bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time visualization of clustering and intracellular transport of gold nanoparticles by correlative imaging
Authors: Liu Mengmeng , Li Qian , Liang Le , Li Jiang , Wang Kun , Li Jiajun , Lv Min , Chen Nan , Song Haiyun , Lee Joon , Shi Jiye , Wang Lihua , Lal Ratnesh , Fan Chunhai 
Published: May 2017

AbstractMechanistic understanding of the endocytosis and intracellular trafficking of nanoparticles is essential for designing smart theranostic carriers. Physico-chemical properties, including size, clustering and surface chemistry of nanoparticles regulate their cellular uptake and transport. Significantly, even single nanoparticles could cluster intracellularly, yet their clustering state and subsequent trafficking are not well understood. Here, we used DNA-decorated gold (fPlas-gold) nanoparticles as a dually emissive fluorescent and plasmonic probe to examine their clustering states and intracellular transport. Evidence from correlative fluorescence and plasmonic imaging shows that endocytosis of fPlas-gold follows multiple pathways. In the early stages of endocytosis, fPlas-gold nanoparticles appear mostly as single particles and they cluster during the vesicular transport and maturation. The speed of encapsulated fPlas-gold transport was critically dependent on the size of clusters but not on the types of organelle such as endosomes and lysosomes. Our results provide key strategies for engineering theranostic nanocarriers for efficient health management.
Biotransformation of p-xylene into terephthalic acid by engineered Escherichia coli
Authors: Luo Zi Wei , Lee Sang Yup 
Published: May 2017

AbstractTerephthalic acid (TPA) is an important industrial chemical currently produced by energy intensive and potentially hazardous p-xylene (pX) oxidation process. Here we report the development of metabolically engineered Escherichia coli system for biological transformation of pX into TPA. The engineered E. coli strain harbours a synthetic TPA pathway optimized through manipulation of expression levels of upstream and downstream modules. The upstream pathway converts pX to p-toluic acid (pTA) and the downstream pathway transforms pTA to TPA. In a two-phase partitioning fermentation, the engineered strain converts 8.8 g pX into 13.3 g TPA, which corresponds to a conversion yield of 96.7 mol%. These results suggest that the E. coli system presented here might be a promising alternative for the large-scale biotechnological production of TPA and lays the foundations for the future development of sustainable approaches for TPA production.
An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
Authors: Salamanca Viloria Juan , Allega Maria Francesca , Lambrughi Matteo , Papaleo Elena 
Published: May 2017

AbstractProteins are highly dynamic entities attaining a myriad of different conformations. Protein side chains change their states during dynamics, causing clashes that are propagated at distal sites. A convenient formalism to analyze protein dynamics is based on network theory using Protein Structure Networks (PSNs). Despite their broad applicability, few efforts have been devoted to benchmarking PSN methods and to provide the community with best practices. In many applications, it is convenient to use the centers of mass of the side chains as nodes. It becomes thus critical to evaluate the minimal distance cutoff between the centers of mass which will provide stable network properties. Moreover, when the PSN is derived from a structural ensemble collected by molecular dynamics (MD), the impact of the MD force field has to be evaluated. We selected a dataset of proteins with different fold and size and assessed the two fundamental properties of the PSN, i.e. hubs and connected components. We identified an optimal cutoff of 5 Å that is robust to changes in the force field and the proteins. Our study builds solid foundations for the harmonization and standardization of the PSN approach.
Protective effect of rosiglitazone on kidney function in high-fat challenged human-CRP transgenic mice: a possible role for adiponectin and miR-21?
Authors: Morrison Martine C. , Yakala Gopala K. , Liang Wen , Wielinga Peter Y. , Salic Kanita , van Koppen Arianne , Tomar Tushar , Kleemann Robert , Heeringa Peter , Kooistra Teake 
Published: May 2017

AbstractObesity-related albuminuria is associated with decline of kidney function and is considered a first sign of diabetic nephropathy. Suggested factors linking obesity to kidney dysfunction include low-grade inflammation, insulin resistance and adipokine dysregulation. Here, we investigated the effects of two pharmacological compounds with established anti-inflammatory properties, rosiglitazone and rosuvastatin, on kidney dysfunction during high-fat diet (HFD)-induced obesity. For this, human CRP transgenic mice were fed standard chow, a lard-based HFD, HFD+rosuvastatin or HFD+rosiglitazone for 42 weeks to study effects on insulin resistance; plasma inflammatory markers and adipokines; and renal pathology. Rosiglitazone but not rosuvastatin prevented HFD-induced albuminuria and renal fibrosis and inflammation. Also, rosiglitazone prevented HFD-induced KIM-1 expression, while levels were doubled with rosuvastatin. This was mirrored by miR-21 expression, which plays a role in fibrosis and is associated with renal dysfunction. Plasma insulin did not correlate with albuminuria. Only rosiglitazone increased circulating adiponectin concentrations. In all, HFD-induced albuminuria, and renal inflammation, injury and fibrosis is prevented by rosiglitazone but not by rosuvastatin. These beneficial effects of rosiglitazone are linked to lowered miR-21 expression but not connected with the selectively enhanced plasma adiponectin levels observed in rosiglitazone-treated animals.
Identification of New Shikonin Derivatives as Antitumor Agents Targeting STAT3 SH2 Domain
Authors: Qiu Han-Yue , Zhu Xiang , Luo Yue-Lin , Lin Hong-Yan , Tang Cheng-Yi , Qi Jin-Liang , Pang Yan-Jun , Yang Rong-Wu , Lu Gui-Hua , Wang Xiao-Ming , Yang Yong-Hua 
Published: May 2017

AbstractSignal transducer and activator of transcription 3 (STAT3) is hyper-activated in diversiform human tumors and has been validated as an attractive therapeutic target. Current research showed that a natural product, shikonin, along with its synthetic analogues, is able to inhibit the activity of STAT3 potently. The potential space of shikonin in developing novel anti-cancer agents encouraged us to carry out the investigation of the probable binding mode with STAT3. From this foundation, we have designed new types of STAT3 SH2 inhibitors. Combined simulations were performed to filter for the lead compound, which was then substituted, synthesized and evaluated by a variety of bioassays. Among the entities, PMM-172 exhibited the best anti-proliferative activity against MDA-MB-231 cells with IC50 value 1.98 ± 0.49 μM. Besides, it was identified to decrease luciferase activity, induce cell apoptosis and reduce mitochondrial transmembrane potential in MDA-MB-231 cells. Also, PMM-172 inhibited constitutive/inducible STAT3 activation without affecting STAT1 and STAT5 in MDA-MB-231 cells, and had no effect in non-tumorigenic MCF-10A cells. Moreover, PMM-172 suppressed STAT3 nuclear localization and STAT3 downstream target genes expression. Overall, these results indicate that the antitumor activity of PMM-172 is at least partially due to inhibition of STAT3 in breast cancer cells.
Quantum – coherent dynamics in photosynthetic charge separation revealed by wavelet analysis
Authors: Romero Elisabet , Prior Javier , Chin Alex W. , Morgan Sarah E. , Novoderezhkin Vladimir I. , Plenio Martin B. , van Grondelle Rienk 
Published: May 2017

AbstractExperimental/theoretical evidence for sustained vibration-assisted electronic (vibronic) coherence in the Photosystem II Reaction Center (PSII RC) indicates that photosynthetic solar-energy conversion might be optimized through the interplay of electronic and vibrational quantum dynamics. This evidence has been obtained by investigating the primary charge separation process in the PSII RC by two-dimensional electronic spectroscopy (2DES) and Redfield modeling of the experimental data. However, while conventional Fourier transform analysis of the 2DES data allows oscillatory signatures of vibronic coherence to be identified in the frequency domain in the form of static 2D frequency maps, the real-time evolution of the coherences is lost. Here we apply for the first time wavelet analysis to the PSII RC 2DES data to obtain time-resolved 2D frequency maps. These maps allow us to demonstrate that (i) coherence between the excitons initiating the two different charge separation pathways is active for more than 500 fs, and (ii) coherence between exciton and charge-transfer states, the reactant and product of the charge separation reaction, respectively; is active for at least 1 ps. These findings imply that the PSII RC employs coherence (i) to sample competing electron transfer pathways, and ii) to perform directed, ultrafast and efficient electron transfer.
Collective navigation of complex networks: Participatory greedy routing
Authors: Kleineberg Kaj-Kolja , Helbing Dirk 
Published: May 2017

AbstractMany networks are used to transfer information or goods, in other words, they are navigated. The larger the network, the more difficult it is to navigate efficiently. Indeed, information routing in the Internet faces serious scalability problems due to its rapid growth, recently accelerated by the rise of the Internet of Things. Large networks like the Internet can be navigated efficiently if nodes, or agents, actively forward information based on hidden maps underlying these systems. However, in reality most agents will deny to forward messages, which has a cost, and navigation is impossible. Can we design appropriate incentives that lead to participation and global navigability? Here, we present an evolutionary game where agents share the value generated by successful delivery of information or goods. We show that global navigability can emerge, but its complete breakdown is possible as well. Furthermore, we show that the system tends to self-organize into local clusters of agents who participate in the navigation. This organizational principle can be exploited to favor the emergence of global navigability in the system.
Pre- and post-diagnostic β-blocker use and lung cancer survival: A population-based cohort study
Authors: Weberpals Janick , Jansen Lina , Haefeli Walter E. , Hoffmeister Michael , Wolkewitz Martin , Herk-Sukel Myrthe P. P. van , Vissers Pauline A. J. , Brenner Hermann 
Published: May 2017

AbstractBeta-blockers have been associated with decreased cancer mortality. However, evidence for lung cancer is sparse and reported beneficial effects might be based on biased analyses. In this so far largest study we investigated the association between β-blocker use and lung cancer survival. Therefore, patients with a lung cancer diagnosis between April 1998 and December 2011 were selected from a database linkage of the Netherlands Cancer Registry and the PHARMO Database Network. After matching eligible patients on the propensity score, adjusted hazard ratios (HRs) and corresponding 95% confidence intervals (CI) were calculated using Cox proportional hazards regression to investigate the association between pre-diagnostic and time-dependent β-blocker use and overall survival. Duration and dose-response analyses and stratified analyses by β-blocker type, histological subgroups and stage were conducted. Of 3,340 eligible lung cancer patients, 1437 (43%) took β-blockers four months prior to diagnosis. Pre-diagnostic β-blocker use was not associated with overall survival (HR 1.00 (0.92–1.08)) in the adjusted model. Time-dependent post-diagnostic analysis showed similar results with a HR of 1.03 (0.94–1.11). Trend analyses showed no association for cumulative dose (HR 0.99 (0.97–1.02)) and cumulative duration (HR 1.00 (0.96–1.05)). In conclusion, β-blocker use is not associated with reduced mortality among lung cancer patients.
Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish
Authors: Silva Gonçalo , Cunha Regina L. , Ramos Ana , Castilho Rita 
Published: May 2017

AbstractSmall pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0–0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53–0.80] Ma) matches a severe drop of sea temperature during the Günz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.
RETRACTED ARTICLE: Protective effects of gingerol on streptozotocin-induced sporadic Alzheimer’s disease: emphasis on inhibition of β-amyloid, COX-2, alpha-, beta - secretases and APH1a
Authors: Halawany Ali M. El , Sayed Nesrine S. EL , Abdallah Hossam M. , Dine Riham Salah El 
Published: May 2017

AbstractGingerol is a major dietary compound that occurs in several plants belonging to the Zingiberaceae family. In the current study, the protective effect of gingerol on STZ-induced sporadic Alzheimer’s disease (SAD) was determined. Gingerol was isolated from the seeds of Aframomum melegueta K. Schum and tested at doses of 10 and 20 mg/kgbwt for its possible effect on the SAD model in mice, using celecoxib (30 mg/kg bwt) as a reference standard. The curative effects of gingerol were assessed through measurement of β-amyloid (Aβ-42), α-, β- secretases, APH1a and COX-2 levels. In addition, improvement in the cognitive deficit in mice after treatment was confirmed using the water maze and Y-maze with intra-maze cues. Gingerol improved the cognitive and behavioral impairment and AD-like pathology in streptozotocin model mice. These beneficial effects occurred with an increase in α-secretase activity and a decrease in cerebral Aβ-42, β- secretase, APH1a activity and COX-2-linked neuro-inflammation.
Plasmon-induced nanoscale quantised conductance filaments
Authors: Kravets Vasyl G. , Marshall Owen P. , Schedin Fred , Rodriguez Francisco J. , Zhukov Alexander A. , Gholinia Ali , Prestat Eric , Haigh Sarah J. , Grigorenko Alexander N. 
Published: May 2017

AbstractPlasmon-induced phenomena have recently attracted considerable attention. At the same time, relatively little research has been conducted on electrochemistry mediated by plasmon excitations. Here we report plasmon-induced formation of nanoscale quantized conductance filaments within metal-insulator-metal heterostructures. Plasmon-enhanced electromagnetic fields in an array of gold nanodots provide a straightforward means of forming conductive CrOx bridges across a thin native chromium oxide barrier between the nanodots and an underlying metallic Cr layer. The existence of these nanoscale conducting filaments is verified by transmission electron microscopy and contact resistance measurements. Their conductance was interrogated optically, revealing quantised relative transmission of light through the heterostructures across a wavelength range of 1–12 μm. Such plasmon-induced electrochemical processes open up new possibilities for the development of scalable devices governed by light.
Alteration of the gut microbiota in Chinese population with chronic kidney disease
Authors: Jiang Shuanghong , Xie Shan , Lv Dan , Wang Pu , He Hanchang , Zhang Ting , Zhou Youlian , Lin Qianyun , Zhou Hongwei , Jiang Jianping , Nie Jing , Hou Fanfan , Chen Ye 
Published: May 2017

AbstractWe evaluated differences in the compositions of faecal microbiota between 52 end stage renal disease (ESRD) patients and 60 healthy controls in southern China using quantitative real-time polymerase chain reaction (qPCR) and high-throughput sequencing (16S ribosomal RNA V4-6 region) methods. The absolute quantification of total bacteria was significantly reduced in ESRD patients (p < 0.01). In three enterotypes, Prevotella was enriched in the healthy group whereas Bacteroides were prevalent in the ESRD group (LDA score > 4.5). 11 bacterial taxa were significantly overrepresented in samples from ESRD and 22 bacterial taxa were overrepresented in samples from healthy controls. The butyrate producing bacteria, Roseburia, Faecalibacterium, Clostridium, Coprococcus and Prevotella were reduced in the ESRD group (LDA values > 2.0). Canonical correspondence analysis (CCA) indicated that Cystatin C (CysC), creatinine and eGFR appeared to be the most important environmental parameters to influence the overall microbial communities. In qPCR analysis, The butyrate producing species Roseburia spp., Faecalibacterium prausnitzii, Prevotella and Universal bacteria, were negatively related to CRP and CysC. Total bacteria in faeces were reduced in patients with ESRD compared to that in healthy individuals. The enterotypes change from Prevotella to Bacteroides in ESRD patients. The gut microbiota was associated with the inflammatory state and renal function of chronic kidney disease.
Down-dip variations in a subducting low-velocity zone linked to episodic tremor and slip: a new constraint from ScSp waves
Authors: Toya Mitsuhiro , Kato Aitaro , Maeda Takuto , Obara Kazushige , Takeda Tetsuya , Yamaoka Koshun 
Published: May 2017

AbstractFluids are thought to play an important role in controlling episodic tremor and slow slip (ETS) in subduction zones. Therefore, constraining the along-dip distribution of fluids is necessary to better understand source mechanism of ETS, and particularly the role played by fluids in ETS generation. Here, we report clear observations of coherent ScSp phases with a dense seismic array in western Shikoku, Japan, where ETS has been most active over the past decade. Using numerical simulations of elastic-wave propagation to reproduce the observed ScSp phases, we demonstrate that, relative to shallower depths, either the Vp/Vs ratio or the thickness of a low-velocity zone (LVZ) within the subducting oceanic crust increases with depth beneath the mantle wedge corner where ETS has been observed. Based on these depth dependences of the structural elements, a wide semi-ductile shear zone appears to be lubricated by high-pressurized fluid in the subducting oceanic crust at ETS source depths, and to be a key factor regulating ETS activity.
Electro-optic comb based real time ultra-high sensitivity phase noise measurement system for high frequency microwaves
Authors: Kuse N. , Fermann M. E. 
Published: May 2017

AbstractRecent progress in ultra low phase noise microwave generation indispensably depends on ultra low phase noise characterization systems. However, achieving high sensitivity currently relies on time consuming averaging via cross correlation, which sometimes even underestimates phase noise because of residual correlations. Moreover, extending high sensitivity phase noise measurements to microwaves beyond 10 GHz is very difficult because of the lack of suitable high frequency microwave components. In this work, we introduce a delayed self-heterodyne method in conjunction with sensitivity enhancement via the use of higher order comb modes from an electro-optic comb for ultra-high sensitivity phase noise measurements. The method obviates the need for any high frequency RF components and has a frequency measurement range limited only by the bandwidth (100 GHz) of current electro-optic modulators. The estimated noise floor is as low as −133 dBc/Hz, −155 dBc/Hz, −170 dBc/Hz and −171 dBc/Hz without cross correlation at 1 kHz, 10 kHz, 100 kHz and 1 MHz Fourier offset frequency for a 10 GHz carrier, respectively. Moreover, since no cross correlation is necessary, RF oscillator phase noise can be directly suppressed via feedback up to 100 kHz frequency offset.
Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis
Authors: Hitomi Yuki , Kojima Kaname , Kawashima Minae , Kawai Yosuke , Nishida Nao , Aiba Yoshihiro , Yasunami Michio , Nagasaki Masao , Nakamura Minoru , Tokunaga Katsushi 
Published: May 2017

AbstractNumerous genome-wide association studies (GWAS) have been performed to identify susceptibility genes to various human complex diseases. However, in many cases, neither a functional variant nor a disease susceptibility gene have been clarified. Here, we show an efficient approach for identification of a functional variant in a primary biliary cholangitis (PBC)-susceptible region, chromosome 17q12-21 (ORMDL3-GSDMB-ZPBP2-IKZF3). High-density association mapping was carried out based on SNP imputation analysis by using the whole-genome sequence data from a reference panel of 1,070 Japanese individuals (1KJPN), together with genotype data from our previous GWAS (PBC patients: n = 1,389; healthy controls: n = 1,508). Among 23 single nucleotide polymorphisms (SNPs) with P < 1.0 × 10−8, rs12946510 was identified as the functional variant that influences gene expression via alteration of Forkhead box protein O1 (FOXO1) binding affinity in vitro. Moreover, expression-quantitative trait locus (e-QTL) analyses showed that the PBC susceptibility allele of rs12946510 was significantly associated with lower endogenous expression of ORMDL3 and GSDMB in whole blood and spleen. This study not only identified the functional variant in chr.17q12-21 and its molecular mechanism through which it conferred susceptibility to PBC, but it also illustrated an efficient systematic approach for post-GWAS analysis that is applicable to other complex diseases.
Identification of MyoD-Responsive Transcripts Reveals a Novel Long Non-coding RNA (lncRNA-AK143003) that Negatively Regulates Myoblast Differentiation
Authors: Guo Yiwen , Wang Jingnan , Zhu Mingfei , Zeng Rui , Xu Zaiyan , Li Guoliang , Zuo Bo 
Published: May 2017

AbstractMyogenic differentiation factor (MyoD) is a master transcription factor in muscle development and differentiation. Although several long non-coding RNAs (lncRNAs) linked to MyoD have been found to influence muscle development, the functions of many lncRNAs have not been explored. Here we utilized lncRNA and mRNA microarray analysis to identify potential lncRNAs regulated by MyoD in muscle cells. A total of 997 differentially expressed lncRNAs (335 up-regulated and 662 down-regulated) and 1,817 differentially expressed mRNAs (148 up-regulated and 1,669 down-regulated) were identified after MyoD knockdown in C2C12 cells. Functional predictions suggested that most lncRNAs are involved in the biological pathways related to muscle differentiation and cell cycle with co-expressed genes. To gain further insight into the MyoD-mediated lncRNA expression in muscle differentiation, tissue expression profiles and MyoD overexpression were performed, and we found one of the candidate lncRNAs-AK143003 was significantly regulated by MyoD. Further analyses showed its noncoding ability and cytoplasmic localisation. Silencing of AK143003 stimulated the accumulation of myogenic marker genes, whereas AK143003 overexpression led to their decreased synthesis. This study identified a multitude of MyoD-mediated lncRNAs for further investigation and identified a novel lncRNA, lnc-AK143003, which plays a role in controlling muscle differentiation.