bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designer substrate library for quantitative, predictive modeling of reaction performance
Authors: Bess Elizabeth N. , Bischoff Amanda J. , Sigman Matthew S. 
Published: September 2014

Significance
Product distributions of chemical reactions are dictated by a myriad of interactions between molecular species. Identifying which of these features affects reaction selectivity is a key facet for mechanistically understanding a transformation. Such insight often facilitates optimization as well as indicates which types of substrates (substrate scope) are well suited to the method. Unfortunately, the assessment of impactful features is frequently a qualitative endeavor that would significantly benefit from quantitation. We demonstrate a robust method for developing a varied substrate scope library of ketones, identifying quantitative descriptors of mechanistic significance, and applying these descriptors to mathematically elucidate trends in enantioselective reaction outcomes of rhodium-catalyzed asymmetric transfer hydrogenation. The developed mathematical relationships were used to predict future outcomes of new ketone substrates.
On inference of causality for discrete state models in a multiscale context
Authors: Gerber Susanne , Horenko Illia 
Published: September 2014

SignificanceThe presented framework is capable of parameter identification and optimal causality inference for discrete/Boolean-valued processes in a multiscale context, allowing us to understand such processes beyond the usual statistical assumptions of standard approaches. By applying this framework to appropriately coarse-grained molecular dynamics data it is demonstrated that the optimal causality of the considered process is localized in time and space. This offers new opportunities for applying localized parameterization tools from other areas in a molecular dynamics context, thus opening up new possibilities to bridge the gap toward long timescales in molecular dynamics simulations. The new methodology is expected to become very useful in various scientific fields (bioinformatics, geoscience) where large amounts of multiscale discrete/Boolean data have been accumulated.
Benefaction proper and surrogation
Authors: Zúñiga Fernando 
Published: September 2014

The semantic role of beneficiary is usually conceptualized in very general terms, typically without an intensive definition of what can constitute a benefit in the particular construction under study. Among those accounts that have proposed to discuss benefaction as related to the notion(s) of surrogation, substituting, and/or deputing, Kittilä (2005) proposes a distinction between recipients, beneficiaries, and recipient-beneficiaries based on the binary features [reception] and [substitutive benefaction]; the recipient includes only reception (and the beneficiary only substitutive benefaction), whereas both features are relevant with recipient-beneficiaries.This paper proposes an alternative account (i) by defining benefaction proper in terms of a prototype related to possession (and thereby to reception) and a periphery, and (ii) by defining surrogation as a separate notion that can, but need not, coalesce with benefaction proper. Thus, the beneficiaries’ condition improves because they are relieved from having to carry out a given action themselves.
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Authors: Ahn Tae-Hyuk , Chai Juanjuan , Pan Chongle 
Published: September 2014

Abstract
Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis.
Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. The algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains.
Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org .
Contact: panc@ornl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
IL-10 enhances the phenotype of M2 macrophages induced by IL-4 and confers the ability to increase eosinophil migration
Authors: Makita Naoyuki , Hizukuri Yoshiyuki , Yamashiro Kyoko , Murakawa Masao , Hayashi Yasuhiro 
Published: September 2014

Abstract
M2 macrophages have been subdivided into subtypes such as IL-4-induced M2a and IL-10-induced M2c in vitro. Although it was reported that IL-10 stimulation leads to an increase in IL-4Rα, the effect of IL-4 and IL-10 in combination with macrophage subtype differentiation remains unclear. Thus, we sought to clarify whether IL-10 enhanced the M2 phenotype induced by IL-4. In this study, we showed that IL-10 enhanced IL-4Rα expression in M-CSF-induced bone marrow-derived macrophages (BMDMs). Global gene expression analysis of M2 macrophages induced by IL-4, IL-10 or IL-4 + IL-10 showed that IL-10 enhanced gene expression of M2a markers induced by IL-4 in M-CSF-induced BMDMs. Moreover, IL-4 and IL-10 synergistically induced CCL24 (Eotaxin-2) production. Enhanced CCL24 expression was also observed in GM-CSF-induced BMDMs and zymosan-elicited, thioglycolate-elicited and naive peritoneal macrophages. CCL24 is a CCR3 agonist and an eosinophil chemoattractant. In vitro, IL-4 + IL-10-stimulated macrophages produced a large amount of CCL24 and increased eosinophil migration, which was inhibited by anti-CCL24 antibody. We also showed that IL-4 + IL-10-stimulated (but not IL-4 or IL-10 alone) macrophages transferred into the peritoneum of C57BL/6J mice increased eosinophil infiltration into the peritoneal cavity. These results demonstrate that IL-4 + IL-10-simulated macrophages have enhanced M2a macrophage-related gene expression, CCL24 production and eosinophil infiltration-inducing activity, thereby suggesting their contribution to eosinophil-related diseases.
Prognostic Scoring Models for Patients Undergoing Sorafenib Treatment for Advanced Stage Hepatocellular Carcinoma in Real-Life Practice
Authors: Choi Gwang Hyeon , Han Seungbong , Shim Ju Hyun , Ryu Min-Hee , Ryoo Baek-Yeol , Kang Yoon-Koo , Kim Kang Mo , Lim Young-Suk , Lee Han Chu 
Published: September 2014

Background:
The purpose of this study was to build prognostic models capable of estimating the outcomes of individual sorafenib-treated advanced stage hepatocellular carcinoma (HCC) patients based on specific patient and tumor factors.

Methods:
A parametric model for time-to-event data was used to construct scoring systems based on the intent-to-treat data set from 480 sorafenib-treated patients with advanced stage HCC: 356 for derivation and 124 for validation. Clinical parameters included in the models were based on importance variable scores generated by a random forest approach and bootstrap resampling. The model’s accuracy was internally and externally assessed using the time-dependent C-index of discrimination and a Hosmer-Lemeshow type test for calibration.

Results:
The models generated for time-to-progression and overall survival based on Child-Pugh score, serum α-fetoprotein, tumor morphology, and vascular invasion and/or extrahepatic involvement had good calibration and discrimination abilities, with C-indexes of 0.669 (3 mo progression) and 0.809 (6 mo survival), respectively. External validation results also showed that these models performed well in terms of goodness-of-fit and discrimination (C-index: 0.746 for 3 mo progression and 0.875 for 6 mo survival). Receiver operating characteristic curve analysis in the validation patients indicated that these models have better predictive power than Child-Pugh scores (C-index: 0.686 for 3 mo progression and 0.777 for 6 mo survival).

Conclusions:
The prognostic tools developed to quantify the potential outcomes for progression and survival expected from sorafenib treatment can serve as useful clinical aids in personalized decision making regarding treatment in advanced stage HCC patients.
Hepatocellular Carcinoma Management in Nonalcoholic Fatty Liver Disease Patients
Authors: Kikuchi Luciana , Oliveira Claudia P. , Alvares-da-Silva Mario R. , Tani Claudia M. , Diniz Marcio A. , Stefano Jose T. , Chagas Aline L. , Alencar Regiane S.S.M. , Vezozzo Denise C.P. , Santos Gilmar R. , Campos Priscila B. , Alves Venancio AF. , Ratziu Vlad , Carrilho Flair J. 
Published: September 2014

Background/Aims:
Nonalcoholic fatty liver disease (NAFLD) has emerged as an important cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma (HCC). The Barcelona Clinic Liver Cancer (BCLC) system is the preferred staging system to evaluate patients with HCC and links prognosis assessment with treatment recommendation. The aim of this retrospective study was to evaluate whether the BCLC staging system and its treatment algorithm are suitable for patients with HCC arising from NAFLD.

Methods:
Forty-two patients with HCC related to either to NAFLD or cryptogenic cirrhosis were retrieved retrospectively from 2 centers in Brazil. Patients were classified according to BCLC staging system. If the proposed HCC therapy could not be applied, the case was considered to represent deviations from the recommended BCLC guideline. Causes of treatment deviations were investigated.

Results:
There were 4 patients without evidence of cirrhosis according to liver biopsy and/or clinical evaluation. One (2%), 21 (50%), 10 (24%), 5 (12%), and 5 patients (12%) were classified initially to the very early (0), early (A), intermediate (B), advanced (C), and terminal (D) BCLC stages, respectively. Thirty-five patients (83%) were treated according to BCLC recommendations. There were 3 cases (of 5) of protocol deviation in BCLC C patients. The 1- and 2-year overall survival rates were 81% and 66%, respectively.

Conclusions:
The BCLC system is applied in most cases of NAFLD-related HCC cases. Deviation of BCLC is found more frequently in BCLC C stage patients.
Self-initiated expatriates
Authors: Selmer Jan , Lauring Jakob 
Published: September 2014

Purpose
– As it has been suggested that adult third-culture kids may be more culturally adaptable than others, they have been labelled “the ideal” expatriates. The purpose of this paper is to explore the adjustment of self-initiated expatriate academics in Hong Kong, comparing adult third-culture kids with adult mono-culture kids.

Design/methodology/approach
– The authors use survey results from 267 self-initiated expatriate academics in Hong Kong.

Findings
– Exploratory results show that adult third-culture kids had a higher extent of general adjustment. No significant results were found in relation to interaction adjustment and job adjustment. The authors also found that recent expatriate experiences generally had a positive association with the adjustment of adult mono-culture kids, but this association only existed in terms of general adjustment for adult third-culture kids.

Originality/value
– Once corroborated by further studies, this exploratory research project may contribute to the understanding of the adjustment of adult third-culture kids as well as the role of experience and multicultural abilities. Few, if any, prior studies, have examined adjustment of this group of self-initiated expatriates.
Parameter identification for a low-density-foam material model using numerical optimisation procedures
Authors: Škrlec Andrej , Klemenc Jernej , Fajdiga Matija 
Published: September 2014

Purpose
– In the event of a crash involving a car, its seats, together with their backrests and head supports, ensure the safety of the passengers. The filling material used for such a car seat is normally made of polyurethane foam. To simulate the behaviour of the seat assembly during a crash, the material characteristics of the seat-filling foam should be appropriately modelled. The purpose of this paper is to present a method, with which the proper parameter values of the selected material model for the seat-filling foam can be easily determined.

Design/methodology/approach
– In the study, an experiment with the specimen from seat-filling foam was carried out. The results from this experiment were the basis for the determination of the parameter values of the low-density-foam material model, which is often used in crash-test simulations. Two different numerical optimisation algorithms – a genetic algorithm and a gradient-descent algorithm – were coupled with LS-DYNA explicit simulations to identify the material parameters.

Findings
– The paper provides comparison of two optimisation algorithms and discusses the engineering applicability of the results.

Originality/value
– This paper presents an approach for the identification of the missing parameter values of the highly non-linear material model, if these cannot be easily determined directly from experimental data.
Numerical simulation of initial mixing of marine wastewater discharge from multiport diffusers
Authors: Xue Wanyun , Huai Wenxin , Qian Zhongdong , Yang Zhonghua , Zeng Yuhong 
Published: September 2014

Purpose
– The purpose of this paper is to examine the initial mixing of wastewater discharged from submerged outfall diffusers and the influence of port configurations on wastewater distribution based on computational results.

Design/methodology/approach
– Marine wastewater discharges from multiport diffusers are investigated by numerically solving three-dimensional and uncompressible two-phase flow fields. A mixture model simulates this flow and the standard k-e model to resolve flow turbulence; inter-phase interactions were described in terms of relative slip velocity between phases. Computations were performed for two values of the port spacings s/H with different current Froude numbers F.

Findings
– Computational results compared well with previous laboratory measurements. Numerical results reveal that for both the closely spaced (s/H=0.21) and widely spaced (s/H=3.0) ports, the normalized dilution Sn becomes independent of F; further, the length of the near field xn and the spreading layer thickness hn are functions of F. For the closely spaced ports, the wastewater discharge behaves like a line plume, the Coanda effect is obvious, quasi-bifurcation is present, horseshoe structures of the jets in the planes are rapidly produced and then squashed and elongated, and the jet trajectories based on maximum velocity precede those based on maximum concentration. For the widely spaced ports, the wastewater discharge behaves like a point plume, the Coanda effect is not obvious, bifurcation is present, horseshoe structures of the jets in the planes are gradually produced and become ellipses, and the jet trajectories based on maximum velocity are similar to those based on maximum concentration.

Originality/value
– Semi-empirical equations are presented to predict major near field characteristics. These provide guidance for designing multiport diffusers and assessing environmental impact.
A comparative study of the stochastic simulation methods applied in structural health monitoring
Authors: Zhang Yanhui , Yang Wenyu 
Published: September 2014

Purpose
– The purpose of this paper is to discuss the characteristics of several stochastic simulation methods applied in computation issue of structure health monitoring (SHM).

Design/methodology/approach
– On the basis of the previous studies, this research focusses on four promising methods: transitional Markov chain Monte Carlo (TMCMC), slice sampling, slice-Metropolis-Hasting (M-H), and TMCMC-slice algorithm. The slice-M-H is the improved slice sampling algorithm, and the TMCMC-slice is the improved TMCMC algorithm. The performances of the parameters samples generated by these four algorithms are evaluated using two examples: one is the numerical example of a cantilever plate; another is the plate experiment simulating one part of the mechanical structure.

Findings
– Both the numerical example and experiment show that, identification accuracy of slice-M-H is higher than that of slice sampling; and the identification accuracy of TMCMC-slice is higher than that of TMCMC. In general, the identification accuracy of the methods based on slice (slice sampling and slice-M-H) is higher than that of the methods based on TMCMC (TMCMC and TMCMC-slice).

Originality/value
– The stochastic simulation methods evaluated in this paper are mainly two categories of representative methods: one introduces the intermediate probability density functions, and another one is the auxiliary variable approach. This paper provides important references about the stochastic simulation methods to solve the ill-conditioned computation issue, which is commonly encountered in SHM.
On a fractional step-splitting scheme for the Cahn-Hilliard equation
Authors: Aderogba A.A. , Chapwanya M. , Djoko J.K. 
Published: September 2014

Purpose
– For a partial differential equation with a fourth-order derivative such as the Cahn-Hilliard equation, it is always a challenge to design numerical schemes that can handle the restrictive time step introduced by this higher order term. The purpose of this paper is to employ a fractional splitting method to isolate the convective, the nonlinear second-order and the fourth-order differential terms.

Design/methodology/approach
– The full equation is then solved by consistent schemes for each differential term independently. In addition to validating the second-order accuracy, the authors will demonstrate the efficiency of the proposed method by validating the dissipation of the Ginzberg-Lindau energy and the coarsening properties of the solution.

Findings
– The scheme is second-order accuracy, the authors will demonstrate the efficiency of the proposed method by validating the dissipation of the Ginzberg-Lindau energy and the coarsening properties of the solution.

Originality/value
– The authors believe that this is the first time the equation is handled numerically using the fractional step method. Apart from the fact that the fractional step method substantially reduces computational time, it has the advantage of simplifying a complex process efficiently. This method permits the treatment of each segment of the original equation separately and piece them together, in a way that will be explained shortly, without destroying the properties of the equation.
Elastic wave propagation and time history analysis in FG nanocomposite cylinders reinforced by carbon nanotubes using a hybrid mesh-free method
Authors: Mahmoud Hosseini Seyed 
Published: September 2014

Purpose
– The purpose of this paper is to propose a hybrid mesh-free method based on generalized finite difference (GFD) and Newmark finite difference methods to study the elastic wave propagation in functionally graded nanocomposite reinforced by carbon nanotubes (FGNRCN). The presented hybrid mesh-free method is applied for a thick hollow cylinder, which is made of FGNRCN and excited by various mechanical shock loadings.

Design/methodology/approach
– The FG nanocomposite cylinder is assumed to be under shock loading. The elastic wave propagation is obtained and studied for various nonlinear grading patterns and distributions of the aligned carbon nanotubes. The distribution of carbon naotubes in FG nanocomposite are considered to vary as nonlinear function of radius, which varies with various nonlinear grading patterns continuously through radial direction. The effective material properties of functionally graded carbon nanotube are estimated using a micro-mechanical model.

Findings
– The mechanical shock analysis of FGNRCN thick hollow cylinder is carried out and the dynamic behavior of displacement field and the time history of radial displacement are obtained for various grading patterns. An effective hybrid mesh-free method based on GFD and Newmark finite difference methods is presented to calculate the average velocity of elastic wave propagation in FGNRCN. The average velocity of elastic wave propagation is obtained for various grading patterns and various kinds of volume fraction. The effects of some parameters on average velocity of elastic wave propagation are obtained and studied in detail.

Originality/value
– The calculation of elastic radial wave propagation in a FGNRCN thick hollow cylinder is presented using a hybrid mesh-free method. The effects of some parameters on wave propagation such as various grading patterns of distribution of carbon nanotubes are studied in details.
Revisiting the “two communities” metaphor of research utilisation
Authors: Newman Joshua 
Published: September 2014

Purpose– The “two communities” metaphor for the relationship between policy and academia is inconsistent with empirical evidence that shows that a sizeable minority of public servants use academic research in their policy-related work. The purpose of this paper is to investigate the two communities metaphor by comparing the personal and professional characteristics of Australian public servants who claim to use research in their policy work with the characteristics of those who claim not to use research.Design/methodology/approach– Using data from a survey of 2,084 public servants from the state and federal levels in Australia carried out from 2011 to 2013, tests of statistical significance were conducted for the relationship between some personal and professional characteristics (e.g. gender, age, work experience) and the claim that research is used in policy-related work.Findings– The “two communities” metaphor is not an accurate description of the relationship between policy and academia. In reality, public servants who claim to use academic research in their policy work are more likely to have much in common with academics, including having postgraduate degrees and work experience in the university sector.Research limitations/implications– Rather than existing as isolated solitudes, the findings in this paper suggest that the policy and academic communities possess links that can encourage the use of research in policy making.Originality/value– The findings presented in this paper are especially important for the evidence-based policy movement, which emphasises the value of the use of research evidence in the creation of public policy.