bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel microscopy-based screening method reveals regulators of contact-dependent intercellular transfer
Authors: Frei Dominik Michael , Hodneland Erlend , Rios-Mondragon Ivan , Burtey Anne , Neumann Beate , Bulkescher Jutta , Schölermann Julia , Pepperkok Rainer , Gerdes Hans-Hermann , Kögel Tanja 
Published: August 2015

AbstractContact-dependent intercellular transfer (codeIT) of cellular constituents can have functional consequences for recipient cells, such as enhanced survival and drug resistance. Pathogenic viruses, prions and bacteria can also utilize this mechanism to spread to adjacent cells and potentially evade immune detection. However, little is known about the molecular mechanism underlying this intercellular transfer process. Here, we present a novel microscopy-based screening method to identify regulators and cargo of codeIT. Single donor cells, carrying fluorescently labelled endocytic organelles or proteins, are co-cultured with excess acceptor cells. CodeIT is quantified by confocal microscopy and image analysis in 3D, preserving spatial information. An siRNA-based screening using this method revealed the involvement of several myosins and small GTPases as codeIT regulators. Our data indicates that cellular protrusions and tubular recycling endosomes are important for codeIT. We automated image acquisition and analysis to facilitate large-scale chemical and genetic screening efforts to identify key regulators of codeIT.
R2O3 (R = La, Y) modified erbium activated germanate glasses for mid-infrared 2.7 μm laser materials
Authors: Cai Muzhi , Zhou Beier , Wang Fengchao , Wei Tao , Tian Ying , Zhou Jiajia , Xu Shiqing , Zhang Junjie 
Published: August 2015

AbstractEr3+ activated germanate glasses modified by La2O3 and Y2O3 with good thermal stability were prepared. 2.7 μm fluorescence was observed and corresponding radiative properties were investigated. A detailed discussion of J–O parameters has been carried out based on absorption spectra and Judd–Ofelt theory. The peak emission cross sections of La2O3 and Y2O3 modified germanate glass are (14.3 ± 0.10) × 10−21 cm2 and (15.4 ± 0.10) × 10−21 cm2, respectively. Non-radiative relaxation rate constants and energy transfer coefficients of 4I11/2 and 4I13/2 levels have been obtained and discussed to understand the 2.7 μm fluorescence behavior. Moreover, the energy transfer processes of 4I11/2 and 4I13/2 level were quantitatively analyzed according to Dexter’s theory and Inokuti–Hirayama model. The theoretical calculations are in good agreement with the observed 2.7 μm fluorescence phenomena. Results demonstrate that the Y2O3 modified germanate glass, which possesses more excellent spectroscopic properties than La2O3 modified germanate glass, might be an attractive candidate for mid-infrared laser.
The ubiquity and ancestry of insect doublesex
Authors: Price Dana C. , Egizi Andrea , Fonseca Dina M. 
Published: August 2015

AbstractThe doublesex (dsx) gene functions as a molecular switch at the base of the insect sex determination cascade and triggers male or female somatic sexual differentiation in Drosophila. Having been reported from only seven current insect orders, the exact phylogenetic distribution of dsx within the largest Arthropod sub-phylum, the Hexapoda, is unknown. To understand the evolution of this integral gene relative to other arthropods, we tested for the presence of dsx within public EST and genome sequencing projects representative of all 32 hexapod orders. We find the dsx gene to be ubiquitous, with putative orthologs recovered from 30 orders. Additionally, we recovered both alternatively spliced and putative paralogous dsx transcripts from several orders of hexapods, including basal lineages, indicating the likely presence of these characteristics in the hexapod common ancestor. Of note, other arthropods such as chelicerates and crustaceans express two dsx genes, both of which are shown to lack alternative splicing. Furthermore, we discovered a large degree of length heterogeneity in the common region of dsx coding sequences within and among orders, possibly resulting from lineage-specific selective pressures inherent to each taxon. Our work serves as a valuable resource for understanding the evolution of sex determination in insects.
Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes
Authors: Mehra Poonam , Pandey Bipin K. , Giri Jitender 
Published: August 2015

AbstractSoil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes.
Stearic acid induces proinflammatory cytokine production partly through activation of lactate-HIF1α pathway in chondrocytes
Authors: Miao Hongming , Chen Liang , Hao Lijun , Zhang Xuan , Chen Yujuan , Ruan Zhihua , Liang Houjie 
Published: August 2015

AbstractThe biomechanics stress and chronic inflammation in obesity are causally linked to osteoarthritis. However, the metabolic factors mediating obesity-related osteoarthritis are still obscure. Here we scanned and identified at least two elevated metabolites (stearic acid and lactate) from the plasma of diet-induced obese mice. We found that stearic acid potentiated LDH-a-dependent production of lactate, which further stabilized HIF1α protein and increased VEGF and proinflammatory cytokine expression in primary mouse chondrocytes. Treatment with LDH-a and HIF1α inhibitors notably attenuated stearic acid-or high fat diet-stimulated proinflammatory cytokine production in vitro and in vivo. Furthermore, positive correlation of plasma lactate, cartilage HIF1α and cytokine levels with the body mass index was observed in subjects with osteoarthritis. In conclusion, saturated free fatty acid induced proinflammatory cytokine production partly through activation of a novel lactate-HIF1α pathway in chondrocytes. Our findings hold promise of developing novel clinical strategies for the management of obesity-related diseases such as osteoarthritis.
High-yield isolation of extracellular vesicles using aqueous two-phase system
Authors: Shin Hyunwoo , Han Chungmin , Labuz Joseph M. , Kim Jiyoon , Kim Jongmin , Cho Siwoo , Gho Yong Song , Takayama Shuichi , Park Jaesung 
Published: August 2015

AbstractExtracellular vesicles (EVs) such as exosomes and microvesicles released from cells are potential biomarkers for blood-based diagnostic applications. To exploit EVs as diagnostic biomarkers, an effective pre-analytical process is necessary. However, recent studies performed with blood-borne EVs have been hindered by the lack of effective purification strategies. In this study, an efficient EV isolation method was developed by using polyethylene glycol/dextran aqueous two phase system (ATPS). This method provides high EV recovery efficiency (~70%) in a short time (~15 min). Consequently, it can significantly increase the diagnostic applicability of EVs.
Identification and characterization of the chromosomal yefM-yoeB toxin-antitoxin system of Streptococcus suis
Authors: Zheng Chengkun , Xu Jiali , Ren Sujing , Li Jinquan , Xia Miaomiao , Chen Huanchun , Bei Weicheng 
Published: August 2015

AbstractToxin-antitoxin (TA) systems are widely prevalent in the genomes of bacteria and archaea. These modules have been identified in Escherichia coli and various other bacteria. However, their presence in the genome of Streptococcus suis, an important zoonotic pathogen, has received little attention. In this study, we describe the identification and characterization of a type II TA system, comprising the chromosomal yefM-yoeB locus of S. suis. The yefM-yoeB locus is present in the genome of most serotypes of S. suis. Overproduction of S. suis YoeB toxin inhibited the growth of E. coli and the toxicity of S. suis YoeB could be alleviated by the antitoxin YefM from S. suis and Streptococcus pneumoniae, but not by E. coli YefM. More importantly, introduction of the S. suis yefM-yoeB system into E. coli could affect cell growth. In a murine infection model, deletion of the yefM-yoeB locus had no effect on the virulence of S. suis serotype 2. Collectively, our data suggested that the yefM-yoeB locus of S. suis is an active TA system without the involvement of virulence.
Lentiviral shRNA against KCa3.1 inhibits allergic response in allergic rhinitis and suppresses mast cell activity via PI3K/AKT signaling pathway
Authors: Lin Hai , Zheng Chunquan , Li Jing , Yang Chen , Hu Li 
Published: August 2015

AbstractCalcium-activated potassium ion channel-3.1 (KCa3.1) plays a pivotal role in the potassium-calcium exchange involved in atopy. This study aimed to explore the impact of lentiviral-mediated shRNA silencing KCa3.1 on allergic response in a murine allergic rhinitis (AR) model. The BALB/c mice were divided into four groups: untreated AR group, negative control AR group, lentiviral KCa3.1-shRNA treated AR group and normal control group. Concentrations of ovalbumin (OVA)-specific IgE, histamine and leukotrienes C4 (LTC4) in serum and IL-4, IL-9 and IL-17 in nasal lavage fluid (NLF) were analyzed. Goblet cells and mast cells were counted. KCa3.1 positive cells were counted after immunolabelling by immunofluorescence method. KCa3.1, Mucin 5AC (MUC5AC) and tryptase mRNA levels were determined using real-time polymerase chain reaction. Furthermore, P815 cell line was used to explore the role and mechanism of lentiviral KCa3.1-shRNA on mast cells. The results showed that LV-KCa3.1-shRNA intervention effectively attenuated allergic responses in LV-KCa3.1-shRNA treated mice. LV-KCa3.1-shRNA intervention effectively suppressed KCa3.1 levels and phosphorylation of AKT in P815 cells, leading to the downregulation of tryptase, IL-6 and IL-8 levels. LV-KCa3.1-shRNA intervention effectively attenuated the allergic responses in AR and suppressed mast cell activity by inhibiting PI3K/AKT signaling pathway.
Histamine deficiency exacerbates myocardial injury in acute myocardial infarction through impaired macrophage infiltration and increased cardiomyocyte apoptosis
Authors: Deng Long , Hong Tao , Lin Jinyi , Ding Suling , Huang Zheyong , Chen Jinmiao , Jia Jianguo , Zou Yunzeng , Wang Timothy C. , Yang Xiangdong , Ge Junbo 
Published: August 2015

AbstractHistamine is a biogenic amine that is widely distributed and has multiple functions, but the role it plays in acute myocardial infarction (AMI) remains unclear. In this study, we investigated the origin and contribution of endogenous histamine to AMI. Histidine decarboxylase (HDC) is the unique enzyme responsible for histamine generation. Using HDC-EGFP bacterial artificial chromosome (BAC) transgenic mice in which EGFP expression is controlled by the HDC promoter, we identified HDC expression primarily in CD11b+Gr-1+ immature myeloid cells (IMCs) that markedly increase in the early stages of AMI. Deficiency of histamine in HDC knockout mice (HDC−/−) reduced cardiac function and exacerbated the injury of infarcted heart. Furthermore, administering either an H1 receptor antagonist (pyrilamine) or an H2 receptor antagonist (cimetidine) demonstrated a protective effect of histamine against myocardial injury. The results of in vivo and in vitro assays showed that histamine deficiency promotes the apoptosis of cardiomyocytes and inhibits macrophage infiltration. In conclusion, CD11b+Gr-1+ IMCs are the predominant HDC-expressing sites in AMI and histamine plays a protective role in the process of AMI through inhibition of cardiomyocyte apoptosis and facilitation of macrophage infiltration.
Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury
Authors: Camp Sara M. , Ceco Ermelinda , Evenoski Carrie L. , Danilov Sergei M. , Zhou Tong , Chiang Eddie T. , Moreno-Vinasco Liliana , Mapes Brandon , Zhao Jieling , Gursoy Gamze , Brown Mary E. , Adyshev Djanybek M. , Siddiqui Shahid S. , Quijada Hector , Sammani Saad , Letsiou Eleftheria , Saadat Laleh , Yousef Mohammed , Wang Ting , Liang Jie , Garcia Joe G. N. 
Published: August 2015

AbstractVentilator-induced inflammatory lung injury (VILI) is mechanistically linked to increased NAMPT transcription and circulating levels of nicotinamide phosphoribosyl-transferase (NAMPT/PBEF). Although VILI severity is attenuated by reduced NAMPT/PBEF bioavailability, the precise contribution of NAMPT/PBEF and excessive mechanical stress to VILI pathobiology is unknown. We now report that NAMPT/PBEF induces lung NFκB transcriptional activities and inflammatory injury via direct ligation of Toll–like receptor 4 (TLR4). Computational analysis demonstrated that NAMPT/PBEF and MD-2, a TLR4-binding protein essential for LPS-induced TLR4 activation, share ~30% sequence identity and exhibit striking structural similarity in loop regions critical for MD-2-TLR4 binding. Unlike MD-2, whose TLR4 binding alone is insufficient to initiate TLR4 signaling, NAMPT/PBEF alone produces robust TLR4 activation, likely via a protruding region of NAMPT/PBEF (S402-N412) with structural similarity to LPS. The identification of this unique mode of TLR4 activation by NAMPT/PBEF advances the understanding of innate immunity responses as well as the untoward events associated with mechanical stress-induced lung inflammation.
Tunable terahertz fishnet metamaterials based on thin nematic liquid crystal layers for fast switching
Authors: Zografopoulos Dimitrios C. , Beccherelli Romeo 
Published: August 2015

AbstractThe electrically tunable properties of liquid-crystal fishnet metamaterials are theoretically investigated in the terahertz spectrum. A nematic liquid crystal layer is introduced between two fishnet metallic structures, forming a voltage-controlled metamaterial cavity. Tuning of the nematic molecular orientation is shown to shift the magnetic resonance frequency of the metamaterial and its overall electromagnetic response. A shift higher than 150 GHz is predicted for common dielectric and liquid crystalline materials used in terahertz technology and for low applied voltage values. Owing to the few micron-thick liquid crystal cell, the response speed of the tunable metamaterial is calculated as orders of magnitude faster than in demonstrated liquid-crystal based non-resonant terahertz components. Such tunable metamaterial elements are proposed for the advanced control of electromagnetic wave propagation in terahertz applications.
Improving the accuracy of the k-shell method by removing redundant links: From a perspective of spreading dynamics
Authors: Liu Ying , Tang Ming , Zhou Tao , Do Younghae 
Published: August 2015

AbstractRecent study shows that the accuracy of thek-shell method in determining node coreness in a spreading process is largely impacted due to the existence of core-like group, which has a largek-shell index but a low spreading efficiency. Based on the analysis of the structure of core-like groups in real-world networks, we discover that nodes in the core-like group are mutually densely connected with very few out-leaving links from the group. By defining a measure of diffusion importance for each edge based on the number of out-leaving links of its both ends, we are able to identify redundant links in the spreading process, which have a relatively low diffusion importance but lead to form the locally densely connected core-like group. After filtering out the redundant links and applying thek-shell method to the residual network, we obtain a renewed corenessksfor each node which is a more accurate index to indicate its location importance and spreading influence in the original network. Moreover, we find that the performance of the ranking algorithms based on the renewed coreness are also greatly enhanced. Our findings help to more accurately decompose the network core structure and identify influential nodes in spreading processes.
Label-Free Biosensing with High Selectivity in Complex Media using Microtoroidal Optical Resonators
Authors: Ozgur Erol , Toren Pelin , Aktas Ozan , Huseyinoglu Ersin , Bayindir Mehmet 
Published: August 2015

AbstractAlthough label-free biosensors comprised of optical microcavities inherently possess the capability of resolving molecular interactions at individual level, this extreme sensitivity restricts their convenience for large scale applications by inducing vulnerability towards non-specific interactions that readily occur within complex media. Therefore, the use of optical microresonators for biosensing is mostly limited within strictly defined laboratory conditions, instead of field applications as early detection of cancer markers in blood, or identification of contamination in food. Here, we propose a novel surface modification strategy suitable for but not limited to optical microresonator based biosensors, enabling highly selective biosensing with considerable sensitivity as well. Using a robust, silane-based surface coating which is simultaneously protein resistant and bioconjugable, we demonstrate that it becomes possible to perform biosensing within complex media, without compromising the sensitivity or reliability of the measurement. Functionalized microtoroids are successfully shown to resist nonspecific interactions, while simultaneously being used as sensitive biological sensors. This strategy could pave the way for important applications in terms of extending the use of state-of-the-art biosensors for solving problems similar to the aforementioned.
Improved human visuomotor performance and pupil constriction after choline supplementation in a placebo-controlled double-blind study
Authors: Naber Marnix , Hommel Bernhard , Colzato Lorenza S. 
Published: August 2015

AbstractOnly few nutrients are known to enhance cognition. Here we explore whether visuomotor performance can be improved through the intake of the nutrient choline, an essential chemical compound in a vertebrate’s diet. Choline is abundant in for example eggs and shrimps and many animal studies suggest that it serves as a cognitive enhancer. As choline is important for the communication between motor neurons and the control of skeletal muscles, we assumed that choline supplementation may have positive effects on action coordination in humans. A group of twenty-eight individuals ingested two grams of choline bitartrate or a placebo in two separate sessions. Seventy minutes post ingestion, participants performed a visuomotor aiming task in which they had to rapidly hit the centers of targets. Results showed that participants hit targets more centrally after choline supplementation. Pupil size (a cognition-sensitive biomarker) also significantly decreased after choline intake and correlated positively with the hit distance to the targets and the number of target misses and negatively with reaction times. These findings point to a choline-induced bias towards action precision in the trade-off between speed and accuracy. The changes in pupil size suggest that choline uptake alters cholinergic functions in the nervous system.
Derivation of a fifteen gene prognostic panel for six cancers
Authors: Khirade Mamata F. , Lal Girdhari , Bapat Sharmila A. 
Published: August 2015

AbstractThe hallmarks of cancer deem biological pathways and molecules to be conserved. This approach may be useful for deriving a prognostic gene signature. Weighted Gene Co-expression Network Analysis of gene expression datasets in eleven cancer types identified modules of highly correlated genes and interactive networks conserved across glioblastoma, breast, ovary, colon, rectal and lung cancers, from which a universal classifier for tumor stratification was extracted. Specific conserved gene modules were validated across different microarray platforms and datasets. Strikingly, preserved genes within these modules defined regulatory networks associated with immune regulation, cell differentiation, metastases, cell migration, metastases, oncogenic transformation and resistance to apoptosis and senescence, with AIF1 and PRRX1 being suggested to be master regulators governing these biological processes. A universal classifier from these conserved networks enabled execution of common set of principles across different cancers that revealed distinct, differential correlation of biological functions with patient survival in a cancer-specific manner. Correlation analysis further identified a panel of 15 risk genes with potential prognostic value, termed as the GBOCRL-IIPr panel [(GBM-Breast-Ovary-Colon-Rectal-Lung)–Immune–Invasion–Prognosis], that surprisingly, were not amongst the master regulators or important network hubs. This panel may now be integrated in predicting patient outcomes in the six cancers.
Hilbert–Huang transform‐based transient busbar protection algorithm
Authors: Guo Zhenwei , Yao Jiangang , Tan Zhewen 
Published: August 2015

A new algorithm for busbar protection is proposed based on the Hilbert–Huang transform in this study. The algorithm decomposes currents of all lines connecting to the busbar into intrinsic‐mode functions and calculates the instantaneous amplitude of the first intrinsic mode function (IMF). Then, the instantaneous amplitude is normalised to eliminate the impact of fault initial angle and transition resistance. When a fault occurs on the busbar, the initial travelling waves on head ends of the lines all have great instantaneous amplitudes; when a fault occurs on any line, the travelling wave on the faulted line is of great instantaneous amplitude, whereas the initial travelling waves on healthy lines are of small instantaneous amplitudes. Thus, through analysing the detected instantaneous amplitudes of travelling waves, a new busbar protection scheme can be constructed, which achieves a high reliability relative to other fault‐travel‐wave‐based algorithms. According to simulation results on a 500 kV substation modelled in ATP‐Draw, the graphical preprocessor to ATP‐EMTP windows version, the proposed algorithm is effective in determining various types of faults.