore Gudrun E. , Stanier Philip , Passos-Bueno Maria Rita 
Published: May 2017

AbstractNon-syndromic cleft lip and/or palate (NSCLP) is a common congenital malformation with a multifactorial model of inheritance. Although several at-risk alleles have been identified, they do not completely explain the high heritability. We postulate that epigenetic factors as DNA methylation might contribute to this missing heritability. Using a Methylome-wide association study in a Brazilian cohort (67 NSCLP, 59 controls), we found 578 methylation variable positions (MVPs) that were significantly associated with NSCLP. MVPs were enriched in regulatory and active regions of the genome and in pathways already implicated in craniofacial development. In an independent UK cohort (171 NSCLP, 177 controls), we replicated 4 out of 11 tested MVPs. We demonstrated a significant positive correlation between blood and lip tissue DNA methylation, indicating blood as a suitable tissue for NSCLP methylation studies. Next, we quantified CDH1 promoter methylation levels in CDH1 mutation-positive families, including penetrants, non-penetrants or non-carriers for NSCLP. We found methylation levels to be significantly higher in the penetrant individuals. Taken together, our results demonstrated the association of methylation at specific genomic locations as contributing factors to both non-familial and familial NSCLP and altered DNA methylation may be a second hit contributing to penetrance.
Density-controlled quantum Hall ferromagnetic transition in a two-dimensional hole system
Authors: Lu T. M. , Tracy L. A. , Laroche D. , Huang S.-H. , Chuang Y. , Su Y.-H. , Li J.-Y. , Liu C. W. 
Published: May 2017

AbstractQuantum Hall ferromagnetic transitions are typically achieved by increasing the Zeeman energy through in-situ sample rotation, while transitions in systems with pseudo-spin indices can be induced by gate control. We report here a gate-controlled quantum Hall ferromagnetic transition between two real spin states in a conventional two-dimensional system without any in-plane magnetic field. We show that the ratio of the Zeeman splitting to the cyclotron gap in a Ge two-dimensional hole system increases with decreasing density owing to inter-carrier interactions. Below a critical density of ~2.4 × 1010 cm−2, this ratio grows greater than 1, resulting in a ferromagnetic ground state at filling factor ν = 2. At the critical density, a resistance peak due to the formation of microscopic domains of opposite spin orientations is observed. Such gate-controlled spin-polarizations in the quantum Hall regime opens the door to realizing Majorana modes using two-dimensional systems in conventional, low-spin-orbit-coupling semiconductors.
Group‐delay‐insensitive linear equaliser for reducing eye‐skew in PAM‐4 receivers
Authors: Wu Kejun , Zhang Huazi 
Published: May 2017

A novel group‐delay‐insensitive linear equaliser (GDILE) is proposed to reduce the eye‐skew in four‐level pulse amplitude modulation (PAM‐4) receivers. With a cross‐coupled positive‐feedback degeneration network, the proposed GDILE employs additional pole and zero into its transfer function to reduce the group‐delay variation with frequency. Simulation results shows a 40 Gbit/s PAM‐4 receiver that employs a GDILE that can reduce the eye‐skew by 73% compared with the conventional linear equaliser with a modest increase of power consumption.
Development of an arc‐extinguishing lightning protection gap for 35 kV overhead power lines
Authors: Wang Ju‐feng , Wu Dong 
Published: May 2017

Given that currently available lightning protection measures cannot effectively protect overhead lines from lightning strikes, this study develops an active and fast arc‐extinguishing lightning protection gap to address this issue. When a power frequency arc is formed within the protection gap due to a lightning strike, the lightning current immediately ignites the device, while strong airflow is synchronously produced. In this manner, the follow‐up power frequency arc can be extinguished within an arc duration that is considerably shorter than the action time of relay protection; thus, relay protection can be avoided, and the lightning trip‐out of overhead lines can be effectively prevented. A test of insulation coordination for impulse flashover and a test of power frequency arc extinction are performed to validate the effectiveness of the device. The arc‐extinguishing test proves that the strong airflow can extinguish the arc within 0.4 ms. The devices have been widely applied in China and have been extremely successful.