bluuebunny/crossref_metadata_2025 huggingface dataset:
Dependence of the SET switching variability on the initial state in HfOx‐based ReRAM
Authors: La Torre Camilla , Fleck Karsten , Starschich Sergej , Linn Eike , Waser Rainer , Menzel Stephan
Published: December 2015

For any application of redox‐based resistive switching devices understanding of variability is of major interest. In this work, we analyze the dependence of the SET switching time in pulse measurements of TiN/HfOx/Pt devices on the initial state before switching. The distribution of the measured SET times covers up to seven decades in one cell. A stochastic as well as a deterministic variability component are identified by relating the initial HRS resistance – obtained from a READ pulse and from the SET pulse for comparison – to the SET time. The different resulting correlations to the SET time for the two descriptions of the initial resistance are analyzed and linked to the polarity and voltage dependence of the HRS. In addition, the origin of the resistance variation is discussed.
Switching of Cu/MoOx/TiN CBRAM at MoOx/TiN interface
Authors: Arita Masashi , Ohno Yuuki , Takahashi Yasuo
Published: December 2015

For dynamical observation of CBRAM microstructure, in situ transmission electron microscopy (in situ TEM) was performed on Cu/MoOx/TiN during the resistive switching. It was confirmed that the local area near the MoOx/TiN interface contributes to resistive switching. The Cu deposit at the bottom of the MoOx layer swelled into the oxidized thin layer of the TiN bottom electrode, and a thin filament of 3–5 nm diameter was formed in the Set process. The reversal change was seen in the Reset process. On increasing the switching power, a microstructural change in the MoOx layer was also seen, and the CBRAM film was finally destroyed.
Recent development of atom‐pairwise van der waals corrections for density functional theory: From molecules to solids
Authors: Kim Minho , Kim Won June , Lee Eok Kyun , Lebègue Sébastien , Kim Hyungjun
Published: December 2015

Van der Waals (vdW) interactions are important in numerous physical, chemical, and biological systems. However, traditional density functional theory (DFT) within local or semi‐local approximations can hardly treat this interaction. Among various attempts to handle vdW interactions in DFT, semi‐empirical correction methods are known to present the advantages of low additional computational costs and easy implementation in conventional DFT codes. In this review, we summarize the state‐of‐the‐art semi‐empirical vdW correction methods based on pairwise summations within the atoms‐in‐molecules scaling framework, such as the Grimme's D3 methods and variants of the Tkatchenko‐Scheffler method. In addition, we compare the performance of these methods for systems ranging from molecules to solids, which have dispersive to ionic interactions: 128 molecular pairs, 23 molecular crystals, 4 noble gas crystals, 27 two‐dimensional layered materials, and 9 ionic crystals. © 2015 Wiley Periodicals, Inc.
The influence of liver‐extract on the oxygen consumption of mammalian erythrocytes: I. Properties of the constituents of the system
Authors: Overbeek G. A.
Published: December 2015

Various aspects of the reaction of Michaelis and Salomon (increased oxygen consumption of mammalian erythrocytes after the addition of liver‐extract) have been studied and compared with the methylene‐blue respiration of the erythrocytes.

The most important facts are the following:

1) Each of the individual components of the system could be made a limiting factor by increasing the concentration of the other components. In methylene‐blue respiration both components are limiting factors at all concentrations.

2) Erythrocytes of man and the rabbit reacted with liver‐extract; those of hogs sometimes did. Rat erythrocytes did not react. An interesting correlations between this reactivity and the blood catalase level was demonstrated No difference was observed in the behaviour of erythrocytes from rabbits and rats with methylene‐blue as an activator.

3) In contradiction with current literature, no abnormal reaction of erythrocytes of patients, suffering from pernicious anaemia, was found.

4) The intactness of the cell proved to be in no way necessary, though other authors suppose that it is. Haemolysed erythrocytes, freed from cell‐remnants reacted like a suspension of erythrocytes, provided the haemoglobin concentration was of the same magnitude. Methylene‐blue does not increase the oxygen consumption of haemolysed erythrocytes.

5) The active principle of the liver‐extract proved to be thermolabile and destroyable by irradiation with ultraviolet light.

6) Antianaemic liver preparations were inactive.

7) Oxygen consumption was increased in the presence of fluoride. This effect is probably caused by an inhibition of glycolysis and therefore suggests consumption of carbohydrates (Pasteur‐Meyerhof reaction).

8) Carbon dioxide was produced during the reaction. The respiratory quotient was about 0.9.
Arsenite‐induced endoplasmic reticulum‐dependent apoptosis through disturbance of calcium homeostasis in HBE cell line
Authors: Chen Chengzhi , Gu Shiyan , Jiang Xuejun , Zhang Zunzhen
Published: December 2015

Calcium (Ca2+) is a ubiquitous cell signal responsible for multiple fundamental cellular functions, including apoptosis. Whether the homeostasis of Ca2+ is involved in arsenite‐induced apoptosis remains unclear. In this study, we observed that arsenite significantly elevated the intracellular Ca2+ concentration in a dose‐ and time‐dependent manner. By using the Ca2+‐ATPase inhibitor, thapsigargin, and the inositol 1,4,5‐ trisphosphate receptors (IP3Rs) inhibitor, heparin, we further confirmed that the disturbance of endoplasmic reticulum (ER) Ca2+ homeostasis caused Ca2+ overload in the cells. Moreover, loss of ER Ca2+ homeostasis also led to ER stress, mitochondrial dysfunction, and NF‐κB activation. Importantly, pretreatment of cells with heparin remarkably attenuated the elevated cell apoptosis induced by arsenite, but inhibition of ER Ca2+ uptake with thapsigargin exacerbated arsenite‐induced cell damage significantly. Together, we demonstrated for the first time that arsenite disturbed the Ca2+ homeostasis in ER, which subsequently led to ER stress, mitochondrial dysfunction, and NF‐κB nuclear translocation, and thus consequently triggering cell apoptosis. Our findings indicate regulation of disrupted Ca2+ homeostasis in ER may be a potential strategy for prevention of arsenite toxicity. © 2015 Wiley Periodicals, Inc. Environ Toxicol 32: 197–216, 2017.
Impact of EMG Changes in Continuous Vagal Nerve Monitoring in High‐Risk Endocrine Neck Surgery
Authors: Brauckhoff Katrin , Vik Renate , Sandvik Lorentz , Heimdal John‐Helge , Aas Turid , Biermann Martin , Brauckhoff Michael
Published: December 2015

Background

Continuous vagal intraoperative neuromonitoring (CIONM) of the recurrent laryngeal nerve (RLN) may reduce the risk of RLN lesions during high‐risk endocrine neck surgery such as operation for large goiter potentially requiring transsternal surgery, advanced thyroid cancer, and recurrence.

Methods

Fifty‐five consecutive patients (41 female, median age 61 years, 87 nerves at risk) underwent high‐risk endocrine neck surgery. CIONM was performed using the commercially available NIM‐Response 3.0 nerve monitoring system with automatic periodic stimulation (APS) and matching endotracheal tube electrodes (Medtronic Inc.). All CIONM events (decreased amplitude/increased latency) were recorded.

Results

APS malfunction occurred on three sides (3 %). A total of 138 CIONM events were registered on 61 sides. Of 138, 47 (34 %) events were assessed as imminent (13 events) or potentially imminent (34 events) lesions, whereas 91 (66 %) were classified as artifacts. Loss of signal was observed in seven patients. Actions to restore the CIONM baseline were undertaken in 58/138 (42 %) events with a median 60 s required per action. Four RLN palsies (3 transient, 1 permanent) occurred: one in case of CIONM malfunction, two sudden without any significant previous CIONM event, and one without any CIONM event. The APS vagus electrode led to temporary damage to the vagus nerve in two patients.

Conclusions

CIONM may prevent RLN palsies by timely recognition of imminent nerve lesions. In high‐risk endocrine neck surgery, CIONM may, however, be limited in its utility by system malfunction, direct harm to the vagus nerve, and particularly, inability to indicate RLN lesions ahead in time.
Normal Magnetic Resonance Imaging Anatomy of the Anterolateral Knee Ligament with a T2/T1-Weighted 3-Dimensional Sequence: A Feasibility Study
Authors: Klontzas Michail E. , Maris Thomas G. , Zibis Aristeidis H. , Karantanas Apostolos H.
Published: December 2015

Purpose

The anatomy of the lateral knee compartment has been recently further explored with description of the anterolateral knee ligament (ALL). The purpose of this study was to confirm the presence of ALL on cadaveric knees and to describe its normal anatomy in young healthy volunteers, utilizing a high-resolution 3-dimensional (3D) pulse sequence.

Methods

Dissection was performed on 9 cadaveric knees in order to confirm the presence of ALL. Conventional 2-dimensional sequences of 10 knees at 1.5 T and 10 knees at 3 T, with a slice thickness of 2-4 mm, were reviewed for the presence of ALL. A 3D T2/T1-weighted gradient echo sequence (constructive interference in steady state [CISS]), yielding in-plane resolution of 0.4 mm × 0.4 mm × 0.4 mm, was applied in 14 healthy volunteers (26 knees). All 3D images were manipulated using multiplanar reconstruction (MPR) and the presence and width of ALL were recorded.

Results

Cadaveric dissection disclosed the presence of ALL in 8 of 9 knees. Conventional knee MR imaging depicted ALL only on coronal images (18 of 20) whereas the CISS revealed ALL on 24 of 26 studied knees (92.3%). ALL has a mean thickness of 1.1 ± 0.27 mm measured on coronal MR images.

Conclusions

ALL can be thoroughly assessed in young healthy individuals with the use of high-resolution 3D MR imaging with MPR at 1.5 T.
Mindfulness and the Transfer of Training
Authors: Saks Alan M. , Gruman Jamie A.
Published: December 2015

Hyland, Lee, and Mills (2015) make a strong case for research and practice on mindfulness within the industrial–organizational community. Their main argument is that mindfulness has the potential to provide physical, psychological, and performance benefits to employees and organizations. However, to realize these benefits, organizations must first provide mindfulness training programs to their employees. Along these lines they note that some organizations have established mindfulness training programs to enhance employee well-being, and some firms specialize in providing workplace mindfulness training.
Which Mindfulness Measures To Choose To Use?
Authors: Qu Yuanmei (Elly) , Dasborough Marie T. , Todorova Gergana
Published: December 2015

Hyland, Lee, and Mills (2015) specified the two most popular scales for mindfulness: the Freiburg Mindfulness Inventory (FMI; 30 items, Buchheld, Grossman, & Walach, 2001; 14 items, Walach, Buchheld, Buttenmüller, Kleinknecht, & Schmidt, 2006) and the Mindfulness Attention and Awareness Scale (MAAS; Brown & Ryan, 2003). However, the popularity of these measures does not necessarily mean that they are of high quality. Especially considering the complex epistemology and ontology of the mindfulness construct, we should apply mindfulness assessments with caution. More specially, according to item development theorists in the industrial and organizational (I-O) area (see Hinkin, 1998; Hinkin & Tracey, 1999; Kerlinger & Lee, 2000; Schriesheim, Powers, Scandura, Gardiner, & Lankau, 1993), scholars must select measures that have (a) a clear operational definition; (b) alignment between definition and measure (content validity); (c) high reliability and (d) high construct validity; and (e) high criterion-related validity. However, it is not clear which of the available mindfulness assessments satisfies these criteria and to what extent. In this commentary, we assess currently used measures based on these criteria and provide directions for future research.
I-Os in the Vanguard of Big Data Analytics and Privacy
Authors: Ducey Adam J. , Guenole Nigel , Weiner Sara P. , Herleman Hailey A. , Gibby Robert E. , Delany Tanya
Published: December 2015

In this response to Guzzo, Fink, King, Tonidandel, and Landis (2015), we suggest industrial–organizational (I-O) psychologists join business analysts, data scientists, statisticians, mathematicians, and economists in creating the vanguard of expertise as we acclimate to the reality of analytics in the world of big data. We enthusiastically accept their invitation to share our perspective that extends the discussion in three key areas of the focal article—that is, big data sources, logistic and analytic challenges, and data privacy and informed consent on a global scale. In the subsequent sections, we share our thoughts on these critical elements for advancing I-O psychology's role in leveraging and adding value from big data.
Minding the Mechanisms: A Discussion of How Mindfulness Leads to Positive Outcomes at Work
Authors: Miksch Dexter , Lindeman Meghan I. H. , Varghese Lebena
Published: December 2015

Hyland, Lee, and Mills (2015) asserted that the many benefits of mindfulness practices have been underutilized and understudied at work. We agree with the focal article's stance that more research is needed on mindfulness at work. We extend this argument to include a request that future research pays attention to the mechanisms responsible for the effects of mindfulness at work. In this commentary, we (a) briefly discuss the practical importance of understanding the mechanisms by which mindfulness practices lead to positive outcomes, (b) outline the mediating mechanisms proposed by the leading theoretical model of mindfulness effects and how those mediators apply to work, and (c) argue that more rigorous, empirical research is needed to understand the mechanisms through which mindfulness practices lead to positive work outcomes.
Mind the Gap: The Link Between Mindfulness and Performance at Work Needs More Attention
Authors: Choi Ellen , Tobias Jutta
Published: December 2015

The concept of mindfulness has become the topic of heated debates among scholars and practitioners alike. Hyland, Lee, and Mills's (2015) focal article has an ambitious goal: distilling how mindfulness fits into workplace research and practice. This is laudable, and we are pleased that the authors are providing a review of the many ways in which mindfulness may benefit employees and organizations. Unfortunately, the authors fall short of their aspiration to produce a comprehensive overview of the link between workplace mindfulness and performance. We outline three points that we find may have helped the authors achieve their main objective.
How Does Employee Mindfulness Reduce Psychological Distress?
Authors: Eatough Erin M.
Published: December 2015

As pointed out by Hyland, Lee, and Mills (2015), the most prominent effect of mindfulness is a significant decrease in experienced stress levels, and one of the most popular mindfulness interventions is mindfulness-based stress reduction. When it comes to psychological stress, desirable outcomes are both expected and documented for employees who adopt a mindful approach to work. But how are these beneficial effects happening, exactly?
Heat-flux enhancement by vapour-bubble nucleation in Rayleigh–Bénard turbulence
Authors: Narezo Guzman Daniela , Xie Yanbo , Chen Songyue , Fernandez Rivas David , Sun Chao , Lohse Detlef , Ahlers Guenter
Published: December 2015

We report on the enhancement of turbulent convective heat transport due to vapour-bubble nucleation at the bottom plate of a cylindrical Rayleigh–Bénard sample (aspect ratio 1.00, diameter 8.8 cm) filled with liquid. Microcavities acted as nucleation sites, allowing for well-controlled bubble nucleation. Only the central part of the bottom plate with a triangular array of microcavities (etched over an area with diameter of 2.5 cm) was heated. We studied the influence of the cavity density and of the superheat $T_{b}-T_{on}$ ($T_{b}$ is the bottom-plate temperature and $T_{on}$ is the value of $T_{b}$ below which no nucleation occurred). The effective thermal conductivity, as expressed by the Nusselt number $\mathit{Nu}$, was measured as a function of the superheat by varying $T_{b}$ and keeping a fixed difference $T_{b}-T_{t}\simeq 16$  K ($T_{t}$ is the top-plate temperature). Initially $T_{b}$ was much larger than $T_{on}$ (large superheat), and the cavities vigorously nucleated vapour bubbles, resulting in two-phase flow. Reducing $T_{b}$ in steps until it was below $T_{on}$ resulted in cavity deactivation, i.e. in one-phase flow. Once all cavities were inactive, $T_{b}$ was increased again, but they did not reactivate. This led to one-phase flow for positive superheat. The heat transport of both one- and two-phase flow under nominally the same thermal forcing and degree of superheat was measured. The Nusselt number of the two-phase flow was enhanced relative to the one-phase system by an amount that increased with increasing $T_{b}$. Varying the cavity density (69, 32, 3.2, 1.2 and $0.3~\text{mm}^{-2}$) had only a small effect on the global $\mathit{Nu}$ enhancement; it was found that $\mathit{Nu}$ per active site decreased as the cavity density increased. The heat-flux enhancement of an isolated nucleating site was found to be limited by the rate at which the cavity could generate bubbles. Local bulk temperatures of one- and two-phase flows were measured at two positions along the vertical centreline. Bubbles increased the liquid temperature (compared to one-phase flow) as they rose. The increase was correlated with the heat-flux enhancement. The temperature fluctuations, as well as local thermal gradients, were reduced (relative to one-phase flow) by the vapour bubbles. Blocking the large-scale circulation around the nucleating area, as well as increasing the effective buoyancy of the two-phase flow by thermally isolating the liquid column above the heated area, increased the heat-flux enhancement.
German Jews in Paris: Traversing Modernity
Authors: Roemer Nils
Published: December 2015

The article traces Central European Jewish visitors of Paris during the Weimar Republic and the 1930s and analyzes the shifting meaning of travel, exile, and the figure of the flaneur. Their travelogues articulated their affection for Paris in the aftermath of World War I and the Treaty of Versailles, marking them as border crossers in multiple ways. Writing about modern capitals such as Paris became a way to temporarily belong to them, to reimagine modernity.
Supercongruences for sporadic sequences
Authors: Osburn Robert , Sahu Brundaban , Straub Armin
Published: December 2015

We prove two-term supercongruences for generalizations of recently discovered sporadic sequences of Cooper. We also discuss recent progress and future directions concerning other types of supercongruences.
Ups and downs of central bank independence from the Great Inflation to the Great Recession: theory, institutions and empirics
Authors: Masciandaro Donato , Romelli Davide
Published: December 2015

This article analyses the pillar of modern central bank governance, i.e. central bank independence, from three perspectives. First, we provide a systematic review of the economics of central bank independence. Second, applying a principal agent model we design a political economy framework, which explains how politicians can shape central bank governance in addressing macroeconomic shocks, while taking into account both the wishes of the citizens and their own personal interests. This framework is then used to interpret the evolution of central bank independence from the Great Inflation (1970s), throughout the Great Moderation (1980s-2000s) and to the Great Recession (2007-14). We provide empirical evidence supporting this evolution using recently developed indices of dynamic central bank independence. Further, our findings stress the importance of macroeconomic shocks in shaping the evolution of central bank independence after the global financial crisis.
Estimation of genetic and phenotypic parameters of some important economic traits in Khazak native hen in Iran
Authors: Ebrahimzadeh-Allahabad Ahmad , Mahmodian Zhila , Pezeshkian Zahra , Mollaei A.
Published: December 2015

The purpose of this study was the estimation of genetic and phenotypic parameters of important economic traits in Khazak native hens in Iran. The registered records of 7 434 Khazak native chickens containing 5 238 hens and 2 196 cocks in the research centre of Zabol University from 2007 to 2011 were used. The results of this study were compared with the results of studies on other native chickens breeding in Iran (Yazd: 4198, Mazandaran: 49 536, Esfahan: 23 108, West Azarbaijan: 24 890 and Fars: 30 279). Genotypic and phenotypic correlations between traits and heritability of traits were evaluated by univariate and bivariate animal models using ASREML software. The quantity of some traits such as the average egg production, weight of eggs produced, fertility, hatchability, age of sexual maturity and broodiness were a month 120, 45.15 g, 65.25 percent, 74.83 percent, 5.54 and 1.90, respectively. The heritability of sexual maturity age, the number of eggs produced and egg weight were 0.22 ± 0.41, 0.16 ± 0.13 and 0.50, respectively. The genetic correlation between the age of sexual maturity and the number of eggs produced were 0.95 ± 0.02 and 0.29 ± 0.07, respectively. The results of the study showed that decreasing the sexual age of maturity will lead to an increase in the number of eggs produced. The results of variance analysis showed that some factors such as hen age, broodiness (P< 0.01) and the weight of hens have a significant effect on hatchability.
A generic strategy for CRISPR-Cas9-mediated gene tagging
Authors: Lackner Daniel H. , Carré Alexia , Guzzardo Paloma M. , Banning Carina , Mangena Ramu , Henley Tom , Oberndorfer Sarah , Gapp Bianca V. , Nijman Sebastian M.B. , Brummelkamp Thijn R. , Bürckstümmer Tilmann
Published: December 2015

Genome engineering has been greatly enhanced by the availability of Cas9 endonuclease that can be targeted to almost any genomic locus using so called guide RNAs (gRNAs). However, the introduction of foreign DNA sequences to tag an endogenous gene is still cumbersome as it requires the synthesis or cloning of homology templates. Here we present a strategy that enables the tagging of endogenous loci using one generic donor plasmid. It contains the tag of interest flanked by two gRNA recognition sites that allow excision of the tag from the plasmid. Co-transfection of cells with Cas9, a gRNA specifying the genomic locus of interest, the donor plasmid and a cassette-specific gRNA triggers the insertion of the tag by a homology-independent mechanism. The strategy is efficient and delivers clones that display a predictable integration pattern. As showcases we generated NanoLuc luciferase- and TurboGFP-tagged reporter cell lines.
Exploring the variation in implementation of a COPD disease management programme and its impact on health outcomes: a post hoc analysis of the RECODE cluster randomised trial
Authors: Boland Melinde R S , Kruis Annemarije L , Huygens Simone A , Tsiachristas Apostolos , Assendelft Willem J J , Gussekloo Jacobijn , Blom Coert M G , Chavannes Niels H , Rutten-van Mölken Maureen P M H
Published: December 2015

This study aims to (1) examine the variation in implementation of a 2-year chronic obstructive pulmonary disease (COPD) management programme called RECODE, (2) analyse the facilitators and barriers to implementation and (3) investigate the influence of this variation on health outcomes. Implementation variation among the 20 primary-care teams was measured directly using a self-developed scale and indirectly through the level of care integration as measured with the Patient Assessment of Chronic Illness Care (PACIC) and the Assessment of Chronic Illness Care (ACIC). Interviews were held to obtain detailed information regarding the facilitators and barriers to implementation. Multilevel models were used to investigate the association between variation in implementation and change in outcomes. The teams implemented, on average, eight of the 19 interventions, and the specific package of interventions varied widely. Important barriers and facilitators of implementation were (in)sufficient motivation of healthcare provider and patient, the high starting level of COPD care, the small size of the COPD population per team, the mild COPD population, practicalities of the information and communication technology (ICT) system, and hurdles in reimbursement. Level of implementation as measured with our own scale and the ACIC was not associated with health outcomes. A higher level of implementation measured with the PACIC was positively associated with improved self-management capabilities, but this association was not found for other outcomes. There was a wide variety in the implementation of RECODE, associated with barriers at individual, social, organisational and societal level. There was little association between extent of implementation and health outcomes.
HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene
Authors: Pandit Aridaman , de Boer Rob J.
Published: December 2015

Highly active antiretroviral therapy (ART) has successfully turned Human immunodeficiency virus type 1 (HIV-1) from a deadly pathogen into a manageable chronic infection. ART is a lifelong therapy which is both expensive and toxic and HIV can become resistant to it. An alternative to lifelong ART is gene therapy that targets the CCR5 co-receptor and creates a population of genetically modified host cells that are less susceptible to viral infection. With generic mathematical models we show that gene therapy that only targets the CCR5 co-receptor fails to suppress HIV-1 (which is in agreement with current data). We predict that the same gene therapy can be markedly improved if it is combined with a suicide gene that is only expressed upon HIV-1 infection.
GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1
Authors: Miglietta Giulia , Cogoi Susanna , Pedersen Erik B. , Xodo Luigi E.
Published: December 2015

HRAS is regulated by two neighbouring quadruplex-forming GC-elements (hras-1 and hras-2), located upstream of the major transcription start sites (doi: 10.1093/nar/gku 5784). In this study we demonstrate that the C-rich strands of hras-1 and hras-2 fold into i-motif conformations (iMs) characterized under crowding conditions (PEG-300, 40% w/v) by semi-transitions at pH 6.3 and 6.7, respectively. Nondenaturing PAGE shows that the HRAS C-rich sequences migrate at both pH 5 and 7 as folded intramolecular structures. Chromatin immunoprecipitation shows that hnRNP A1 is associated under in vivo conditions to the GC-elements, while EMSA proves that hnRNP A1 binds tightly to the iMs. FRET and CD show that hnRNP A1 unfolds the iM structures upon binding. Furthermore, when hnRNP A1 is knocked out in T24 bladder cancer cells by a specific shRNA, the HRAS transcript level drops to 44 ± 5% of the control, suggesting that hnRNP A1 is necessary for gene activation. The sequestration by decoy oligonucleotides of the proteins (hnRNP A1 and others) binding to the HRAS iMs causes a significant inhibition of HRAS transcription. All these outcomes suggest that HRAS is regulated by a G-quadruplex/i-motif switch interacting with proteins that recognize non B-DNA conformations.
Effect of edge pruning on structural controllability and observability of complex networks
Authors: Mengiste Simachew Abebe , Aertsen Ad , Kumar Arvind
Published: December 2015

Controllability and observability of complex systems are vital concepts in many fields of science. The network structure of the system plays a crucial role in determining its controllability and observability. Because most naturally occurring complex systems show dynamic changes in their network connectivity, it is important to understand how perturbations in the connectivity affect the controllability of the system. To this end, we studied the control structure of different types of artificial, social and biological neuronal networks (BNN) as their connections were progressively pruned using four different pruning strategies. We show that the BNNs are more similar to scale-free networks than to small-world networks, when comparing the robustness of their control structure to structural perturbations. We introduce a new graph descriptor, ‘the cardinality curve’, to quantify the robustness of the control structure of a network to progressive edge pruning. Knowing the susceptibility of control structures to different pruning methods could help design strategies to destroy the control structures of dangerous networks such as epidemic networks. On the other hand, it could help make useful networks more resistant to edge attacks.
The N-terminal domain of the thermo-regulated surface protein PrpA of Enterococcus faecium binds to fibrinogen, fibronectin and platelets
Authors: Guzmán Prieto Ana M. , Urbanus Rolf T. , Zhang Xinglin , Bierschenk Damien , Koekman C. Arnold , van Luit-Asbroek Miranda , Ouwerkerk Janneke P. , Pape Marieke , Paganelli Fernanda L. , Wobser Dominique , Huebner Johannes , Hendrickx Antoni P. A. , Bonten Marc J. M. , Willems Rob J. L. , van Schaik Willem
Published: December 2015

Enterococcus faecium is a commensal of the mammalian gastrointestinal tract, but is also found in non-enteric environments where it can grow between 10 °C and 45 °C. E. faecium has recently emerged as a multi-drug resistant nosocomial pathogen. We hypothesized that genes involved in the colonization and infection of mammals exhibit temperature-regulated expression control and we therefore performed a transcriptome analysis of the clinical isolate E. faecium E1162, during mid-exponential growth at 25 °C and 37 °C. One of the genes that exhibited differential expression between 25 °C and 37 °C, was predicted to encode a peptidoglycan-anchored surface protein. The N-terminal domain of this protein is unique to E. faecium and closely related enterococci, while the C-terminal domain is homologous to the Streptococcus agalactiae surface protein BibA. This region of the protein contains proline-rich repeats, leading us to name the protein PrpA for proline-rich protein A. We found that PrpA is a surface-exposed protein which is most abundant during exponential growth at 37 °C in E. faecium E1162. The heterologously expressed and purified N-terminal domain of PrpA was able to bind to the extracellular matrix proteins fibrinogen and fibronectin. In addition, the N-terminal domain of PrpA interacted with both non-activated and activated platelets.
Diiron centre mutations in Ciona intestinalis alternative oxidase abolish enzymatic activity and prevent rescue of cytochrome oxidase deficiency in flies
Authors: Andjelković Ana , Oliveira Marcos T. , Cannino Giuseppe , Yalgin Cagri , Dhandapani Praveen K. , Dufour Eric , Rustin Pierre , Szibor Marten , Jacobs Howard T.
Published: December 2015

The mitochondrial alternative oxidase, AOX, carries out the non proton-motive re-oxidation of ubiquinol by oxygen in lower eukaryotes, plants and some animals. Here we created a modified version of AOX from Ciona instestinalis, carrying mutations at conserved residues predicted to be required for chelation of the diiron prosthetic group. The modified protein was stably expressed in mammalian cells or flies, but lacked enzymatic activity and was unable to rescue the phenotypes of flies knocked down for a subunit of cytochrome oxidase. The mutated AOX transgene is thus a potentially useful tool in studies of the physiological effects of AOX expression.
Metabolomic analysis with GC-MS to reveal potential metabolites and biological pathways involved in Pb & Cd stress response of radish roots
Authors: Wang Yan , Xu Liang , Shen Hong , Wang Juanjuan , Liu Wei , Zhu Xianwen , Wang Ronghua , Sun Xiaochuan , Liu Liwang
Published: December 2015

The radish (Raphanus sativus L.) is an important root vegetable crop. In this study, the metabolite profiling analysis of radish roots exposed to lead (Pb) and cadmium (Cd) stresses has been performed using gas chromatography-mass spectrometry (GC-MS). The score plots of principal component analysis (PCA) and partial least squares-discriminate analysis (PLS-DA) showed clear discrimination between control and Pb- or Cd-treated samples. The metabolic profiling indicated Pb or Cd stress could cause large metabolite alteration mainly on sugars, amino acids and organic acids. Furthermore, an integrated analysis of the effects of Pb or Cd stress was performed on the levels of metabolites and gene transcripts from our previous transcriptome work in radish roots. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of integration data demonstrated that exposure of radish to Pb stress resulted in profound biochemical changes including carbohydrate metabolism, energy metabolism and glutathione metabolism, while the treatment of Cd stress caused significant variations in energy production, amino acid metabolism and oxidative phosphorylation-related pathways. These results would facilitate further dissection of the mechanisms of heavy metal (HM) accumulation/tolerance in plants and the effective management of HM contamination in vegetable crops by genetic manipulation.
Development of a real-time flexible multiphoton microendoscope for label-free imaging in a live animal
Authors: Ducourthial Guillaume , Leclerc Pierre , Mansuryan Tigran , Fabert Marc , Brevier Julien , Habert Rémi , Braud Flavie , Batrin Renaud , Vever-Bizet Christine , Bourg-Heckly Geneviève , Thiberville Luc , Druilhe Anne , Kudlinski Alexandre , Louradour Frédéric
Published: December 2015

We present a two-photon microendoscope capable of in vivo label-free deep-tissue high-resolution fast imaging through a very long optical fiber. First, an advanced light-pulse spectro-temporal shaping device optimally precompensates for linear and nonlinear distortions occurring during propagation within the endoscopic fiber. This enables the delivery of sub-40-fs duration infrared excitation pulses at the output of 5 meters of fiber. Second, the endoscopic fiber is a custom-made double-clad polarization-maintaining photonic crystal fiber specifically designed to optimize the imaging resolution and the intrinsic luminescence backward collection. Third, a miniaturized fiber-scanner of 2.2 mm outer diameter allows simultaneous second harmonic generation (SHG) and two-photon excited autofluorescence (TPEF) imaging at 8 frames per second. This microendoscope’s transverse and axial resolutions amount respectively to 0.8 μm and 12 μm, with a field-of-view as large as 450 μm. This microendoscope’s unprecedented capabilities are validated during label-free imaging, ex vivo on various fixed human tissue samples and in vivo on an anesthetized mouse kidney demonstrating an imaging penetration depth greater than 300 μm below the surface of the organ. The results reported in this manuscript confirm that nonlinear microendoscopy can become a valuable clinical tool for real-time in situ assessment of pathological states.
TALEN-mediated homologous recombination in Daphnia magna
Authors: Nakanishi Takashi , Kato Yasuhiko , Matsuura Tomoaki , Watanabe Hajime
Published: December 2015

Transcription Activator-Like Effector Nucleases (TALENs) offer versatile tools to engineer endogenous genomic loci in various organisms. We established a homologous recombination (HR)-based knock-in using TALEN in the crustacean Daphnia magna, a model for ecological and toxicological genomics. We constructed TALENs and designed the 67 bp donor insert targeting a point deletion in the eyeless mutant that shows eye deformities. Co-injection of the TALEN mRNA with donor DNA into eggs led to the precise integration of the donor insert in the germ line, which recovered eye deformities in offspring. The frequency of HR events in the germ line was 2% by using both plasmid and single strand oligo DNA with 1.5 kb and 80 nt homology to the target. Deficiency of ligase 4 involved in non-homologous end joining repair did not increase the HR efficiency. Our data represent efficient HR-based knock-in by TALENs in D. magna, which is a promising tool to understand Daphnia gene functions.
The effect of androgens on ovarian follicle maturation: Dihydrotestosterone suppress FSH-stimulated granulosa cell proliferation by upregulating PPARγ-dependent PTEN expression.
Authors: Chen Mei-Jou , Chou Chia-Hung , Chen Shee-Uan , Yang Wei-Shiung , Yang Yu-Shih , Ho Hong-Nerng
Published: December 2015

Intraovarian hyperandrogenism is one of the determining factors of follicular arrest in women with polycystic ovary syndrome (PCOS). Using androgenized rat models, we investigated the effects of androgens on metabolism, as well as on factors involved in follicular arrest and the reduced number of estrus cycles. The dihydrotestosterone (DHT)-treated rats had fewer estrus cycles, higher numbers of large arrested follicles and an increased in body weight gain compared with the dehydroepiandrostenedione (DHEA)- and placebo-treated rats. In cultured rat granulosa cells, DHT suppressed follicle stimulating hormone (FSH)-induced granulosa cell proliferation and increased the accumulation of cells in the G2/M phase. DHT decreased phosphorylated Akt (p-Akt) and cyclin D1 levels through increasing PTEN. DHT-promoted PTEN expression was regulated by peroxisome proliferator-activated receptor gamma (PPARγ) in granulosa cells. Meanwhile, in the large follicles of the DHT-treated rats, the expressions of PPARγ and PTEN were higher, but the expression of p-Akt and proliferating cell nuclear antigen (PCNA) were lower. Conclusively, DHT and DHEA produced differential effects on metabolism in prepubertal female rats like clinical manifestations of women with PCOS. DHT treatment may affect ovarian follicular maturation by altering granulosa cell proliferation through the regulation of enhancing PPARγ dependent PTEN/p-Akt expression in the granulosa cells.
Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals
Authors: Liu Chuang , Xie Liping , Zhang Rongqing
Published: December 2015

Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites.
Synthesis of heavy hydrocarbons at the core-mantle boundary
Authors: Belonoshko Anatoly B. , Lukinov Timofiy , Rosengren Anders , Bryk Taras , Litasov Konstantin D.
Published: December 2015

The synthesis of complex organic molecules with C-C bonds is possible under conditions of reduced activity of oxygen. We have found performing ab initio molecular dynamics simulations of the C-O-H-Fe system that such conditions exist at the core-mantle boundary (CMB). H2O and CO2 delivered to the CMB by subducting slabs provide a source for hydrogen and carbon. The mixture of H2O and CO2 subjected to high pressure (130 GPa) and temperature (4000 to 4500 K) does not lead to synthesis of complex hydrocarbons. However, when Fe is added to the system, C-C bonds emerge. It means that oil might be a more abundant mineral than previously thought.
Fully epitaxial C1b-type NiMnSb half-Heusler alloy films for current-perpendicular-to-plane giant magnetoresistance devices with a Ag spacer
Authors: Wen Zhenchao , Kubota Takahide , Yamamoto Tatsuya , Takanashi Koki
Published: December 2015

Remarkable magnetic and spin-dependent transport properties arise from well-designed spintronic materials and heterostructures. Half-metallic Heusler alloys with high spin polarization exhibit properties that are particularly advantageous for the development of high-performance spintronic devices. Here, we report fully (001)-epitaxial growth of a high-quality half-metallic NiMnSb half-Heusler alloy films and their application to current-perpendicular-to-plane giant magnetoresistance (CPP-GMR) devices with Ag spacer layers. Fully (001)-oriented NiMnSb epitaxial films with very flat surface and high magnetization were prepared on Cr/Ag-buffered MgO(001) single crystalline substrates by changing the substrate temperature. Epitaxial CPP-GMR devices using the NiMnSb films and a Ag spacer were fabricated and room-temperature (RT) CPP-GMR ratios for the C1b-type half-Heusler alloy were determined for the first time. A CPP-GMR ratio of 8% (21%) at RT (4.2 K) was achieved in the fully epitaxial NiMnSb/Ag/NiMnSb structures. Furthermore, negative anisotropic magnetoresistance (AMR) ratio and small discrepancy of the AMR amplitudes between RT and 10 K were observed in a single epitaxial NiMnSb film, indicating robust bulk half metallicity against thermal fluctuation in the half-Heusler compound. The modest CPP-GMR ratios could be attributed to interface effects between NiMnSb and Ag. This work provides a pathway for engineering a new class of ordered alloy materials with particular emphasis on spintronics.
IL-8 as mediator in the microenvironment-leukaemia network in acute myeloid leukaemia
Authors: Kuett Alexander , Rieger Christina , Perathoner Deborah , Herold Tobias , Wagner Michaela , Sironi Silvia , Sotlar Karl , Horny Hans-Peter , Deniffel Christian , Drolle Heidrun , Fiegl Michael
Published: December 2015

The bone marrow microenvironment is physiologically hypoxic with areas being as low as 1% O2, e.g. the stem cell niche. Acute myeloid leukaemia (AML) blasts misuse these bone marrow niches for protection by the local microenvironment, but also might create their own microenvironment. Here we identify IL-8 as a hypoxia-regulated cytokine in both AML cell lines and primary AML samples that is induced within 48 hours of severe hypoxia (1% O2). IL-8 lacked effects on AML cells but induced migration in mesenchymal stromal cells (MSC), an integral part of the bone marrow. Accordingly, MSC were significantly increased in AML bone marrow as compared to healthy bone marrow. Interestingly, mononuclear cells obtained from healthy bone marrow displayed both significantly lower endogenous and hypoxia-induced production of IL-8. IL-8 mRNA expression in AML blasts from 533 patients differed between genetic subgroups with significantly lower expression of IL-8 in acute promyelocytic leukaemia (APL), while in non APL-AML patients with FLT ITD had the highest IL-8 expression. In this subgroup, high IL-8 expression was also prognostically unfavourable. In conclusion, hypoxia as encountered in the bone marrow specifically increases IL-8 expression of AML, which in turn impacts niche formation. High IL-8 expression might be correlated with poor prognosis in certain AML subsets.
DockTope: a Web-based tool for automated pMHC-I modelling
Authors: Menegatti Rigo Maurício , Amaral Antunes Dinler , Vaz de Freitas Martiela , Fabiano de Almeida Mendes Marcus , Meira Lindolfo , Sinigaglia Marialva , Fioravanti Vieira Gustavo
Published: December 2015

The immune system is constantly challenged, being required to protect the organism against a wide variety of infectious pathogens and, at the same time, to avoid autoimmune disorders. One of the most important molecules involved in these events is the Major Histocompatibility Complex class I (MHC-I), responsible for binding and presenting small peptides from the intracellular environment to CD8+T cells. The study of peptide:MHC-I (pMHC-I) molecules at a structural level is crucial to understand the molecular mechanisms underlying immunologic responses. Unfortunately, there are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number of complexes that could be formed combining different peptides) and pMHC-I modelling tools are scarce. Here, we present DockTope, a free and reliable web-based tool for pMHC-I modelling, based on crystal structures from the PDB. DockTope is fully automated and allows any researcher to construct a pMHC-I complex in an efficient way. We have reproduced a dataset of 135 non-redundant pMHC-I structures from the PDB (Cα RMSD below 1 Å). Modelling of pMHC-I complexes is remarkably important, contributing to the knowledge of important events such as cross-reactivity, autoimmunity, cancer therapy, transplantation and rational vaccine design.
Disintegration of Carbon Dioxide Molecules in a Microwave Plasma Torch
Authors: Kwak Hyoung S. , Uhm Han S. , Hong Yong C. , Choi Eun H.
Published: December 2015

A pure carbon dioxide torch is generated by making use of 2.45 GHz microwave. Carbon dioxide gas becomes the working gas and produces a stable carbon dioxide torch. The torch volume is almost linearly proportional to the microwave power. Temperature of the torch flame is measured by making use of optical spectroscopy and thermocouple. Two distinctive regions are exhibited, a bright, whitish region of high-temperature zone and a bluish, dimmer region of relatively low-temperature zone. Study of carbon dioxide disintegration and gas temperature effects on the molecular fraction characteristics in the carbon dioxide plasma of a microwave plasma torch under atmospheric pressure is carried out. An analytical investigation of carbon dioxide disintegration indicates that substantial fraction of carbon dioxide molecules disintegrate and form other compounds in the torch. For example, the normalized particle densities at center of plasma are given by nCO2/nN = 6.12 × 10−3, nCO/nN = 0.13, nC/nN = 0.24, nO/nN = 0.61, nC2/nN = 8.32 × 10−7, nO2/nN = 5.39 × 10−5, where nCO2, nCO, nC, nO, nC2 and nO2 are carbon dioxide, carbon monoxide, carbon and oxygen atom, carbon and oxygen molecule densities, respectively. nN is the neutral particle density. Emission profiles of the oxygen and carbon atom radicals and the carbon monoxide molecules confirm the theoretical predictions of carbon dioxide disintegration in the torch.
Estimating the Attack Ratio of Dengue Epidemics under Time-varying Force of Infection using Aggregated Notification Data
Authors: Coelho Flavio Codeço , Carvalho Luiz Max de
Published: December 2015

Quantifying the attack ratio of disease is key to epidemiological inference and public health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation of the attack ratio of an epidemic and the initial fraction of susceptibles using aggregated incidence data. We derive the probability distribution of the effective reproductive number,Rtand use MCMC to obtain posterior distributions of the parameters of a single-strain SIR transmission model with time-varying force of infection. Our method is showcased in a data set consisting of 18 years of dengue incidence in the city of Rio de Janeiro, Brazil. We demonstrate that it is possible to learn about the initial fraction of susceptibles and the attack ratio even in the absence of serotype specific data. On the other hand, the information provided by this approach is limited, stressing the need for detailed serological surveys to characterise the distribution of serotype-specific immunity in the population.