bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus
Authors: Zhang Qi-Lin , Zhu Qian-Hua , Liao Xin , Wang Xiu-Qiang , Chen Tao , Xu Han-Ting , Wang Juan , Yuan Ming-Long , Chen Jun-Yuan 
Published: November 2016

AbstractAmphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder). The results showed that the top two stable RGs were the following: (1)S20and18 Sin thirteen developmental stages, (2)EF1AandACTin seven normal tissues, (3)S20andL13in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4)S20andEF1Ain gill challenged with LPS. The expression profiles of two target genes (EYAandHHEX) in thirteen developmental stages were used to confirm the reliability of chosen RGs. This study identified optimal RGs that can be used to accurately measure gene expression under these conditions, which will benefit evolutionary and functional genomics studies in amphioxus.
GeS2–In2S3–CsI Chalcogenide Glasses Doped with Rare Earth Ions for Near- and Mid-IR Luminescence
Authors: Li Legang , Bian Junyi , Jiao Qing , Liu Zijun , Dai Shixun , Lin Changgui 
Published: November 2016

AbstractChalcogenide glass has been considered as a promising host for the potential laser gain and amplifier media operating in near- and mid-IR spectral region. In this work, the IR luminescence spectra of rare earth ions (Tm3+, Er3+, and Dy3+) doped 65GeS2–25In2S3–10CsI chalcogenide glasses were measured under the excitation of an 808 nm laser diode. To the best of our knowledge, it firstly provides the luminescence spectra of a full near- and mid-IR spectral range from 1 to 4 μm in rare earth ions doped chalcogenide glasses. The results of absorption spectra, luminescence spectra, and fluorescence decay curves were obtained in these samples with singly-, co- and triply-doping behaviors of Tm3+, Er3+, and Dy3+ ions. In order to search possible efficient IR emissions, the luminescence behavior was investigated specifically with the variation of doping behaviors and dopant ions, especially in the samples co- and triply-doped active ions. The results suggest that favorable near- and mid-IR luminescence of rare earth ions can be further modified in chalcogenide glasses through an elaborated design of doping behavior and optically active ions.
Regulation of Anticancer Styrylpyrone Biosynthesis in the Medicinal Mushroom Inonotus obliquus Requires Thioredoxin Mediated Transnitrosylation of S-nitrosoglutathione Reductase
Authors: Zhao Yanxia , He Meihong , Ding Jianing , Xi Qi , Loake Gary J. , Zheng Weifa 
Published: November 2016

AbstractThe medicinal macrofungus Inonotus obliquus widely utilized as folk medicine in Russia and Baltic countries is a source of phenylpropanoid-derived styrylpyrone polyphenols that can inhibit tumor proliferation. Insights into the regulatory machinery that controls I. obliquus styrylpyrone polyphenol biosynthesis will enable strategies to increase the production of these molecules. Here we show that Thioredoxin (Trx) mediated transnitrosylation of S-nitrosoglutathione reductase (GSNOR) underpins the regulation of styrylpyrone production, driven by nitric oxide (NO) synthesis triggered by P. morii coculture. NO accumulation results in the S-nitrosylation of PAL and 4CL required for the synthesis of precursor phenylpropanoids and styrylpyrone synthase (SPS), integral to the production of styrylpyrone, inhibiting their activities. These enzymes are targeted for denitrosylation by Trx proteins, which restore their activity. Further, this Trx S-nitrosothiol (SNO) reductase activity was potentiated following S-nitrosylation of Trx proteins at a non-catalytic cysteine (Cys) residue. Intriguingly, this process was counterbalanced by Trx denitrosylation, mediated by Trx-dependent transnitrosylation of GSNOR. Thus, unprecedented interplay between Trx and GSNOR oxidoreductases regulates the biosynthesis of styrylpyrone polyphenols in I. obliquus.
Quantitative secretomic analysis of pancreatic cancer cells in serum-containing conditioned medium
Authors: Liu Peng , Weng Yejing , Sui Zhigang , Wu Yunhao , Meng Xiangli , Wu Mengwei , Jin Haoyi , Tan Xiaodong , Zhang Lihua , Zhang Yukui 
Published: November 2016

AbstractPancreatic cancer is a highly metastatic and chemo-resistant disease. Secreted proteins involved in cell-cell interactions play an important role in changing the tumor microenvironment. Previous studies generally focus on the secretome of cancer cell line from serum-free media, due to the serious interference of fetal bovine serum (FBS). However, serum-starvation may alter expression patterns of secreted proteins. Hence, efforts to decrease the interference of serum in proteomic analysis of serum-containing media have been hampered to quantitatively measure the tumor secretion levels. Recently, the metabolic labeling, protein equalization, protein fractionation and filter-aided sample preparation (FASP) strategy (MLEFF) has been successfully used to avoid the disturbance of serum on secretome analysis. Here, this efficient method was applied for comparative secretome analysis of two hamster pancreatic cancer cells with differentially metastatic potentials, enabling the observation of 161 differentially expressed proteins, including 106 proteins that had been previously reported and detected in plasma. By integrated analysis of our data and publicly available bioinformatics resources, we found that a combination panel consisting of CDH3, PLAU, and LFNG might improve the prognosis of overall pancreatic cancer survival. These secreted proteins may serve as a potential therapeutic targets for pancreatic cancer metastasis.
Anion-controlled dimer distance induced unique solid-state fluorescence of cyano substituted styrene pyridinium
Authors: Zhang Gaobin , Zhang Xuanjun , Kong Lin , Wang Shichao , Tian Yupeng , Tao Xutang , Yang Jiaxiang 
Published: November 2016

AbstractMolecular packing arrangements play a key role in dominating the photophysical properties of luminophores in aggregated state but fine control of the molecular packing is a great challenge. This article describes a unique cyano substituted styrene pyridinium with interesting solid-state fluorescence that can be finely tuned by simple change of counteranions. The dilute solutions of the organic salts (PyCl, PyNO3, PyOTs and PyPh4B) exhibit very weak fluorescence. The crystals of the organic salts (PyCl, PyNO3, and PyOTs) show much enhanced fluorescence compared with their dilute solutions. It is interesting that the emissions changed from bluish-green to deep-blue and fluorescence quantum yields increase from 2.5% to 13.1% with the increasing of steric hindrance of the anions from chloridion, nitrate, to p-toluenesulfonate. Crystal and DFT studies reveal that the enhanced fluorescence is ascribed to the formation of dimers and bigger anions induce larger molecular separation in dimers. Tetraphenylboron anion with very large steric hindrance impedes the formation of dimers and thus results in non-fluorescent salt (PyPh4B). Meanwhile, this unique dimeric packing endows the crystal of PyNO3 with anisotropic fluorescence.
Investigating the rotational evolution of very low-mass stars and brown dwarfs in young clusters using Monte Carlo simulations
Authors: Vasconcelos M. J. , Bouvier J. 
Published: November 2016

Context. Very low-mass (VLM) stars and brown dwarfs (BDs) present a different rotational behaviour from their solar mass counterparts.
Aims. We investigate the rotational evolution of young VLM stars and BDs using Monte Carlo simulations under the hypothesis of disk locking and stellar angular momentum conservation.
Methods. We built a set of objects with masses ranging from 0.01 M⊙ to 0.4 M⊙ and considered models with single- and double-peaked initial period distributions with and without disk locking. An object is considered to be diskless when its mass accretion rate is below a given threshold.
Results. Models with initial single-peaked period distributions reproduce the observations well given that BDs rotate faster than VLM stars. We observe a correlation between rotational period and mass when we relax the disk locking hypothesis, but with a shallower slope compared to some observational results. The angular momentum evolution of diskless stars is flatter than it is for stars with a disk which occurs because the moment of inertia of objects less massive than 0.2 M⊙ remains pratically constant for a time scale that increases with decreasing stellar mass.
Conclusions. Comparing our results with the available observational data we see that disk locking is not as important in the low-mass regime and that the rotational behaviour of VLM stars and BDs is different from what is seen in their solar mass counterparts.
A study of the effect of rotational mixing on massive stars evolution: surface abundances of Galactic O7-8 giant stars
Authors: Martins F. , Simón-Díaz S. , Barbá R. H. , Gamen R. C. , Ekström S. 
Published: November 2016

Context. Massive star evolution remains only partly constrained. In particular, the exact role of rotation has been questioned by puzzling properties of OB stars in the Magellanic Clouds.
Aims. Our goal is to study the relation between surface chemical composition and rotational velocity, and to test predictions of evolutionary models including rotation.
Methods. We have performed a spectroscopic analysis of a sample of fifteen Galactic O7-8 giant stars. This sample is homogeneous in terms of mass, metallicity and evolutionary state. It is made of stars with a wide range of projected rotational velocities.
Results. We show that the sample stars are located on the second half of the main sequence, in a relatively narrow mass range (25–40 M⊙). Almost all stars with projected rotational velocities above 100 km s-1 have N/C ratios about ten times the initial value. Below 100 km s-1 a wide range of N/C values is observed. The relation between N/C and surface gravity is well reproduced by various sets of models. Some evolutionary models including rotation are also able to consistently explain slowly rotating, highly enriched stars. This is due to differential rotation which efficiently transports nucleosynthesis products and allows the surface to rotate slower than the core. In addition, angular momentum removal by winds amplifies surface braking on the main sequence. Comparison of the surface composition of O7-8 giant stars with a sample of B stars with initial masses about four times smaller reveal that chemical enrichment scales with initial mass, as expected from theory.
Conclusions. Although evolutionary models that include rotation face difficulties in explaining the chemical properties of O- and B-type stars at low metallicity, some of them can consistently account for the properties of main-sequence Galactic O stars in the mass range 25–40 M⊙.
Kinematics of the Local Universe
Authors: Theureau G. , Coudreau N. , Hallet N. , Hanski M. O. , Poulain M. 
Published: November 2016

Aims.This paper presents 828 new 21 cm neutral hydrogen line measurements carried out with the FORT receiver of the meridian transit Nançay radio telescope (NRT) in the years 2000–2007.Methods.This observational program was part of a larger project aimed at collecting an exhaustive and magnitude-complete HI extragalactic catalog for Tully-Fisher applications. Through five massive data releases, the KLUN series has collected a homogeneous sample of 4876 HI-spectra of spiral galaxies, complete down to a flux of 5 Jy km s-1and with declinationδ> −40°.Results.We publish here the last release of the KLUN HI observational program, corresponding to the faint end of the survey, with HI masses ranging from 5 × 108to 5 × 1010solar masses. The size of this final sample is comparable to the catalogs based on the Arecibo and Parkes radio telescope campaigns, and it allows general HI mass distribution studies from a set of homogeneous radio measurements.
Orientation diagnostique d’un cas de « Rigid spine » familial par IRM musculaire corps entier
Authors: Cavassa Eliana , Tordjman Mickael , Ferreiro Ana , Carlier Robert , Quijano-Roy Susana 
Published: November 2016

La maladie de Pompe est une maladie lysosomale avec atteinte musculaire prédominante. On distingue la forme sévère du nourrisson avec troubles cardiaques des formes tardives de l’enfant, de l’adolescent et de l’adulte qui n’ont en général pas de manifestations cardiaques. L’association d’une maladie de Pompe et d’un « rigid spine » a été occasionnellement rapportée. Plusieurs profils ont été décrits. La présentation la plus fréquente est un déficit des muscles des ceintures et du diaphragme. Une scoliose est rapportée dans un tiers des patients, mais seulement 15 % associent une raideur spinale. L’atteinte extra-musculaire, en particulier des symptômes cardio-cérébrovasculaires sont observés dans un tiers des patients. L’observation rapportée ici présente un tableau de myopathie avec un phénotype typique de raideur spinale sélective, associé à une augmentation modérée des enzymes musculaires, des signes myopathiques à la biopsie, et une atteinte cardiaque.
Prediction of Outcome From Adult Bacterial Meningitis in a High-HIV-Seroprevalence, Resource-Poor Setting Using the Malawi Adult Meningitis Score (MAMS)
Authors: Wall Emma C. , Mukaka Mavuto , Scarborough Matthew , Ajdukiewicz Katherine M. A. , Cartwright Katharine E. , Nyirenda Mulinda , Denis Brigitte , Allain Theresa J. , Faragher Brian , Lalloo David G. , Heyderman Robert S. 
Published: November 2016

Abstract

Background.
Acute bacterial meningitis (ABM) in adults residing in resource-poor countries is associated with mortality rates &gt;50%. To improve outcome, interventional trials and standardized clinical algorithms are urgently required. To optimize these processes, we developed and validated an outcome prediction tool to identify ABM patients at greatest risk of death.

Methods.
We derived a nomogram using mortality predictors derived from a logistic regression model of a discovery database of adult Malawian patients with ABM (n = 523 [65%] cerebrospinal fluid [CSF] culture positive). We validated the nomogram internally using a bootstrap procedure and subsequently used the nomogram scores to further interpret the effects of adjunctive dexamethasone and glycerol using clinical trial data from Malawi.

Results.
ABM mortality at 6-week follow-up was 54%. Five of 15 variables tested were strongly associated with poor outcome (CSF culture positivity, CSF white blood cell count, hemoglobin, Glasgow Coma Scale, and pulse rate), and were used in the derivation of the Malawi Adult Meningitis Score (MAMS) nomogram. The C-index (area under the curve) was 0.76 (95% confidence interval, .71–.80) and calibration was good (Hosmer-Lemeshow C-statistic = 5.48, df = 8, P = .705). Harmful effects of adjunctive glycerol were observed in groups with relatively low predicted risk of poor outcome (25%–50% risk): Case Fatality Rate of 21% in the placebo group and 52% in the glycerol group (P &lt; .001). This effect was not seen with adjunctive dexamethasone.

Conclusions.
MAMS provides a novel tool for predicting prognosis and improving interpretation of ABM clinical trials by risk stratification in resource-poor settings. Whether MAMS can be applied to non-HIV-endemic countries requires further evaluation.
Standard-based comprehensive detection of adverse drug reaction signals from nursing statements and laboratory results in electronic health records
Authors: Lee Suehyun , Choi Jiyeob , Kim Hun-Sung , Kim Grace Juyun , Lee Kye Hwa , Park Chan Hee , Han Jongsoo , Yoon Dukyong , Park Man Young , Park Rae Woong , Kang Hye-Ryun , Kim Ju Han 
Published: November 2016

Abstract
Objective. We propose 2 Medical Dictionary for Regulatory Activities–enabled pharmacovigilance algorithms, MetaLAB and MetaNurse, powered by a per-year meta-analysis technique and improved subject sampling strategy.
Matrials and methods. This study developed 2 novel algorithms, MetaLAB for laboratory abnormalities and MetaNurse for standard nursing statements, as significantly improved versions of our previous electronic health record (EHR)–based pharmacovigilance method, called CLEAR. Adverse drug reaction (ADR) signals from 117 laboratory abnormalities and 1357 standard nursing statements for all precautionary drugs (n  = 101) were comprehensively detected and validated against SIDER (Side Effect Resource) by MetaLAB and MetaNurse against 11 817 and 76 457 drug-ADR pairs, respectively.
Results. We demonstrate that MetaLAB (area under the curve, AUC = 0.61 ± 0.18) outperformed CLEAR (AUC = 0.55 ± 0.06) when we applied the same 470 drug-event pairs as the gold standard, as in our previous research. Receiver operating characteristic curves for 101 precautionary terms in the Medical Dictionary for Regulatory Activities Preferred Terms were obtained for MetaLAB and MetaNurse (0.69 ± 0.11; 0.62 ± 0.07), which complemented each other in terms of ADR signal coverage. Novel ADR signals discovered by MetaLAB and MetaNurse were successfully validated against spontaneous reports in the US Food and Drug Administration Adverse Event Reporting System database.
Discussion. The present study demonstrates the symbiosis of laboratory test results and nursing statements for ADR signal detection in terms of their system organ class coverage and performance profiles.
Conclusion. Systematic discovery and evaluation of the wide spectrum of ADR signals using standard-based observational electronic health record data across many institutions will affect drug development and use, as well as postmarketing surveillance and regulation.
A multi-agent systems-based contractor pre-qualification model
Authors: Kog Faikcan , Yaman Hakan 
Published: November 2016

Purpose
The selection of the contractor, as a main participant of a construction project, is the most important and challenging decision process for a client. The purpose of this paper is to propose a multi-agent systems (MAS)-based contractor pre-qualification (CP) model for the construction sector in the frame of the tender management system.

Design/methodology/approach
The meta-classification and analysis study of the existing literature on CP, contractor selection and criteria weighting issues, which examines the current and important CP criteria, other than price, is introduced structurally. A quantitative survey, which is carried out to estimate initial weightings of the identified criteria, is overviewed. MAS are used to model the pre-qualification process and workflows are shown in Petri nets formalism. A user-friendly prototype program is created in order to simulate the tendering process. In addition, a real case regarding the construction work in Turkey is analyzed.

Findings
There is a lack of non-human-driven solutions and automation in CP and in the selection problem. The proposed model simulates the pre-qualification process and provides consistent results.

Research limitations/implications
The meta-classification study consists of only peer-reviewed papers between 1992 and 2013 and the quantitative survey initiates the perspectives of the actors of Turkish construction sector. Only the traditional project delivery method is selected for the proposed model, that is other delivery methods such as design/build, project management, etc., are not considered. Open, selective limited and negotiated tendering processes are examined in the study and the direct supply is not considered in the scope.

Practical implications
The implications will help to provide an objective CP and selection process and to prevent the delays, costs and other troubles, which are caused by the false selection of a contractor.

Originality/value
Automation and simulation in the pre-qualification and the selection of the contractor with a non-human-driven intelligent solution ease the decision processes of clients in terms of cost, time and quality.
Using augmented reality video in enhancing masonry and roof component comprehension for construction management students
Authors: Shanbari Hamzah , Blinn Nathan , Issa Raja R.A. 
Published: November 2016

Purpose
New methods to introduce topics in classrooms are needed to enhance the construction management educational experience. One of these new methods is showing real time videos that highlight the various elements of concern in the classroom lecture. The purpose of this paper is to use augmented reality technology (ART) and a layer of artificial visualizations to simulate the environmental context and spatio-temporal constraints of various construction processes. The superimposition of images serves as an instructional mechanism to virtually incorporate jobsite experiences into classrooms. This enhancement of spatio-temporal constraints enables learners to visualize context and hidden processes otherwise unattainable through traditional classroom lectures.

Design/methodology/approach
A significantly improved perception of reality is created through the combination of the learners’ ability to understand the complexity of construction products (e.g. assemblies) and associated jobsite processes by viewing the real environment augmented with computer-generated information layers.

Findings
Testing the ART video in a classroom with undergraduate construction management students showed that students who were exposed to the ART video were able to remember and identify the highlighted elements in the corresponding assembly more effectively than those who were not.

Originality/value
ART is a valuable tool in enhancing classroom learning and gives educators a teaching advantage when they combine traditional classroom lectures with ART enabled media.
Free vs hate speech on social media: the Indian perspective
Authors: Alam Iftikhar , Raina Roshan Lal , Siddiqui Faizia 
Published: November 2016

PurposeThe Hon’ble Supreme Court of India, in a landmark judgment, scrapped a draconian law [Section 66 (A)] that gave the police absolute power to put behind bars anybody who was found posting offensive or annoying comments online. This paper aims to examine the take of people on the “Free Speech via Social Media” issue and their attitude towards the way sensitive messages/information are posted, shared and forwarded on social media, especially, Facebook.Design/methodology/approachThe research was carried out on a sample of 200 social media users, all picked up randomly, from five Indian states/Union Territories. Data were collected through a questionnaire, and users were contacted through e-mail. Data collected were analyzed through the Kolmogorov–Smirnov (K-S)Ztest.FindingsThe findings indicate that hate posts/messages are on the rise, and more and more users are joining in. Besides, prosecution happens only when the aggrieved party is influential or powerful.Practical implicationsThe findings of this research give a strong insight into the social media behaviour of users in relation to hate contents/posts. The study establishes the fact that Indian people are in favour of free speech, but with a sense of restraint and responsibility. The work could form the basis for future research on various aspects of hate speech on social media. Researchers could study the trials and prosecutions that have happened over the past few years and whether punishment has acted as a deterrent.Originality/valueThe research is likely to be important for those involved in work on freedom of speech or hate speech through social media. Social networking sites such as Facebook would also get some insights into users’ perception towards free and hate speech mechanism on social media.