bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Pluripotent Stem-Cell Marker Alkaline Phosphatase is Highly Expressed in Refractory Glioblastoma with DNA Hypomethylation
Authors: Iwadate Yasuo , Suganami Akiko , Tamura Yutaka , Matsutani Tomoo , Hirono Seiichiro , Shinozaki Natsuki , Hiwasa Takaki , Takiguchi Masaki , Saeki Naokatsu 
Published: February 2017

Abstract

BACKGROUND: Hypomethylation of genomic DNA induces stem-cell properties in cancer cells and contributes to the treatment resistance of various malignancies.

OBJECTIVE: To examine the correlation between the methylation status of stem-cell-related genes and the treatment outcomes in patients with glioblastoma (GBM).

METHODS: The genome-wide DNA methylation status was determined using HumanMethylation450 BeadChips, and the methylation status was compared between a group of patients with good prognosis (survival > 4 yr) and a group with poor prognosis (survival < 1 yr). Immunohistochemistry for proteins translated from hypomethylated genes, including alkaline phosphatase (ALPL), CD133, and CD44, was performed in 70 GBMs and 60 oligodendroglial tumors.

RESULTS: The genomic DNA in refractory GBM was more hypomethylated than in GBM from patients with relatively long survival (P = .0111). Stem-cell-related genes including ALPL, CD133, and CD44 were also significantly hypomethylated. A validation study using immunohistochemistry showed that DNA hypomethylation was strongly correlated with high protein expression of ALPL, CD133, and CD44. GBM patients with short survival showed high expression of these stem-cell markers. Multivariate analysis confirmed that co-expression of ALPL + CD133 or ALPL + CD44 was a strong predictor of short survival. Anaplastic oligodendroglial tumors without isocitrate dehydrogenase 1 mutation were significantly correlated with high ALPL expression and poor survival.

CONCLUSION: Accumulation of stem-cell properties due to aberrant DNA hypomethylation is associated with the refractory nature of GBM.
Chemosensory Transduction in Arthropods
Authors: Stengl Monika 
Published: February 2017

Abstract
Reception of chemicals via olfaction and gustation are prerequisites to find, distinguish, and recognize food and mates and to avoid dangers. Several receptor gene superfamilies are employed in arthropod chemosensation: inverse 7-transmembrane (7-TM) gustatory and olfactory receptors (GRs, ORs), 3-TM ionotropic glutamate-related receptors (IRs), receptor-guanylyl cyclases, transient receptor potential ion channels, and epithelial sodium channels. Some of these receptor gene families have ancient origins and expanded in several taxa, producing very large, variant gene families adapted to the respectively relevant odor ligands in species-specific environments. Biochemical and electrophysiological studies in situ as well as molecular genetics found evidence for G-protein-dependent signal transduction cascades for ORs, GRs, and IRs, suggesting that signal amplification is paramount for chemical senses. In contrast, heterologous expression studies argued for primarily ionotropic transduction as a prerequisite to interstimulus intervals in the range of microseconds.
Self-sustaining processes at all scales in wall-bounded turbulent shear flows
Authors: Cossu Carlo , Hwang Yongyun 
Published: February 2017

We collect and discuss the results of our recent studies which show evidence of the existence of a whole family of self-sustaining motions in wall-bounded turbulent shear flows with scales ranging from those of buffer-layer streaks to those of large-scale and very-large-scale motions in the outer layer. The statistical and dynamical features of this family of self-sustaining motions, which are associated with streaks and quasi-streamwise vortices, are consistent with those of Townsend’s attached eddies. Motions at each relevant scale are able to sustain themselves in the absence of forcing from larger- or smaller-scale motions by extracting energy from the mean flow via a coherent lift-up effect. The coherent self-sustaining process is embedded in a set of invariant solutions of the filtered Navier–Stokes equations which take into full account the Reynolds stresses associated with the residual smaller-scale motions.
This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’.
Iroki: automatic customization and visualization of phylogenetic trees
Authors: Moore Ryan M. , Harrison Amelia O. , McAllister Sean M. , Polson Shawn W. , Wommack K. Eric 
Published: February 2017

ABSTRACTPhylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available athttps://www.iroki.netor through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available athttps://github.com/mooreryan/iroki.
Unsupervised idealization of ion channel recordings by Minimum Description Length: Application to human PIEZO1-channels
Authors: Gnanasambandam Radhakrishnan , Nielsen Morten Schak , Nicolai Christopher , Sachs Frederick , Hofgaard Johannes Pauli , Dreyer Jakob Kisbye 
Published: February 2017

AbstractResearchers can investigate the mechanistic and molecular basis of many physiological phenomena in cells by analyzing the fundamental properties of single ion channels. These analyses entail recording single channel currents and measuring current amplitudes and transition rates between conductance states. Since most electrophysiological recordings contain noise, the data analysis can proceed by idealizing the recordings to isolate the true currents from the noise. This de-noising can be accomplished with threshold crossing algorithms and Hidden Markov Models, but such procedures generally depend on inputs and supervision by the user, thus requiring some prior knowledge of underlying processes. Channels with unknown gating and/or functional sub-states and the presence in the recording of currents from uncorrelated background channels present substantial challenges to unsupervised analyses.Here we describe and characterize an idealization algorithm based on Rissanen’s Minimum Description Length (MDL) Principle. This method uses minimal assumptions and idealizes ion channel recordings without requiring a detailed user input or aprioriassumptions about channel conductance and kinetics.. Furthermore, we demonstrate that correlation analysis of conductance steps can resolve properties of single ion channels in recordings contaminated by signals from multiple channels. We first validated our methods on simulated data defined with a range of different signal-to-noise levels, and then showed that our algorithm can recover channel currents and their substates from recordings with multiple channels, even under conditions of high noise. We then tested the MDL algorithm on real experimental data from human PIEZO1 channels and found that our method revealed the presence of substates with alternate conductances.
Bayesian molecular dating as a “doubly intractable” problem
Authors: Guindon Stéphane 
Published: February 2017

1AbstractThis study focuses on a conceptual issue with Bayesian inference of divergence times using Markov chain Monte Carlo. The influence of fossil data on the probabilistic distribution of trees is the crux of the matter considered here. More specifically, among all the phylogenies that a tree model (e.g., the birth-death process) generates, only a fraction of them “agree” with the fossil data at hands. Bayesian inference of divergence times using Markov Chain Monte Carlo requires taking this fraction into account. Yet, doing so is challenging and most Bayesian samplers have simply overlooked this hurdle so far, thereby providing approximate estimates of divergence times and tree process parameters. A generic solution to this issue is presented here. This solution relies on an original technique, the so-called exchange algorithm, dedicated to drawing samples from “doubly intractable” distributions. A small example illustrates the problem of interest and the impact of the approximation aforementioned on tree parameter estimates. The analysis of land plant sequences and multiple fossils further illustrates the importance of proper mathematical handling of calibration data in order to derive accurate estimates of node age.
The performance of China’s stock market price limits: noise mitigator or noise maker?
Authors: Tao Juan , Yingying Wu , Jingyi Zhang 
Published: February 2017

Purpose
The purpose of this paper is to re-examine the effectiveness of price limits on stock volatilities in China over a more recent time period spanning from 2007 to 2012. The motivation stems from the fact that very high stock market volatilities are observed in China and we are sceptical of the volatility mitigating effect claimed by advocates of price limits.

Design/methodology/approach
The effectiveness of price limits on volatilities is examined using an event study methodology and within an expanded framework of volatility-volume relationships. The sample stocks include the 300 component stocks of the CSI300 Index.

Findings
Both event study and regression analysis suggest that price limits exaggerate market volatilities by causing volatility spillovers. The destabilising effect is much more pronounced for small firm stocks and when the market falls. In addition to the informational source of volatilities (represented by volume), price limits create another non-trivial frictional source of volatilities in China’s stock market.

Originality/value
This research is the first to re-examine the price limit effect in China’s stock market in an expanded framework of volatility-volume relationships. It identifies price limits, in addition to information, as another non-trivial frictional source of volatilities. The findings derived from a recent sample period confirm the conventional view of inefficiency of price limits raised by Fama (1989) and provide evidence in support of the pervasive trend of stock market deregulations.
A novel message authentication method for VANET without RSU
Authors: Yein Alan Dahgwo , Lin Chih-Hsueh , Huang Yu-Hsiu , Hsieh Wen-Shyong , Lee Chung-Nan , Kuo Pin-Chun 
Published: February 2017

Purpose
Riding on the wave of intelligent transportation systems, the vehicular ad hoc network (VANET) is becoming a popular research topic. VANET is designed to build an environment where the vehicles can exchange information about the traffic conditions or vehicle situation to help the vehicles avoid traffic accidents or traffic jams. In order to keep the privacy of vehicles, the vehicles must be anonymous and the routing must be untraceable while still being able to be verified as legal entities. The paper aims to discuss these issues.

Design/methodology/approach
The exchanged messages must be authenticated to be genuine and verified that they were sent by a legal vehicle. The vehicles also can mutually trust and communicate confidentially. In VANETs, road-side units (RSUs) are installed to help the vehicles to obtain message authentication or communicate confidentially. However, the coverage of RSUs is limited due to the high cost of wide area installation. Therefore the vehicles must be able to obtain message authentication by themselves – without an RSU.

Findings
The authors take the concept of random key pre-distribution used in wireless sensor networks, modify it into a random secret pre-distribution, and integrate it with identity-based cryptography to make anonymous message authentication and private communication easier and safer. The authors construct a two-tier structure. The tier 1, trust authority, assigns n anonymous identities and embeds n secrets into these identities to be the private secret keys for the tier 2, registered vehicles. At any time, the vehicles can randomly choose one of n anonymous identities to obtain message authentication or communicate confidentially with other vehicles.

Originality/value
The processes of building neighbor set, setting pairing value, and message authenticating are proposed in this paper. The proposed method can protect against the attacks of compromising, masquerading, forging, and replying, and can also achieve the security requirements of VANET in message authentication, confidential communication, anonymity, and un-traceability. The performance of the proposed method is superior to the related works.
The application of simultaneous elimination and back-substitution method (SEBSM) in finite element method
Authors: Liu Yunfei , Lv Jun , Gao Xiaowei 
Published: February 2017

Purpose
The purpose of this paper is to introduce a new method called simultaneous elimination and back-substitution method (SEBSM) to solve a system of linear equations as a new finite element method (FEM) solver.

Design/methodology/approach
In this paper, a new technique assembling the global stiffness matrix will be proposed and meanwhile the direct method SEBSM will be applied to solve the equations formed in FEM.

Findings
The SEBSM solver for FEM with the present assembling technique has distinct advantages in both computational time and memory space occupation over the conventional methods, such as the Gauss elimination and LU decomposition methods.

Originality/value
The developed solver requires less memory space no matter the coefficient matrix is a typical sparse matrix or not, and it is applicable to both symmetric and unsymmetrical linear systems of equations. The processes of assembling matrix and dealing with constraints are straightforward, so it is convenient for coding. Compared to the previous solvers, the proposed solver has favorable universality and good performances.
Diverse approaches to negative treatment in the workplace: sector differences and their effects
Authors: Verheij Jesper , Groeneveld Sandra , Kuyper Lisette 
Published: February 2017

PurposeThis purpose of this paper is to examine whether and how different diversity approaches of public, semi-public and private sector organizations affect negative treatment experienced in the workplace. Broadly speaking, organizations might either approach diversity as a problem of inequality or as a resource and an added value for the organization. As such, a pro-equality and a pro-diversity approach can be distinguished which are both examined in this paper.Design/methodology/approachIn a quantitative study, structural equation modeling was used on survey data of a representative sample of Dutch employees.FindingsResults show that while both approaches are negatively associated with negative treatment, the pro-diversity is most strongly so. Sector differences were less pronounced than expected, although employees across different sectors of employment benefit from both the approaches to a different extent.Research limitations/implicationsFurther research examining the effect of diversity approaches to negative treatment across sectors is required. Suggestions for further research are discussed.Practical implicationsLooking at sector differences, the findings showed that employees across public, semi-public and private sector organizations benefitted from the diversity approaches to a different extent. Organizations across different sectors are therefore suggested to adopt different diversity approaches to combat negative treatment in the workplace.Originality/valueMost studies either focus on a pro-equality or pro-diversity approach. The present study combines both and, moreover, pays attention to the way both approaches affect negative treatment experienced in the semi-public sector. Examining variation within the public sector is unique in the context of diversity research.
A comparative study of population-based algorithms for a political districting problem
Authors: Rincón-García Eric Alfredo , Gutiérrez-Andrade Miguel Ángel , de-los-Cobos-Silva Sergio Gerardo , Mora-Gutiérrez Roman Anselmo , Ponsich Antonin , Lara-Velázquez Pedro 
Published: February 2017

Purpose
This paper aims to propose comparing the performance of three algorithms based on different population-based heuristics, particle swarm optimization (PSO), artificial bee colony (ABC) and method of musical composition (DMMC), for the districting problem.

Design/methodology/approach
In order to compare the performance of the proposed algorithms, they were tested on eight instances drawn from the Mexican electoral institute database, and their respective performance levels were compared. In addition, a simulated annealing-based (simulated annealing – SA) algorithm was used as reference to evaluate the proposed algorithms. This technique was included in this work because it has been used for Federal districting in Mexico since 1994. The performance of the algorithms was evaluated in terms of the quality of the approximated Pareto front and efficiency. Regarding solution quality, convergence and dispersion of the resulting non-dominated solutions were evaluated.

Findings
The results show that the quality and diversification of non-dominated solutions generated by population-based algorithms are better than those produced by Federal Electoral Institute’s (IFE’s) SA-based technique. More accurately, among population-based techniques, discrete adaptation of ABC and MMC outperform PSO.

Originality/value
The performance of three population-based techniques was evaluated for the districting problem. In this paper, the authors used the objective function proposed by the Mexican IFE, a weight aggregation function that seeks for a districting plan that represents the best balance between population equality and compactness. However, the weighting factors can be modified by political agreements; thus, the authors decided to produce a set of efficient solutions, using different weighting factors for the computational experiments. This way, the best algorithm will produce high quality solutions no matter the weighting factors used for a real districting process. The computational experiments proved that the proposed artificial bee colony and method of musical composition-based algorithms produce better quality efficient solutions than its counterparts. These results show that population-based algorithms can outperform traditional local search strategies. Besides, as far as we know, this is the first time that the method of musical composition is used for this kind of problems.
A fuzzy model for the valuation of quality management system
Authors: Brotons Jose M. , Sansalvador Manuel E. 
Published: February 2017

Purpose
The economic effects resulting from the commitment to ISO 9001 certification is a controversial issue. Many authors have concluded about the positive economic effects resulting from the establishment of quality systems in accordance with the requirements established in the ISO 9001 standard, but other authors have not appreciated this positive relationship. The purpose of this paper is to provide a model that facilitates the valuation of the ISO 9001 quality system.

Design/methodology/approach
In the process of developing a valuation model, given the uncertainty this process involves, the use of fuzzy math is very useful. First, as for an internal valuation method, the authors highlight the discounted cash flow in a fuzzy environment. The internal valuation will be completed by external expert opinions. To improve the information supplied by experts, the paper makes use of the experton theory. In this context, the authors propose the aggregation of the experts’ opinion by using basic defuzzification distribution (BADD)-fuzzy induced ordered weighted averaging. Finally, the results undergo contra-expertise. After presenting the theoretical model, the authors proceed with its application by using a case study.

Findings
The paper develops a new method for the economic evaluation of the ISO 9001 certification.

Originality/value
The authors propose the valuation of ISO 9001 quality management system, and they do it using some interesting tools which fuzzy logic offers. In this way, it is possible to eliminate subjectivity and improve the final results.
A fuzzy methodology for innovation management measurement
Authors: Alfaro-García Victor G. , Gil-Lafuente Anna M. , Alfaro Calderón Gerardo G. 
Published: February 2017

PurposeInnovation has been recognized as one of the main sources of competitive advantage for organizations and nations. The purpose of this study is to present an innovation management measurement approach by applying fuzzy techniques to small- and medium-sized manufacturing enterprises.Design/methodology/approachThis study presents a survey focusing on seven innovation measurement areas: innovation strategy, knowledge management, project management, portfolio management, internal enablers, organization and structure and external enablers. A total of 91 small- and medium-sized enterprises (SMEs) located in the city of Morelia, Mexico, participated in the study. Furthermore, the data collected were analyzed under a multi-criteria decision-making approach using the theory of expertons and the induced generalized ordered weighted averaging operator.FindingsThe results show that the most valued areas are innovation strategy, organization and structure, knowledge management and project management. Furthermore, portfolio management, external drivers and internal drivers are the areas with the lowest valuations.Originality/valueThis paper presents an original methodological structure based on an expertise process designed to achieve well-founded results from uncertain and subjective opinions directly from the managers of the surveyed SMEs.