bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring bivariate and trivariate mean vectors with a Shewhart chart
Authors: Leoni Roberto Campos , Costa Antonio Fernando Branco 
Published: May 2017

AbstractIn this article, we propose the use of the mean chart to control multivariate processes. The basic idea is to control the mean vector of bivariate (X, Y) and trivariate (X, Y, Z) processes by alternating the charting statistic of the Shewhart chart. If the mean of X observations was the charting statistic to obtain the current sample point, then the mean of Y observations will be the charting statistic to obtain the next sample point (for the trivariate case, the mean of Z observations will be the charting statistic to obtain the sample point subsequent to the next one). As a Shewhart chart, the signal is given anytime a sample point is plotted beyond the control limits, independent of the charting statistic in use. A fair comparison between the proposed chart and the Hotelling chart is based on an equal number of measurements per sample. The Shewhart chart with alternated charting statistic (ACS) always outperforms the Hotelling chart, except for specific types of disturbances in quality characteristics highly correlated (ρ = 0.7). The ACS chart is substantially easier to operate and faster than the Hotelling chart in signaling changes in the mean vector of bivariate and trivariate processes. Even with fewer measurements per sample, the trivariate ACS chart outperforms the Hotelling chart.
Zanthoxylum avicennae extract enhances GSK‐3β to attenuate β‐catenin via phosphatase 2A to block metastatic effects of HA22T cells and hepatocellular carcinoma xenografted nude mice
Authors: Wu Hsi‐Chin , Lay Ing‐Shiow , Shibu Marthandam Asokan , Ho Tsung‐Jung , Cheng Shiu‐Min , Lin Chih‐Hao , Dung Tran Duc , Jeng Long‐Bin , Viswanadha Vijaya Padma , Huang Chih‐Yang 
Published: May 2017

AbstractHepatocellular carcinoma (HCC) metastasis is often associated with the activation of Wnt/β‐catenin signaling pathway. Zanthoxylum avicennae (Ying Bu Bo, YBB), a traditional herb with hepatoprotective effect, has been proven to inhibit human HCC in in vivo models however, the in vitro and in vivo effect of YBB on tumor metastasis is not clear yet. To determine whether YBB could inhibit HA22T human HCC cell by acting on β‐catenin metastatic signaling in vitro and in vivo, HA22T cells were treated with different concentrations of YBB extracts (YBBE) and analyzed by Immunofluorescence staining assay, western blot analysis, siRNA mediated gene knock‐down assays and co‐immunoprecipitation assay. Additionally, the HA22T‐implanted xenograft nude mice were used to confirm the assessed cellular effects. Mice treated with YBBEs showed a strong increasing trend in PP2Acα, GSK‐3β, APC, and β‐TrCP/HOS levels, however the expression of β‐catenin, p‐GSK‐3β, TBX 3, and IL8 proteins showed a decreasing trend. YBBE significantly downregulated the nuclear and cytosolic β‐catenin levels by facilitating the proteosomal degradation of β‐catenin. Moreover, as observed by co‐immunoprecipitation assay, YBBE directly promoted the protein interactions between GSK‐3β, β‐TrCP, APC, PP2A, and β‐catenin. In conclusion, both in vitro and in vivo models clearly demonstrated that YBBE inhibits β‐catenin involved metastatic signaling in highly metastatic HA22T cells through PP2A activation.
Predictive Business Process Monitoring Considering Reliability Estimates
Authors: Metzger Andreas , Föcker Felix 
Published: May 2017

AbstractPredictive business process monitoring aims at predicting potential problems during process execution so that these problems can be proactively managed and mitigated. Compared to aggregate prediction accuracy indicators (e.g., precision or recall), prediction reliability estimates provide additional information about the prediction error for an individual business process. Intuitively, it appears appealing to consider reliability estimates when deciding on whether to adapt a running process instance or not. However, we lack empirical evidence to support this intuition, as research on predictive business process monitoring focused on aggregate prediction accuracy. We experimentally analyze the effect of considering prediction reliability estimates for proactive business process adaptation. We use ensemble prediction techniques, which we apply to an industry data set from the transport and logistics domain. In our experiments, proactive business process adaptation in general had a positive effect on cost in 52.5% of the situations. In 82.9% of these situations, considering reliability estimates increased the positive effect, leading to cost savings of up to 54%, with 14% savings on average.
Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations
Authors: Chang Jiang , Tan Wenle , Ling Zhiqiang , Xi Ruibin , Shao Mingming , Chen Mengjie , Luo Yingying , Zhao Yanjie , Liu Yun , Huang Xiancong , Xia Yuchao , Hu Jinlin , Parker Joel S. , Marron David , Cui Qionghua , Peng Linna , Chu Jiahui , Li Hongmin , Du Zhongli , Han Yaling , Tan Wen , Liu Zhihua , Zhan Qimin , Li Yun , Mao Weimin , Wu Chen , Lin Dongxin 
Published: May 2017

AbstractApproximately half of the world’s 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1–E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion. The most frequently affected genes by structural variation are LRP1B and TTC28. The aberrant cell cycle and PI3K-AKT pathways seem critical in ESCC. These results establish a comprehensive genomic landscape of ESCC and provide potential targets for precision treatment and prevention of the cancer.
Design of live attenuated bacterial vaccines based on D-glutamate auxotrophy
Authors: Cabral Maria P. , García Patricia , Beceiro Alejandro , Rumbo Carlos , Pérez Astrid , Moscoso Miriam , Bou Germán 
Published: May 2017

AbstractVaccine development is a priority for global health due to the growing multidrug resistance in bacteria. D-glutamate synthesis is essential for bacterial cell wall formation. Here we present a strategy for generating effective bacterial whole-cell vaccines auxotrophic for D-glutamate. We apply this strategy to generate D-glutamate auxotrophic vaccines for three major pathogens, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus. These bacterial vaccines show virulence attenuation and self-limited growth in mice, and elicit functional and cross-reactive antibodies, and cellular immunity. These responses correlate with protection against acute lethal infection with other strains of the same species, including multidrug resistant, virulent and/or high-risk clones such as A. baumannii AbH12O-A2 and Ab307-0294, P. aeruginosa PA14, and community-acquired methicillin-resistant S. aureus USA300LAC. This approach can potentially be applied for the development of live-attenuated vaccines for virtually any other bacterial pathogens, and does not require the identification of virulence determinants, which are often pathogen-specific.
All pure bipartite entangled states can be self-tested
Authors: Coladangelo Andrea , Goh Koon Tong , Scarani Valerio 
Published: May 2017

AbstractQuantum technologies promise advantages over their classical counterparts in the fields of computation, security and sensing. It is thus desirable that classical users are able to obtain guarantees on quantum devices, even without any knowledge of their inner workings. That such classical certification is possible at all is remarkable: it is a consequence of the violation of Bell inequalities by entangled quantum systems. Device-independent self-testing refers to the most complete such certification: it enables a classical user to uniquely identify the quantum state shared by uncharacterized devices by simply inspecting the correlations of measurement outcomes. Self-testing was first demonstrated for the singlet state and a few other examples of self-testable states were reported in recent years. Here, we address the long-standing open question of whether every pure bipartite entangled state is self-testable. We answer it affirmatively by providing explicit self-testing correlations for all such states.
Direct observation of coherent energy transfer in nonlinear micromechanical oscillators
Authors: Chen Changyao , Zanette Damián H. , Czaplewski David A. , Shaw Steven , López Daniel 
Published: May 2017

AbstractEnergy dissipation is an unavoidable phenomenon of physical systems that are directly coupled to an external environmental bath. In an oscillatory system, it leads to the decay of the oscillation amplitude. In situations where stable oscillations are required, the energy dissipated by the vibrations is usually compensated by replenishment from external energy sources. Consequently, if the external energy supply is removed, the amplitude of oscillations start to decay immediately, since there is no means to restitute the energy dissipated. Here, we demonstrate a novel dissipation engineering strategy that can support stable oscillations without supplying external energy to compensate losses. The fundamental intrinsic mechanism of resonant mode coupling is used to redistribute and store mechanical energy among vibrational modes and coherently transfer it back to the principal mode when the external excitation is off. To experimentally demonstrate this phenomenon, we exploit the nonlinear dynamic response of microelectromechanical oscillators to couple two different vibrational modes through an internal resonance.
Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals
Authors: Yu Tao , Zhou Yongjin J. , Wenning Leonie , Liu Quanli , Krivoruchko Anastasia , Siewers Verena , Nielsen Jens , David Florian 
Published: May 2017

AbstractProduction of chemicals and biofuels through microbial fermentation is an economical and sustainable alternative for traditional chemical synthesis. Here we present the construction of a Saccharomyces cerevisiae platform strain for high-level production of very-long-chain fatty acid (VLCFA)-derived chemicals. Through rewiring the native fatty acid elongation system and implementing a heterologous Mycobacteria FAS I system, we establish an increased biosynthesis of VLCFAs in S. cerevisiae. VLCFAs can be selectively modified towards the fatty alcohol docosanol (C22H46O) by expressing a specific fatty acid reductase. Expression of this enzyme is shown to impair cell growth due to consumption of VLCFA-CoAs. We therefore implement a dynamic control strategy for separating cell growth from docosanol production. We successfully establish high-level and selective docosanol production of 83.5 mg l−1 in yeast. This approach will provide a universal strategy towards the production of similar high value chemicals in a more scalable, stable and sustainable manner.
Neonicotinoid-induced pathogen susceptibility is mitigated by Lactobacillus plantarum immune stimulation in a Drosophila melanogaster model
Authors: Daisley Brendan A. , Trinder Mark , McDowell Tim W. , Welle Hylke , Dube Josh S. , Ali Sohrab N. , Leong Hon S. , Sumarah Mark W. , Reid Gregor 
Published: May 2017

AbstractPesticides are used extensively in food production to maximize crop yields. However, neonicotinoid insecticides exert unintentional toxicity to honey bees (Apis mellifera) that may partially be associated with massive population declines referred to as colony collapse disorder. We hypothesized that imidacloprid (common neonicotinoid; IMI) exposure would make Drosophila melanogaster (an insect model for the honey bee) more susceptible to bacterial pathogens, heat stress, and intestinal dysbiosis. Our results suggested that the immune deficiency (Imd) pathway is necessary for D. melanogaster survival in response to IMI toxicity. IMI exposure induced alterations in the host-microbiota as noted by increased indigenous Acetobacter and Lactobacillus spp. Furthermore, sub-lethal exposure to IMI resulted in decreased D. melanogaster survival when simultaneously exposed to bacterial infection and heat stress (37 °C). This coincided with exacerbated increases in TotA and Dpt (Imd downstream pro-survival and antimicrobial genes, respectively) expression compared to controls. Supplementation of IMI-exposed D. melanogaster with Lactobacillus plantarum ATCC 14917 mitigated survival deficits following Serratia marcescens (bacterial pathogen) septic infection. These findings support the insidious toxicity of neonicotinoid pesticides and potential for probiotic lactobacilli to reduce IMI-induced susceptibility to infection.
Coordination Between the Sexes Constrains the Optimization of Reproductive Timing in Honey Bee Colonies
Authors: Lemanski Natalie J. , Fefferman Nina H. 
Published: May 2017

AbstractHoneybees are an excellent model system for examining how trade-offs shape reproductive timing in organisms with seasonal environments. Honeybee colonies reproduce two ways: producing swarms comprising a queen and thousands of workers or producing males (drones). There is an energetic trade-off between producing workers, which contribute to colony growth, and drones, which contribute only to reproduction. The timing of drone production therefore determines both the drones’ likelihood of mating and when colonies reach sufficient size to swarm. Using a linear programming model, we ask when a colony should produce drones and swarms to maximize reproductive success. We find the optimal behavior for each colony is to produce all drones prior to swarming, an impossible solution on a population scale because queens and drones would never co-occur. Reproductive timing is therefore not solely determined by energetic trade-offs but by the game theoretic problem of coordinating the production of reproductives among colonies.
Resveratrol Pretreatment Attenuates Concanavalin A-induced Hepatitis through Reverse of Aberration in the Immune Response and Regenerative Capacity in Aged Mice
Authors: Huang Tse-Hung , Chen Chin-Chang , Liu Hsuan-Miao , Lee Tzung-Yan , Shieh Sue-Heui 
Published: May 2017

AbstractLoss of regenerative capacity plays a critical role in age-related autoimmune hepatitis. Evidence implicates SIRT1 and p66shc in cell senescence, apoptosis, oxidative stress, and proliferation. This study investigated the effect of resveratrol on concanavalin A (Con A)-induced hepatitis in aged mice and the roles of SIRT1 and p66shc. Aged mice were administrated resveratrol (30 mg/kg orally) seven times at an interval of 12 h before a single intravenous injection of Con A (20 mg/kg). Results showed that the cytokines, TNF-α, IL-6, IFN-γ, and MCP-1, as well as infiltration of macrophages, neutrophils, and T lymphocytes in liver were dramatically enhanced in the mice given only Con A. The aged mouse livers showed markedly raised oxidative stress and cell apoptosis. This oxidative stress further aggravated regenerative dysfunction as indicated by the decreased levels of Ki67, PCNA, Cyclin D1, and Cdk2. Conversely, these phenomena were attenuated by pretreatment with resveratrol. Moreover, resveratrol suppressed the elevation of p66shc in the liver by reversing Con-A-mediated downregulation of SIRT1. The findings suggest that resveratrol protected against Con A-induced hepatitis in aged mice by attenuating an aberration of immune response and liver regeneration, partially via the mechanism of SIRT1-mediated repression of p66shc expression.
Ancestral protein resurrection and engineering opportunities of the mamba aminergic toxins
Authors: Blanchet Guillaume , Alili Doria , Protte Adèle , Upert Gregory , Gilles Nicolas , Tepshi Livia , Stura Enrico A. , Mourier Gilles , Servent Denis 
Published: May 2017

AbstractMamba venoms contain a multiplicity of three-finger fold aminergic toxins known to interact with various α-adrenergic, muscarinic and dopaminergic receptors with different pharmacological profiles. In order to generate novel functions on this structural scaffold and to avoid the daunting task of producing and screening an overwhelming number of variants generated by a classical protein engineering strategy, we accepted the challenge of resurrecting ancestral proteins, likely to have possessed functional properties. This innovative approach that exploits molecular evolution models to efficiently guide protein engineering, has allowed us to generate a small library of six ancestral toxin (AncTx) variants and associate their pharmacological profiles to key functional substitutions. Among these variants, we identified AncTx1 as the most α1A-adrenoceptor selective peptide known to date and AncTx5 as the most potent inhibitor of the three α2 adrenoceptor subtypes. Three positions in the ρ-Da1a evolutionary pathway, positions 28, 38 and 43 have been identified as key modulators of the affinities for the α1 and α2C adrenoceptor subtypes. Here, we present a first attempt at rational engineering of the aminergic toxins, revealing an epistasis phenomenon.
Pelvic Floor Reconstruction After Radical Prostatectomy: A Systematic Review and Meta-analysis of Different Surgical Techniques
Authors: Cui Jianfeng , Guo Hu , Li Yan , Chen Shouzhen , Zhu Yaofeng , Wang Shiyu , Wang Yong , Liu Xigao , Wang Wenbo , Han Jie , Chen Pengxiang , Nie Shuping , Yin Gang , Shi Benkang 
Published: May 2017

AbstractRadical prostatectomy (RP) is the gold standard for the treatment of localized PCa. A meta-analysis was conducted to evaluate the effect of different techniques of pelvic floor reconstruction on urinary continence. A comprehensive search was made for trials that evaluated the efficacy of pelvic floor reconstruction. Relevant databases included PubMed, Embase, Cochrane, Ovid, Web of Science databases and relevant trials from the references. Random-effects model was used to estimate risk ratios (RRs) statistics. Pooled results of patients treated with posterior reconstruction (PR) demonstrated complete urinary continence improved at 1–4, 28–42, 90, 180 and 360 days following catheter removal. Anterior suspension (AS) was associated with improvement only at 28–42 days. The anterior reconstruction (AR) + PR was associated with urinary continence at 1–4, 90 and 180 days. AS + PR was not associated with any benefit. And PR improved social urinary continence at 7–14 and 28–42 days. No benefit was associated with AS. AR + PR had better outcomes at 90 and 180 days. AS + PR was significant improved at 28–42 and 90 days. Patients who underwent RP and PR had the least urinary incontinence. No significant benefit was observed after AS. AR + PR and AS + PR had little benefit in the post-operative period.
karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
Authors: Gel Bernat , Serra Eduard 
Published: May 2017

Abstract

Motivation
Data visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species.

Results
We have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation.

Availability and implementation
karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR) and at the examples and tutorial page at https://bernatgel.github.io/karyoploter_tutorial.
Magnetotelluric distortions directly observed with lightning data
Authors: Hennessy Lachlan , Macnae James 
Published: May 2017

AbstractGalvanic distortions complicate magnetotelluric (MT) soundings. In this research, we use lightning network data to identify specific sferics in MT measurements and analyse these events on the basis of the lightning source location. Without source information, identification and removal of galvanic distortion is a fundamentally ill-posed problem, unless data are statistically decomposed into determinable and indeterminable parts. We use realistic assumptions of the earth-ionosphere waveguide propagation velocity to accurately predict the time of arrival, azimuth and amplitude for every significant sferic in our time-series data. For each sferic with large amplitude, we calculate the rotation of the electric field from the measured to the predicted arrival azimuth. This rotation of the electric field is a primary parameter of distortion. Our results demonstrate that a rudimentary model for near-surface galvanic distortion consistently fits observed electric field rotations. When local features rotate regional electric fields, then counter-rotating data to predicted arrival azimuths should correct the directional dependence of static shift. Although we used amplitude thresholds to simplify statistical processing, future developments should incorporate both signal-to-noise improvements and multisite decompositions. Lower amplitude signal may also be useful after the appropriate signal processing for noise reduction. We anticipate our approach will be useful for further work on MT distortion.
No AGN evidence in NGC 1614 from deep radio VLBI observations
Authors: Herrero-Illana Rubén , Alberdi Antxon , Pérez-Torres Miguel Ángel , Alonso-Herrero Almudena , González-Millán Daniel , Pereira-Santaella Miguel 
Published: May 2017

Abstract
We present deep dual-band 5.0- and 8.4-GHz European VLBI Network (EVN) observations of NGC 1614, a local luminous infrared galaxy with a powerful circumnuclear starburst ring, and whose nuclear engine origin is still controversial. We aim at detecting and characterizing compact radio structures both in the nuclear region and in the circumnuclear ring. We do not find any compact source in the central 200 pc region, setting a very tight 5σ upper limit of 3.7 × 1036 and 5.8 × 1036 erg s−1, at 5.0 and 8.4 GHz, respectively. However, we report a clear detection at both frequencies of a compact structure in the circumnuclear ring, 190 pc to the north of the nucleus, whose luminosity and spectral index are compatible with a core-collapse supernova, giving support to the high star formation rate in the ring. Our result favours the pure starburst scenario, even for the nucleus of NGC 1614, and shows the importance of radio VLBI (very long baseline interferometry) observations when dealing with the obscured environments of dusty galaxies.