bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1
Authors: Le Douce Valentin , Forouzanfar Faezeh , Eilebrecht Sebastian , Van Driessche Benoit , Ait-Ammar Amina , Verdikt Roxane , Kurashige Yoshihito , Marban Céline , Gautier Virginie , Candolfi Ermanno , Benecke Arndt G. , Van Lint Carine , Rohr Olivier , Schwartz Christian 
Published: October 2016

AbstractAmong many cellular transcriptional regulators, Bcl11b/CTIP2 and HGMA1 have been described to control the establishment and the persistence of HIV-1 latency in microglial cells, the main viral reservoir in the brain. In this present work, we identify and characterize a transcription factor i.e. HIC1, which physically interacts with both Bcl11b/CTIP2 and HMGA1 to co-regulate specific subsets of cellular genes and the viral HIV-1 gene. Our results suggest that HIC1 represses Tat dependent HIV-1 transcription. Interestingly, this repression of Tat function is linked to HIC1 K314 acetylation status and to SIRT1 deacetylase activity. Finally, we show that HIC1 interacts and cooperates with HGMA1 to regulate Tat dependent HIV-1 transcription. Our results also suggest that HIC1 repression of Tat function happens in a TAR dependent manner and that this TAR element may serve as HIC1 reservoir at the viral promoter to facilitate HIC1/TAT interaction.
Plasmonic Nanoparticle-based Hybrid Photosensitizers with Broadened Excitation Profile for Photodynamic Therapy of Cancer Cells
Authors: Wang Peng , Tang Hong , Zhang Peng 
Published: October 2016

AbstractPhotodynamic therapy combining nanotechnology has shown great potential with improved therapeutic efficacy and fewer side effects. Ideal photosensitizers for cancer treatment should both have good singlet oxygen production capability and be excitable by light illuminations with deep tissue penetration. Here we report a type of hybrid photosensitizers consisting of plasmonic silver nanoparticles and photosensitizing molecules, where strong resonance coupling between the two leads to a broadened excitation profile and exceptionally high singlet oxygen production under both visible light and infrared light excitations. Our results indicate that the hybrid photosensitizers display low cytotoxicity without light illumination yet highly enhanced photodynamic inhibition efficacy against Hela cells under a broad spectrum of light illuminations including the near-infrared light, which has great implication in photodynamic therapy of deep-tissue cancers.
circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations
Authors: Chen Xiaoping , Han Ping , Zhou Tao , Guo Xuejiang , Song Xiaofeng , Li Yan 
Published: October 2016

AbstractIt has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.
Stoichiometry patterns in the androdioecious Acer tegmentosum
Authors: Zhang Xinna , Yao Jie , Fan Chunyu , Tan Lingzhao , Zhang Chunyu , Wang Juan , Zhao Xiuhai , von Gadow Klaus 
Published: October 2016

AbstractThis study evaluates stoichiometry patterns in the androdioecious Acer tegmentosum, a species characterized by a rare reproductive system where males and hermaphrodites coexist. Altogether 31 hermaphrodites and 29 male plants were harvested and samples of leaves, current-year shoots, branches and coarse roots were analyzed to explore gender differences in biomass, C, N and P concentrations of these four components. The nitrogen to phosphorus relationship of each component was examined using SMA estimates. Males had significantly greater amounts of leaf and coarse root dry matter content than hermaphrodites. C, N and P stoichiometry differed significantly between genders, especially in the newly emerging vegetative components (leaves and shoots). Males had higher C/N and C/P ratios in current-year shoots and lower C/P ratios in leaves and branches. Hermaphrodites had higher N/P ratios in the leaves and branches. Males had higher rates of increase in leaf P content than hermaphrodites. This study suggests that stoichiometry patterns may be significantly affected by gender.
Ring-shaped Racetrack memory based on spin orbit torque driven chiral domain wall motions
Authors: Zhang Yue , Zhang Xueying , Hu Jingtong , Nan Jiang , Zheng Zhenyi , Zhang Zhizhong , Zhang Youguang , Vernier Nicolas , Ravelosona Dafine , Zhao Weisheng 
Published: October 2016

AbstractRacetrack memory (RM) has sparked enormous interest thanks to its outstanding potential for low-power, high-density and high-speed data storage. However, since it requires bi-directional domain wall (DW) shifting process for outputting data, the mainstream stripe-shaped concept certainly suffers from the data overflow issue. This geometrical restriction leads to increasing complexity of peripheral circuits or programming as well as undesirable reliability issue. In this work, we propose and study ring-shaped RM, which is based on an alternative mechanism, spin orbit torque (SOT) driven chiral DW motions. Micromagnetic simulations have been carried out to validate its functionality and exhibit its performance advantages. The current flowing through the heavy metal instead of ferromagnetic layer realizes the “end to end” circulation of storage data, which remains all the data in the device even if they are shifted. It blazes a promising path for application of RM in practical memory and logic.
Contrast-Enhanced Ultrasonography with Quantitative Analysis allows Differentiation of Renal Tumor Histotypes
Authors: Sun Di , Wei Cong , Li Yi , Lu Qijie , Zhang Wei , Hu Bing 
Published: October 2016

AbstractTotally 85 patients with 93 renal lesions who underwent contrast-enhanced ultrasound (CEUS) were retrospectively studied with quantitative analysis to evaluate its value in the differential diagnosis of renal tumor histotypes. CEUS characteristics were analysed including the enhancement patterns, peak intensity, homogeneity of enhancement, and pseudocapsule. Quantitative parameters of peak intensity (P) and time to peak (TP) were measured with QontraXt software, and the index “relative enhancement percentage” ΔP% and “difference in TP between tumor and cortex” ΔTP were used to quantify the CEUS features of renal tumors. There are significant difference in CEUS features between the 46 clear cell renal cell carcinoma (CCRCC) and other types of renal tumors, including 17 low malignant lesions, 11 urothelial carcinoma of the renal pelvis, and 19 renal angiomyolipoma. The differences lie in the peak intensity, the homogeneity, the time of wash-in, peak, clearance and presence of pseudocapsule. The ΔTP and ΔP% of the CCRCC is significantly different from other tumors. With “fast to peak + high peak intensity” as the main criterion, assisted with “heterogeneous enhancement” and “fast wash-in” as the secondary criteria, the diagnostic accuracy of CCRCC is 91.4%, demonstrating quantitative CEUS imaging is highly valuable in differentiating CCRCC from other tumors.
Transparency and tunable slow and fast light in a nonlinear optomechanical cavity
Authors: Li Ling , Nie Wenjie , Chen Aixi 
Published: October 2016

AbstractWe investigate theoretically the optical response of the output field and the tunable slow and fast light in a nonlinear optomechanical cavity with a degenerate optical parametric amplifier (OPA) and a higher order excited atomic ensemble. Studies show that the higher-order-excitation atom which is similar to the degenerate OPA that acts as a nonlinear medium, induces an additional dip in absorption spectrum of the probe field. The coherence of the mechanical oscillator leads to split the peak in absorption in the probe field spectrum so that the phenomenon of optomechanically induced transparency (OMIT) is generated from the output probe field. In particular, the presence of nonlinearities with the degenerate OPA and the higher order excited atoms can affect significantly the width of the transparency windows, providing an additional flexibility for controlling optical properties. Furthermore, in the presence of the degenerate OPA, the optical-response properties for the probe field become phase-sensitive so that a tunable switch from slow to fast light can be realized.
A Novel Computer-Assisted Approach to evaluate Multicellular Tumor Spheroid Invasion Assay
Authors: Cisneros Castillo Liliana R. , Oancea Andrei-Dumitru , Stüllein Christian , Régnier-Vigouroux Anne 
Published: October 2016

AbstractMulticellular tumor spheroids (MCTSs) embedded in a matrix are re-emerging as a powerful alternative to monolayer-based cultures. The primary information gained from a three-dimensional model is the invasiveness of treatment-exposed MCTSs through the acquisition of light microscopy images. The amount and complexity of the acquired data and the bias arisen by their manual analysis are disadvantages calling for an automated, high-throughput analysis. We present a universal algorithm we developed with the scope of being robust enough to handle images of various qualities and various invasion profiles. The novelty and strength of our algorithm lie in: the introduction of a multi-step segmentation flow, where each step is optimized for each specific MCTS area (core, halo, and periphery); the quantification through the density of the two-dimensional representation of a three-dimensional object. This latter offers a fine-granular differentiation of invasive profiles, facilitating a quantification independent of cell lines and experimental setups. Progression of density from the core towards the edges influences the resulting density map thus providing a measure no longer dependent on the sole area size of MCTS, but also on its invasiveness. In sum, we propose a new method in which the concept of quantification of MCTS invasion is completely re-thought.
Antisense oligonucleotide-mediated exon skipping as a strategy to reduce proteolytic cleavage of ataxin-3
Authors: Toonen Lodewijk J. A. , Schmidt Iris , Luijsterburg Martijn S. , van Attikum Haico , van Roon-Mom Willeke M. C. 
Published: October 2016

AbstractSpinocerebellar ataxia type-3 (SCA3) is a neurodegenerative disorder caused by a polyglutamine repeat expansion in the ataxin-3 protein. Cleavage of mutant ataxin-3 by proteolytic enzymes yields ataxin-3 fragments containing the polyglutamine stretch. These shorter ataxin-3 fragments are thought to be involved in SCA3 pathogenesis due to their increased cellular toxicity and their involvement in formation of the characteristic neuronal aggregates. As a strategy to prevent formation of toxic cleavage fragments, we investigated an antisense oligonucleotide-mediated modification of the ataxin-3 pre-mRNA through exon skipping of exon 8 and 9, resulting in the removal of a central 88 amino acid region of the ataxin-3 protein. This removed protein region contains several predicted cleavage sites and two ubiquitin-interacting motifs. In contrast to unmodified mutant ataxin-3, the internally truncated ataxin-3 protein did not give rise to potentially toxic cleavage fragments when incubated with caspases. In vitro experiments did not show cellular toxicity of the modified ataxin-3 protein. However, the modified protein was incapable of binding poly-ubiquitin chains, which may interfere with its normal deubiquitinating function. Low exon skipping efficiencies combined with reduction in important ataxin-3 protein functions suggest that skipping of exon 8 and 9 is not a viable therapeutic option for SCA3.
Multistate Redox Switching and Near-Infrared Electrochromism Based on a Star-Shaped Triruthenium Complex with a Triarylamine Core
Authors: Tang Jian-Hong , He Yan-Qin , Shao Jiang-Yang , Gong Zhong-Liang , Zhong Yu-Wu 
Published: October 2016

AbstractA star-shaped cyclometalated triruthenium complex 2(PF6)n (n = 3 and 4) with a triarylamine core was synthesized, which functions as a molecular switch with five well-separated redox states in both solution and film states. The single-crystal X-ray structure of 2(PF6)3 is presented. This complex displays four consecutive one-electron redox waves at +0.082, +0.31, +0.74, and +1.07 V vs Ag/AgCl. In each redox state, it shows significantly different NIR absorptions with λmax of 1590 nm for 24+, 1400 nm for 25+, 1060 nm for 26+, and 740 nm for 27+, respectively. Complex 24+ shows a single-line EPR signal at g = 2.060, while other redox states are all EPR inactive. The spin density distributions and NIR absorptions in different redox states were rationalized by DFT and TDDFT calculations. A vinyl-substituted triruthenium analogous 3(PF6)4 was prepared, which was successfully polymerized on ITO glass electrode surfaces by reductive electropolymerization. The obtained poly-3n+/ITO film was characterized by FTIR, AFM, and SEM analysis. It shows four well-defined redox couples and reversible multistate NIR electrochromism. In particular, a contrast ratio (ΔT%) up to 63% was achieved at the optic telecommunication wavelength (1550 nm).
High pressure die casting of Fe-based metallic glass
Authors: Ramasamy Parthiban , Szabo Attila , Borzel Stefan , Eckert Jürgen , Stoica Mihai , Bárdos András 
Published: October 2016

AbstractSoft ferromagnetic Fe-based bulk metallic glass key-shaped specimens with a maximum and minimum width of 25.4 and 5 mm, respectively, were successfully produced using a high pressure die casting (HPDC) method, The influence of die material, alloy temperature and flow rate on the microstructure, thermal stability and soft ferromagnetic properties has been studied. The results suggest that a steel die in which the molten metal flows at low rate and high temperature can be used to produce completely glassy samples. This can be attributed to the laminar filling of the mold and to a lower heat transfer coefficient, which avoids the skin effect in the steel mold. In addition, magnetic measurements reveal that the amorphous structure of the material is maintained throughout the key-shaped samples. Although it is difficult to control the flow and cooling rate of the molten metal in the corners of the key due to different cross sections, this can be overcome by proper tool geometry. The present results confirm that HPDC is a suitable method for the casting of Fe-based bulk glassy alloys even with complex geometries for a broad range of applications.
The wake-promoting drug modafinil stimulates specific hypothalamic circuits to promote adaptive stress responses in an animal model of PTSD
Authors: Cohen S , Ifergane G , Vainer E , Matar M A , Kaplan Z , Zohar J , Mathé A A , Cohen H 
Published: October 2016

AbstractPharmacotherapeutic intervention during traumatic memory consolidation has been suggested to alleviate or even prevent the development of posttraumatic stress disorder (PTSD). We recently reported that, in a controlled, prospective animal model, depriving rats of sleep following stress exposure prevents the development of a PTSD-like phenotype. Here, we report that administering the wake-promoting drug modafinil to rats in the aftermath of a stressogenic experience has a similar prophylactic effect, as it significantly reduces the prevalence of PTSD-like phenotype. Moreover, we show that the therapeutic value of modafinil appears to stem from its ability to stimulate a specific circuit within the hypothalamus, which ties together the neuropeptide Y, the orexin system and the HPA axis, to promote adaptive stress responses. The study not only confirms the value of sleep prevention and identifies the mechanism of action of a potential prophylactic treatment after traumatic exposure, but also contributes to understanding mechanisms underlying the shift towards adaptive behavioral response.
400–450 MHz power amplifier with high‐order harmonic suppression for multi‐protocol transceiver
Authors: Weng Zhaoyang , Jiang Hanjun , Dong Jingjing , Li Fule , Wang Zhihua 
Published: October 2016

A combinational biasing technique is presented for a 400–450 MHz power amplifier (PA). By combining two class AB amplifiers with different conduction angles and optimising the design parameters as well, the 5th and 6th harmonics are greatly suppressed in the PA's output. The designed PA is fabricated in 65 nm CMOS technology. Measurement results show that with the presented technique the 5th and 6th harmonic suppressions can be improved by 13 and 17 dB, respectively, compared with a PA with a fixed conduction angle. The presented PA technique can find its important use in multi‐protocol transceivers.
CW operation of high‐power blue laser diodes with polished facets on semi‐polar GaN substrates
Authors: Pourhashemi A. , Farrell R.M. , Cohen D.A. , Becerra D.L. , DenBaars S.P. , Nakamura S. 
Published: October 2016

Continuous wave (CW) operation of high‐power blue laser diodes (LDs) with polished facets on semi‐polar (202̅1̅) gallium nitride (GaN) substrates is demonstrated. Ridge waveguide LDs were fabricated using indium GaN waveguiding layers and GaN cladding layers. At a lasing wavelength of 452 nm, the peak two‐facet CW output power from an LD with uncoated facets was 1.71 W at a current of 3 A, corresponding to an optical power density of 32.04 MW/cm2 on each facet. The dependence of output power on current did not change with repeated CW measurements, indicating that the polished facets did not degrade under high‐power CW operation. These results show that polished facets are a viable alternative to cleaved or etched facets for high‐power CW semi‐polar LDs.
80 GBd 6‐bit DAC in InP DHBT for arbitrary waveform generator
Authors: Arayashiki Y. , Ikeda M. , Amano Y. 
Published: October 2016

A high‐speed 6‐bit resolution digital‐to‐analogue converter (DAC) for generating four‐level pulse amplitude modulation (PAM4) signals with high waveform quality is designed and fabricated using InP double‐heterojunction bipolar transistor (DHBT) technology. The DAC outputs a clean PAM4 signal at 80 GBd and a sawtooth signal at 80 GS/s.
Analysis of voltage fluctuation impact on induction motors by an innovative equivalent circuit considering the speed changes
Authors: Ghaseminezhad Morteza , Doroudi Aref , Hosseinian Seyed Hossein , Jalilian Alireza 
Published: October 2016

The most commonly used motor in industries is induction motor. This motor is exposed to various power quality disturbances. A frequent power quality disturbance which has an adverse effect on induction motor is voltage fluctuations. In this study, the behaviour of three‐phase induction motors under voltage fluctuation conditions is studied. By using the theory of dynamic phasor, an innovative equivalent circuit in which the speed fluctuations are taken into account is presented. The currents, efficiency and power factor under voltage fluctuation conditions are evaluated by the proposed equivalent circuit. The variations of these quantities due to different voltage fluctuation characteristics are also investigated. The simulation results are validated by measurements on the laboratory test setup which comprises a 1.1 kW induction motor excited by a programmable power supply unit.
Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data
Authors: Abdelmoula Walid M. , Balluff Benjamin , Englert Sonja , Dijkstra Jouke , Reinders Marcel J. T. , Walch Axel , McDonnell Liam A. , Lelieveldt Boudewijn P. F. 
Published: October 2016

Significance
Mass spectrometry imaging provides untargeted spatiomolecular information necessary to uncover molecular intratumor heterogeneity. The challenge has been to identify those tumor subpopulations that drive patient outcomes within the highly complex datasets (hyperdimensional data, intratumor heterogeneity, and patient variation). Here we report an automatic, unbiased pipeline to nonlinearly map the hyperdimensional data into a 3D space, and identify molecularly distinct, clinically relevant tumor subpopulations. We demonstrate this pipeline’s ability to uncover subpopulations statistically associated with patient survival in primary tumors of gastric cancer and with metastasis in primary tumors of breast cancer.
Notch3 drives development and progression of cholangiocarcinoma
Authors: Guest Rachel V. , Boulter Luke , Dwyer Benjamin J. , Kendall Timothy J. , Man Tak-Yung , Minnis-Lyons Sarah E. , Lu Wei-Yu , Robson Andrew J. , Gonzalez Sofia Ferreira , Raven Alexander , Wojtacha Davina , Morton Jennifer P. , Komuta Mina , Roskams Tania , Wigmore Stephen J. , Sansom Owen J. , Forbes Stuart J. 
Published: October 2016

Significance
Clinical outcomes in cholangiocarcinoma (CC) are poor; few patients are candidates for curative resection, and palliative chemotherapy produces only modest effects on survival. With an increasing incidence, new targets are urgently needed. Notch has been identified as having potential to induce CC when transgenically overexpressed, and this study aimed to characterize how endogenous Notch might drive tumorigenesis. We identify the atypical receptor Notch3 as differentially overactivated in CCs in humans, rats, and mice, with genetic deletion significantly reducing CC growth. Notch3 sustains tumor cell survival through PI3k/Akt activation via a noncanonical mechanism independent of Recombinant Signal Binding Protein for Immunoglobulin Kappa J Region (RBPJ), presenting an opportunity to target the pathway without disrupting classical Notch and bypassing toxicities associated with γ-secretase inhibitors.
Hurricane Sandy’s flood frequency increasing from year 1800 to 2100
Authors: Lin Ning , Kopp Robert E. , Horton Benjamin P. , Donnelly Jeffrey P. 
Published: October 2016

Significance
This study demonstrates quantitatively that the frequency of Hurricane Sandy-like extreme flood events has increased significantly over the past two centuries and is very likely to increase more sharply over the 21st century, due to the compound effects of sea level rise and storm climatology change.