bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electric pulses: a flexible tool to manipulate cytosolic calcium concentrations and generate spontaneous-like calcium oscillations in mesenchymal stem cells
Authors: de Menorval Marie-Amelie , Andre Franck M. , Silve Aude , Dalmay Claire , Français Olivier , Le Pioufle Bruno , Mir Lluis M. 
Published: August 2016

AbstractHuman adipose mesenchymal stem cells (haMSCs) are multipotent adult stem cells of great interest in regenerative medicine or oncology. They present spontaneous calcium oscillations related to cell cycle progression or differentiation but the correlation between these events is still unclear. Indeed, it is difficult to mimic haMSCs spontaneous calcium oscillations with chemical means. Pulsed electric fields (PEFs) can permeabilise plasma and/or organelles membranes depending on the applied pulses and therefore generate cytosolic calcium peaks by recruiting calcium from the external medium or from internal stores. We show that it is possible to mimic haMSCs spontaneous calcium oscillations (same amplitude, duration and shape) using 100 μs PEFs or 10 ns PEFs. We propose a model that explains the experimental situations reported. PEFs can therefore be a flexible tool to manipulate cytosolic calcium concentrations. This tool, that can be switched on and off instantaneously, contrary to chemicals agents, can be very useful to investigate the role of calcium oscillations in cell physiology and/or to manipulate cell fate.
A spiral plasmonic lens with directional excitation of surface plasmons
Authors: Guo Qingrui , Zhang Chi , Hu Xinhua 
Published: August 2016

AbstractConventional plasmonic lenses are composed of curved slits carved through metallic films. Here, we propose a new plasmonic lens based on a metallic slit with an auxiliary groove. When the lens is illumined normally, only inward surface plasmon polaritons (SPPs) can be generated and then focused into a hot spot at the center of the lens. The focusing effect is theoretically investigated by varying the groove parameters and incident polarizations. It is found that this phenomenon exists for both the circular and linear polarizations of incidence. Under optimal groove parameters, the intensity of the focal spot in our lens can be 2.5 times of that in one without grooves for both linearly and circularly polarized illuminations.
Proteomic comparison reveals the contribution of chloroplast to salt tolerance of a wheat introgression line
Authors: Xu Wenjing , Lv Hongjun , Zhao Mingming , Li Yongchao , Qi Yueying , Peng Zhenying , Xia Guangmin , Wang Mengcheng 
Published: August 2016

AbstractWe previously bred a salt tolerant wheat cv. SR3 with bread wheat cv. JN177 as the parent via asymmetric somatic hybridization and found that the tolerance is partially attributed to the superior photosynthesis capacity. Here, we compared the proteomes of two cultivars to unravel the basis of superior photosynthesis capacity. In the maps of two dimensional difference gel electrophoresis (2D-DIGE), there were 26 differentially expressed proteins (DEPs), including 18 cultivar-based and 8 stress-responsive ones. 21 of 26 DEPs were identified and classified into four categories, including photosynthesis, photosynthesis system stability, linolenic acid metabolism and protein synthesis in chloroplast. The chloroplast localization of some DEPs confirmed that the identified DEPs function in the chloroplast. The overexpression of a DEP enhanced salt tolerance in Arabidopsis thaliana. In line with these data, it is concluded that the contribution of chloroplast to high salinity tolerance of wheat cv. SR3 appears to include higher photosynthesis efficiency by promoting system protection and ROS clearance, stronger production of phytohormone JA by enhancing metabolism activity and modulating the in chloroplast synthesis of proteins.
AIM 2 inflammasomes regulate neuronal morphology and influence anxiety and memory in mice
Authors: Wu Pei-Jung , Liu Hsin-Yu , Huang Tzyy-Nan , Hsueh Yi-Ping 
Published: August 2016

AbstractInflammasomes are the protein assemblies that consist of inflammasome sensors, adaptor apoptosis-associated speck-like proteins containing a CARD (ASC) and inflammasome caspase. Inflammasomes sense multiple danger signals via various inflammasome sensors and consequently use caspase to trigger proteolytic processing and secretion of IL-1β cytokines. Recent studies have suggested that neurons use their own innate immune system to detect danger signals and regulate neuronal morphology. Here, we investigate whether inflammasomes, the critical components of innate immunity, participate in regulation of neuronal morphology and function. Among various sensors, Absent in melanoma 2 (Aim2) expression in neurons is most prominent. Adding synthetic double-stranded DNA (dsDNA) to cultured neurons induces IL-1β secretion in an AIM2-dependent manner and consequently downregulates dendritic growth but enhances axon extension. The results of Aim2 knockout and knockdown show that AIM2 acts cell-autonomously to regulate neuronal morphology. Behavioral analyses further reveal that Aim2−/− mice exhibit lower locomotor activity, increased anxious behaviors and reduced auditory fear memory. In conclusion, our study suggests that AIM2 inflammasomes regulate neuronal morphology and influence mouse behaviors.
Accurate Morphology Preserving Segmentation of Overlapping Cells based on Active Contours
Authors: Molnar Csaba , Jermyn Ian H. , Kato Zoltan , Rahkama Vesa , Östling Päivi , Mikkonen Piia , Pietiäinen Vilja , Horvath Peter 
Published: August 2016

AbstractThe identification of fluorescently stained cell nuclei is the basis of cell detection, segmentation, and feature extraction in high content microscopy experiments. The nuclear morphology of single cells is also one of the essential indicators of phenotypic variation. However, the cells used in experiments can lose their contact inhibition, and can therefore pile up on top of each other, making the detection of single cells extremely challenging using current segmentation methods. The model we present here can detect cell nuclei and their morphology even in high-confluency cell cultures with many overlapping cell nuclei. We combine the “gas of near circles” active contour model, which favors circular shapes but allows slight variations around them, with a new data model. This captures a common property of many microscopic imaging techniques: the intensities from superposed nuclei are additive, so that two overlapping nuclei, for example, have a total intensity that is approximately double the intensity of a single nucleus. We demonstrate the power of our method on microscopic images of cells, comparing the results with those obtained from a widely used approach, and with manual image segmentations by experts.
Deep sexual dimorphism in adult medaka fish liver highlighted by multi-omic approach
Authors: Qiao Qin , Le Manach Séverine , Sotton Benoit , Huet Hélène , Duvernois-Berthet Evelyne , Paris Alain , Duval Charlotte , Ponger Loïc , Marie Arul , Blond Alain , Mathéron Lucrèce , Vinh Joelle , Bolbach Gérard , Djediat Chakib , Bernard Cécile , Edery Marc , Marie Benjamin 
Published: August 2016

AbstractSexual dimorphism describes the features that discriminate between the two sexes at various biological levels. Especially, during the reproductive phase, the liver is one of the most sexually dimorphic organs, because of different metabolic demands between the two sexes. The liver is a key organ that plays fundamental roles in various physiological processes, including digestion, energetic metabolism, xenobiotic detoxification, biosynthesis of serum proteins and also in endocrine or immune response. The sex-dimorphism of the liver is particularly obvious in oviparous animals, as the female liver is the main organ for the synthesis of oocyte constituents. In this work, we are interested in identifying molecular sexual dimorphism in the liver of adult medaka fish and their sex-variation in response to hepatotoxic exposures. By developing an integrative approach combining histology and different high-throughput omic investigations (metabolomics, proteomics and transcriptomics), we were able to globally depict the strong sexual dimorphism that concerns various cellular and molecular processes of hepatocytes comprising protein synthesis, amino acid, lipid and polysaccharide metabolism, along with steroidogenesis and detoxification. The results of this work imply noticeable repercussions on the biology of oviparous organisms environmentally exposed to chemical or toxin issues.
BCD to 7‐segment decoder with oxide thin film transistors
Authors: Hwang J.Y. , Kim J.K. , Moon S.J. , Hong M.T. , Yun E.J. , Bae B.S. 
Published: August 2016

Binary coded decimal (BCD) to 7‐segment decoder with oxide thin film transistors (TFTs) was implemented on a glass to display 7‐segment display from BCD. The developed BCD to the 7‐segment decoder with indium–gallium–zinc oxide thin film transistors was verified up to 1 kHz operation frequency under the power supply voltage of 5 V, and converted successfully 4‐bit binary input code to 7‐segment inputs. The binary output voltages were 0.4 V for the low and 4.1 V for the high at an operation frequency of 500 Hz, respectively. The output signals of the developed 7‐segment decoder matched well the BCD to the decimal values. The result showed that oxide TFT can be used for the integrated BCD to 7‐segment decoder for the various sensing applications, particularly for wearable devices and the integrated bio sensing platform.
Stability improvement of mode‐locked laser by passing simply EDF
Authors: Hussain S. , Won Y.‐Y. , Seo D.S. 
Published: August 2016

A 10 GHz mode‐locked fibre laser has been treated to improve its stability and the quality of generated pulses. An unpumped 3 m erbium‐doped fibre (EDF) is incorporated outside the cavity at the output of the mode‐locked laser and a setup is designed so as to form the strong standing waves inside the EDF that leads to spatial hole burning effect. This reduces the phase noise of the mode‐locked laser, resulting in the timing jitter reduction from 260 to 130 fs.
Hydrogenated amorphous silicon waveguide with vertical pin structure for infrared detection
Authors: Maegami Y. , Takei R. , Cong G. , Ohno M. , Okano M. , Horikawa T. , Yamada K. , Kamei T. 
Published: August 2016

Infrared light detection capability of a hydrogenated amorphous silicon waveguide with a vertically stacked pin structure by utilising defect absorption, i.e. transition between dangling bond defect and extended states is demonstrated. The responsivities for a 0.6 mm‐long device are ∼6.2 and ∼0.22 mA/W at 1300 and 1550 nm wavelength, respectively.
Intrinsically microwave tunable resonator designed on silicon
Authors: Allanic R. , Quéré Y. , Le Berre D. , Quendo C. 
Published: August 2016

The potential of an intrinsically microwave tunable resonator consisting in a switchable diode and a stub directly co‐designed on the same silicon substrate is presented. Thanks to this substrate, the semiconductors properties can be associated directly to the electromagnetic wave propagation. Compared with the current technology, the absence of soldered components offers a great flexibility in the design of microwave tunable devices. The active element is based on an integrated and distributed N+PP+ junction which allows the tunability of the resonator by simply applying a low bias voltage. It is demonstrated that high doping levels of the diode and resonator can lead to good performances. Two stubs, switchable from open‐ended (λ/2 at 4 and 3 GHz) to short‐ended (λ/4 at 2.1 GHz) using a low bias voltage, were designed, fabricated and characterised. A good agreement was obtained between simulations and measurements and each resonator presents insertion losses lesser than 2 dB.
Prediction of multidimensional drug dose responses based on measurements of drug pairs
Authors: Zimmer Anat , Katzir Itay , Dekel Erez , Mayo Avraham E. , Alon Uri 
Published: August 2016

Significance
We present a mechanism-free formula that predicts effects of multiple drugs at all doses based on measurements of drug pairs at a few doses. The formula bypasses the combinatorial explosion problem by greatly reducing the number of measurements needed to design optimal cocktails for cancer and infection.
Zinc-sensitive MRI contrast agent detects differential release of Zn(II) ions from the healthy vs. malignant mouse prostate
Authors: Clavijo Jordan M. Veronica , Lo Su-Tang , Chen Shiuhwei , Preihs Christian , Chirayil Sara , Zhang Shanrong , Kapur Payal , Li Wen-Hong , De Leon-Rodriguez Luis M. , Lubag Angelo J. M. , Rofsky Neil M. , Sherry A. Dean 
Published: August 2016

Significance
The normal prostate gland contains the most Zn(II) of all mammalian tissues, and there are marked differences in Zn(II) content between the healthy, malignant, and benign hyperplastic prostate. Given that multiparametric MRI does not always reliably distinguish between these tissue conditions, the release of Zn(II) ions from the prostate in response to an external stimulus may prove valuable as a specific biomarker of prostate cancer progression. In this work, we show that glucose stimulates the release of Zn(II) from intracellular stores in healthy prostate tissue and that Zn(II) secretion is reduced in a transgenic adenocarcinoma of the mouse prostate (TRAMP) model.
Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy
Authors: Zhang Xi , Zhang Mingshu , Li Dong , He Wenting , Peng Jianxin , Betzig Eric , Xu Pingyong 
Published: August 2016

Significance
To understand the cell, it is necessary to study its dynamics at high resolution in space and time in a way that does not adversely affect it. Superresolution microscopy offers the requisite spatial resolution but usually at the cost of slow imaging speed and excessive damage. In this work, a fluorescent protein is described that enables substantial improvements in the speed, duration, and noninvasiveness of live-cell superresolution microscopy.
“El valencià no se pedrà mai”: la manipulació mediàtica de les emocions col·lectives en l’anticatalanisme valencià durant la transició (1976-1982) / “El valencià no se pedrà mai”: Media manipulation of collective emotions in Valencian Anti-Catalanism during the Transition (1976-1982)
Authors: Nicolàs Miquel 
Published: August 2016

Political identities reflect social inequalities and are rewritten at every historical conjuncture with symbolic materials, arguments and states of consciousness that prevail. Languages that use a human group in this context are vehicles for such reconstruction and act simultaneously as a reflection and a mental space where tensions generated by the socio-political struggle are crystallized. In this dual role, languages are powerful catalysts for group emotions. They incorporate these emotions into to socio-communicative dynamism and express them as a complement to other systems of social semiosis. Furthermore, language is quite a malleable material that infiltrates social practices, shapes ideological enunciation and lends itself to political manipulation, triggered by the media.
However, for political manipulation to exist, certain conditions for the receptivity of such messages must also exist. The breeding ground of emotions has to be rich enough and respond to external stimuli in an intelligible way.
Under these assumptions, we consider three interdependent objectives: (a) to make a provisional balance of academic research on the so-called phenomenon of blaverisme, (b) to consider the problems in the method inherent to understanding the conflict and (c) to analyze the historical and cultural substrate of fear towards the other and fear of linguistic impersonation, emotions, in our opinion, that are the genesis of Valencian anti-Catalanism.
Growth-Increment Formation Using Otoliths and Scales for Age-0 Chinook Salmon
Authors: Walker Brian M. , Sutton Trent M. 
Published: August 2016

Abstract
Retrospective analysis is used to reconstruct fish body size at previous ages, with size and growth assumed to be accurately reflected by scale circuli and otolith increments. Using a 122-d laboratory experiment, this study validated the relationship between fish body size and growth with scale circuli and otolith daily growth increments for age-0 Chinook Salmon Oncorhynchus tshawytscha. Somatic growth was accurately reflected by growth in scale radius and growth in otolith diameter, indicating that growth in these two measures was proportional to growth in fish length. Although the width between scale circuli reflected somatic growth, daily growth was not accurately reflected by the width between corresponding otolith daily increments. Study results showed that fish deposited new otolith increments on a daily basis, but that new scale circuli were deposited at each successive increase of 5 to 6 mm in total length. These findings provide a foundation for future retrospective growth analyses involving Chinook Salmon and allow for the conversion of otolith and scale measurements into fish lengths, which are meaningful in studies of growth and survival.
Received November 5, 2015; accepted April 8, 2016 Published online August 26, 2016
Daily consumption of tea catechins improves aerobic capacity in healthy male adults: a randomized double-blind, placebo-controlled, crossover trial
Authors: Ota Noriyasu , Soga Satoko , Shimotoyodome Akira 
Published: August 2016

Abstract
Our previous studies demonstrated that dietary supplementation with tea catechins combined with exercise improved endurance capacity in mice. This study aimed to demonstrate the effect of daily tea catechin consumption on aerobic capacity in humans. Sixteen Japanese non-athlete male subjects (aged 25–47 years) took 500 mL of a test beverage with or without tea catechins (570 mg) daily for 8 weeks and attended a training program twice a week. Aerobic capacity was evaluated by indirect calorimetry and near-infrared spectroscopy during graded cycle exercise. Catechin beverage consumption was associated with a significantly higher ventilation threshold during exercise and a higher recovery rate of oxygenated hemoglobin and myoglobin levels after graded cycle exercise when compared to subjects receiving the placebo beverage. These results indicate that daily consumption of tea catechins increases aerobic capacity when combined with semiweekly light exercise, which may be due to increased skeletal muscle aerobic capacity.
Reversible changes of canavalin solubility controlled by divalent cation concentration in crude sword bean extract
Authors: Nishizawa Kaho , Arii Yasuhiro 
Published: August 2016

Abstract
Canavalin is a vicilin-class (7S) storage protein found in sword bean (Canavalia gladiata). Our previous report indicated that canavalin is precipitated by the addition of 20 mM MgCl2 to crude sword bean extract. Here, we examined the solubility changes induced by the addition of Mg2+ and Ca2+ at various concentrations. Canavalin tended to be insolubilized at relatively low concentrations of MgCl2 (&lt; 20 mM) and solubilized at relatively high concentrations (&gt; 20 mM). In addition, canavalin was slightly insolubilized in the presence of NaCl. Overall, the results revealed that solubility changes are reversible and depend on the concentration of divalent cations. Therefore, we suggested a reaction scheme that describes the effects of divalent cations on the solubility of canavalin, which would facilitate the study of its physiological function and the application of canavalin in the food processing industry.
Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition
Authors: Awazu Akinori 
Published: August 2016

Abstract

Motivation
Nucleosome positioning plays important roles in many eukaryotic intranuclear processes, such as transcriptional regulation and chromatin structure formation. The investigations of nucleosome positioning rules provide a deeper understanding of these intracellular processes.

Results
Nucleosome positioning prediction was performed using a model consisting of three types of variables characterizing a DNA sequence—the number of five-nucleotide sequences, the number of three-nucleotide combinations in one period of a helix, and mono- and di-nucleotide distributions in DNA fragments. Using recently proposed stringent benchmark datasets with low biases for Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster, the present model was shown to have a better prediction performance than the recently proposed predictors. This model was able to display the common and organism-dependent factors that affect nucleosome forming and inhibiting sequences as well. Therefore, the predictors developed here can accurately predict nucleosome positioning and help determine the key factors influencing this process.

Supplementary information
Supplementary data are available at Bioinformatics online.
Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii
Authors: R. Marcelino Vanessa , Cremen Ma Chiela M. , Jackson Chistopher J. , Larkum Anthony A. W. , Verbruggen Heroen 
Published: August 2016

Abstract
Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.