bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding
Authors: Keilwagen Jens , Posch Stefan , Grau Jan 
Published: December 2017

Computational prediction of cell type-specific, in-vivo transcription factor binding sites is still one of the central challenges in regulatory genomics, and a variety of approaches has been proposed for this purpose.Here, we present our approach that earned a shared first rank in the “ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge” in 2017. This approach employs features derived from chromatin accessibility, binding motifs, gene expression, genomic sequence and annotation to train classifiers using a supervised, discriminative learning principle. Two further key aspects of this approach are learning classifier parameters in an iterative training procedure that successively adds additional negative examples to the training set, and creating an ensemble prediction by averaging over classifiers obtained for different training cell types.In post-challenge analyses, we benchmark the influence of different feature sets and find that chromatin accessiblity and binding motifs are sufficient to yield state-of-the-art performance for in-vivo binding site predictions. We also show that the iterative training procedure and the ensemble prediction are pivotal for the final prediction performance.To make predictions of this approach readily accessible, we predict 682 peak lists for a total of 31 transcription factors in 22 primary cell types and tissues, which are available for download at https://www.synapse.org/#!Synapse:syn11526239, and we demonstrate that these may help to yield biological conclusions. Finally, we provide a user-friendly version of our approach as open source software at http://jstacs.de/index.php/Catchitt.Contactgrau@informatik.uni-halle.de
Network analysis of mass spectrometry imaging data from colorectal cancer identifies key metabolites common to metastatic development
Authors: Inglese Paolo , Strittmatter Nicole , Doria Luisa , Mroz Anna , Speller Abigail , Poynter Liam , Dannhorn Andreas , Kudo Hiromi , Mirnezami Reza , Goldin Robert D , Nicholson Jeremy K , Takats Zoltan , Glen Robert C 
Published: December 2017

AbstractA deeper understanding of inter-tumor and intra-tumor heterogeneity is a critical factor for the advancement of next generation strategies against cancer. The heterogeneous morphology exhibited by solid tumors is mirrored by their metabolic heterogeneity. Defining the basic biological mechanisms that underlie tumor cell variability will be fundamental to the development of personalized cancer treatments. Variability in the molecular signatures found in local regions of cancer tissues can be captured through an untargeted analysis of their metabolic constituents. Here we demonstrate that DESI mass spectrometry imaging (MSI) combined with network analysis can provide detailed insight into the metabolic heterogeneity of colorectal cancer (CRC). We show that network modules capture signatures which differentiate tumor metabolism in the core and in the surrounding region. Moreover, module preservation analysis of network modules between patients with and without metastatic recurrence explains the inter-subject metabolic differences associated with diverse clinical outcomes such as metastatic recurrence.SignificanceNetwork analysis of DESI-MSI data from CRC human tissue reveals clinically relevant co-expression ion patterns associated with metastatic susceptibility. This delineates a more complex picture of tumor heterogeneity than conventional hard segmentation algorithms. Using tissue sections from central regions and at a distance from the tumor center, ion co-expression patterns reveal common features among patients who developed metastases (up of > 5 years) not preserved in patients who did not develop metastases. This offers insight into the nature of the complex molecular interactions associated with cancer recurrence. Presently, predicting CRC relapse is challenging, and histopathologically like-for-like cancers frequently manifest widely varying metastatic tendencies. Thus, the methodology introduced here more robustly defines the risk of metastases based on tumor biochemical heterogeneity.Author contributionsP.I., Z.T., R.C.G.: designed the study, developed the workflow, analyzed the data, interpreted the results, wrote the paper; N.S. collected the MS, performed the H…E staining, wrote the paper; L.D.: interpreted the results, wrote the paper; A.M.: collected the MS; A.S.: histological assessment; L.P.: collected the tissue specimens and clinical metadata; A.D.: collected the MS; H.K.: performed the H…E staining; R.M.: collected the tissue specimens and clinical metadata. R.G.: histological assessment; J.K.N: designed the study, edited the paper.
Evolutionary plasticity in the innate immune function of Akirin
Authors: Polanowska Jolanta , Chen Jia-Xuan , Soulé Julien , Omi Shizue , Belougne Jerome , Taffoni Clara , Pujol Nathalie , Selbach Matthias , Zugasti Olivier , Ewbank Jonathan J. 
Published: December 2017

ABSTRACTEukaryotic gene expression requires the coordinated action of transcription factors, chromatin remodelling complexes and RNA polymerase. The conserved nuclear protein Akirin plays a central role in immune gene expression in insects and mammals, linking the SWI/SNF chromatin-remodelling complex with the transcription factor NFκB. Although nematodes lack NFκB, Akirin is also indispensable for the expression of defence genes in the epidermis of Caenorhabditis elegans following natural fungal infection. Through a combination of reverse genetics and biochemistry, we discovered that in C. elegans Akirin has conserved its role of bridging chromatin-remodellers and transcription factors, but that the identity of its functional partners is different since it forms a physical complex with NuRD proteins and the POU-class transcription factor CEH-18. In addition to providing a substantial step forward in our understanding of innate immune gene regulation in C. elegans, our results give insight into the molecular evolution of lineage-specific signalling pathways.
Shell Nigeria’s Global Memorandum of Understanding and corporate-community accountability relations
Authors: Egbon Osamuyimen , Idemudia Uwafiokun , Amaeshi Kenneth 
Published: December 2017

PurposeThe purpose of this paper is to examine whether Shell Nigeria’s Global Memorandum of Understanding (GMoU) promotes corporate-community accountability as a basis for fostering sustainable community development in the Niger Delta.Design/methodology/approachShell Nigeria’s GMoU stand-alone reports were analysed through the lenses of accountability and transparency theoretical frameworks to explore the extent to which GMoU, as a corporate social responsibility (CSR) initiative, is dialogically embedded and practised. Meaning-oriented content analysis was deductively used to isolate pertinent themes and generate findings from the background theoretical literature.FindingsThe authors find that Shell discursively appropriates the meaning of accountability and transparency in a manner that allows it to maintain its social legitimacy and the asymmetric power relations between itself and host communities whilst restricting communities’ agency to hold it accountable. Shell does this by interpreting the notion of participation restrictively, selectively deploying the concept of transparency and accountability and subtly exerting excessive control over the GMoU. Thus, the GMoU’s potential to contribute to sustainable community development and positive corporate-community relation is unlikely tenable.Originality/valueAccountability and transparency are core and critical to corporate-community relations and for achieving community development CSR objectives, but are often taken for granted or ignored in the CSR literature on the Niger Delta of Nigeria. This paper addresses this gap in the literature by using accountability and transparency lenses to unpick GMoU model and contribute to studies on CSR practices by oil multinational corporations (MNCs) in developing countries. Indeed, the use of these lenses to explore CSR process offers new insights as to why CSR practices have failed to contribute to sustainable community development despite increased community spending by oil MNCs.
Transparency fallacy
Authors: Gold Stefan , Heikkurinen Pasi 
Published: December 2017

PurposeThe purpose of this paper is to focus on the research question of how stakeholder claims for transparency work as a means to support responsibility in the international supply chain.Design/methodology/approachThis theoretical study analyses the relationship between stakeholder claims for corporate transparency and responsible business in the global context, and develops a conceptual model for further theoretical and empirical work.FindingsThe study finds that the call for corporate transparency is insufficient as a means to increase responsibility within international supply chains. The erroneous belief that stakeholder claims for transparency will lead to responsible behaviour is identified as the “transparency fallacy”. The fallacy emerges from the denial of opacity in organisations and the blindness to the conditions of international supply chains (including complexity, distance, and resistance) that work against attempts to increase transparency.Research limitations/implicationsAcknowledging the limits of the transparency mechanism in both management theory and practice is necessary in order to advance responsible business in the international arena. Being conceptual in nature, the generic limitations of the type of research apply.Practical implicationsWhile acknowledging opacity, corporate managers and stakeholders should focus on changing the supply chain conditions to support responsible behaviour. This includes reducing complexity, distance, and resistance in the supply network.Originality/valueThis study contests the commonly assumed link between corporate transparency and responsibility, and sheds light on the limits and unintended consequences of stakeholder attempts to impose transparency on business organisations.
Practice variation in Big-4 transparency reports
Authors: Girdhar Sakshi , Jeppesen Kim K. 
Published: December 2017

PurposeThe purpose of this paper is to examine the transparency reports published by the Big-4 public accounting firms in the UK, Germany and Denmark to understand the determinants of their content within the networks of big accounting firms.Design/methodology/approachThe study draws on a qualitative research approach, in which the content of transparency reports is analyzed and semi-structured interviews are conducted with key people from the Big-4 firms who are responsible for developing the transparency reports.FindingsThe findings show that the content of transparency reports is inconsistent and the transparency reporting practice is not uniform within the Big-4 networks. Differences were found in the way in which the transparency reporting practices are coordinated globally by the respective central governing bodies of the Big-4. The content of the transparency reports is particularly influenced by the national institutional environment in which the Big-4 member firms operate, thus leading them to introduce practice variation and resulting in cross-national differences.Practical implicationsThe study results have important implications for standard setters, regulators and practitioners, as the research provides insights into the variation taking place within the common regulatory frame.Originality/valueThis is the first study to analyze how transparency reporting practices are developed within the networks of Big-4 firms, thereby influencing the content of transparency reports.
Semi-empirical heat transfer correlations for turbulent tube flow of liquid metals
Authors: Taler Dawid 
Published: December 2017

Purpose
The purpose of this paper is to develop new semi-empirical heat transfer correlations for turbulent flow of liquid metals in the tubes, and then to compare these correlations with the experimental data. The Prandtl and Reynolds numbers can vary in the ranges: 0.0001 ≤ Pr ≤ 0.1 and 3000 ≤ Re ≤ 106.

Design/methodology/approach
The energy conservation equation averaged by Reynolds was integrated using the universal velocity profile determined experimentally by Reichardt for the turbulent tube flow and four different models for the turbulent Prandtl number. Turbulent heat transfer in the circular tube was analyzed for a constant heat flux at the inner surface. Some constants in different models for the turbulent Prandtl number were adjusted to obtain good agreement between calculated and experimentally obtained Nusselt numbers. Subsequently, new correlations for the Nusselt number as a function of a Peclet number was proposed for different models of the turbulent Prandtl number.

Findings
The inclusion of turbulent Prandtl number greater than one and the experimentally determined velocity profile of the fluid in the tube while solving the energy conservation equation improved the compatibility of calculated Nusselt numbers, with Nusselt numbers determined experimentally. The correlations proposed in the paper have a sound theoretical basis and give Nusselt number values that are in good agreement with the experimental data.

Research limitations/implications
Heat transfer correlations proposed in this paper were derived assuming a constant heat flux at the inner surface of the tube. However, they can also be used for a constant wall temperature, as for the turbulent flow (Re > 3,000), the relative difference between the Nusselt number for uniform wall heat flux and uniform wall temperature is very low.

Originality/value
Unified, systematic approach to derive correlations for the Nusselt number for liquid metals was proposed in the paper. The Nusselt number was obtained from the solution of the energy conservation equation using the universal velocity profile and eddy diffusivity determined experimentally, and various models for the turbulent Prandtl number. Four different relationships for the Nusselt number proposed in the paper were compared with the experimental data.
Identification of three-dimensional transient temperature fields in thick-walled elements using the inverse method
Authors: Jaremkiewicz Magdalena 
Published: December 2017

Purpose
The purpose of this paper is to propose a method of determining the transient temperature of the inner surface of thick-walled elements. The method can be used to determine thermal stresses in pressure elements.

Design/methodology/approach
An inverse marching method is proposed to determine the transient temperature of the thick-walled element inner surface with high accuracy.

Findings
Initially, the inverse method was validated computationally. The comparison between the temperatures obtained from the solution for the direct heat conduction problem and the results obtained by means of the proposed inverse method is very satisfactory. Subsequently, the presented method was validated using experimental data. The results obtained from the inverse calculations also gave good results.

Originality/value
The advantage of the method is the possibility of determining the heat transfer coefficient at a point on the exposed surface based on the local temperature distribution measured on the insulated outer surface. The heat transfer coefficient determined experimentally can be used to calculate thermal stresses in elements with a complex shape. The proposed method can be used in online computer systems to monitor temperature and thermal stresses in thick-walled pressure components because the computing time is very short.
Effectiveness in incorporating Brownian and thermophoresis effects in modelling convective flow of water-Al2O3 nanoparticles
Authors: Saghir M. Ziad , Mohamed Abdulmajeed 
Published: December 2017

Purpose
Nanofluids are widely used in heat transfer phenomena owing to the higher rate of heat removal as compared to their base fluids. Nanoparticle’s motion in nanofluids is analysed by slip mechanisms that consider physical properties, which can be found in literature. It is assumed that among few, only Brownian motion and thermophoresis affect the slip mechanism to produce a relative velocity between the nanoparticles and the base fluid. The purpose of this paper is to study the effects of Brownian motion and thermophoresis in a square cavity by considering it pure fluid as well as porous cavity.

Design/methodology/approach
A finite element method is used to solve the flow porous equations together with the heat transfer equation and the mass transfer equation numerically. The heat and mass transfer equations were modified to take into consideration the Brownian motion as well as the thermophoresis effect.

Findings
A negligible amount of Brownian motion and thermophoresis effect has been found by considering 1 to 3 Vol.% of aluminium oxide as nanoparticles suspended in base fluid of water.

Practical implications
This study has provided an interesting insight into the importance of Brownian motion as well as the thermophoresis effect in heat enhancement.

Originality/value
The present study is believed to be an interesting and original contribution on nanofluid thermal behaviours.
An efficient solving method for nonlinear convection diffusion equation
Authors: Cui Xia , Yuan GuangWei , Shen ZhiJun 
Published: December 2017

Purpose
This paper aims to provide a well-behaved nonlinear scheme and accelerating iteration for the nonlinear convection diffusion equation with fundamental properties illustrated.

Design/methodology/approach
A nonlinear finite difference scheme is studied with fully implicit (FI) discretization used to acquire accurate simulation. A Picard–Newton (PN) iteration with a quadratic convergent ratio is designed to realize fast solution. Theoretical analysis is performed using the discrete function analysis technique. By adopting a novel induction hypothesis reasoning technique, the L∞ (H1) convergence of the scheme is proved despite the difficulty because of the combination of conservative diffusion and convection operator. Other properties are established consequently. Furthermore, the algorithm is extended from first-order temporal accuracy to second-order temporal accuracy.

Findings
Theoretical analysis shows that each of the two FI schemes is stable, its solution exists uniquely and has second-order spatial and first/second-order temporal accuracy. The corresponding PN iteration has the same order of accuracy and quadratic convergent speed. Numerical tests verify the conclusions and demonstrate the high accuracy and efficiency of the algorithms. Remarkable acceleration is gained.

Practical implications
The numerical method provides theoretical and technical support to accelerate resolving convection diffusion, non-equilibrium radiation diffusion and radiation transport problems.

Originality/value
The FI schemes and iterations for the convection diffusion problem are proposed with their properties rigorously analyzed. The induction hypothesis reasoning method here differs with those for linearization schemes and is applicable to other nonlinear problems.
A theoretical, numerical and experimental verification of the Reynolds thermal transpiration law
Authors: Ziółkowski Paweł , Badur Janusz 
Published: December 2017

Purpose
The purpose of this paper is the theoretical presentation of tensorial formulation with surface mobility forces and numerical verification of Reynolds thermal transpiration law in a contemporary experiment with nanoflow.

Design/methodology/approach
The velocity profiles in a single microchannel are calculated by solving the momentum equations and using thermal transpiration force as the boundary conditions. The mass flow rate and pressure of unstationary thermal transpiration modeling of the benchmark experiment has been achieved by the implementation of the thermal transpiration mobility force closure for the thermal momentum accommodation coefficient.

Findings
An original and easy-to-implement method has been developed to numerically prove that at the final equilibrium, i.e. zero-flow state, there is a connection between the Poiseuille flow in the center of channel and counter thermal transpiration flow on the surface. The numerical implementation of the Reynolds model of thermal transpiration has been performed, and its usefulness for the description of the benchmark experiment has been verified.

Research limitations/implications
The simplified procedure requires the measurement or assumption of the helium-glass slip length.

Practical implications
The procedure can be very useful in the design of micro-electro-mechanical systems and nano-electro-mechanical systems, especially for accommodation pumping.

Originality/value
The paper discussed possible constitutive equations in the transpiration shell-like layer. The new approach can be helpful for modeling phenomena occurring at a fluid–solid phase interface at the micro- and nanoscales.
Hybrid atomistic-continuum multiscale method for fluid flow with density variation in microchannels
Authors: Vu Van Huyen , Trouette Benoît , TO Quy Dong , Chénier Eric 
Published: December 2017

Purpose
This paper aims to extend the hybrid atomistic-continuum multiscale method developed by Vu et al. (2016) to study the gas flow problems in long microchannels involving density variations.

Design/methodology/approach
The simulation domain is decomposed into three regions: the bulk where the continuous Navier–Stokes and energy equations are solved, the neighbourhood of the wall simulated by molecular dynamics and the overlap region which connects the macroscopic variables (density, velocity and temperature) between the two former regions. For the simulation of long micro/nanochannels, a strategy with multiple molecular blocks all along the fluid/solid interface is adopted to capture accurately the macroscopic velocity and temperature variations.

Findings
The validity of the hybrid method is shown by comparisons with a simplified analytical model in the molecular region. Applications to compressible and condensation problems are also presented, and the results are discussed.

Originality/value
The hybrid method proposed in this paper allows cost-effective computer simulations of large-scale problems with an accurate modelling of the transfers at small scales (velocity slip, temperature jump, thin condensation films, etc.).
Domestic water demand forecasting in the Yellow River basin under changing environment
Authors: Wang Xiao-jun , Zhang Jian-yun , Shahid Shamsuddin , Yu Lang , Xie Chen , Wang Bing-xuan , Zhang Xu 
Published: December 2017

Purpose
The purpose of this paper is to develop a statistical-based model to forecast future domestic water demand in the context of climate change, population growth and technological development in Yellow River.

Design/methodology/approach
The model is developed through the analysis of the effects of climate variables and population on domestic water use in eight sub-basins of the Yellow River. The model is then used to forecast water demand under different environment change scenarios.

Findings
The model projected an increase in domestic water demand in the Yellow River basin in the range of 67.85 × 108 to 62.20 × 108 m3 in year 2020 and between 73.32 × 108 and 89.27 × 108 m3 in year 2030. The general circulation model Beijing Normal University-Earth System Model (BNU-ESM) predicted the highest increase in water demand in both 2020 and 2030, while Centre National de Recherches Meteorologiques Climate Model v.5 (CNRM-CM5) and Model for Interdisciplinary Research on Climate- Earth System (MIROC-ESM) projected the lowest increase in demand in 2020 and 2030, respectively. The fastest growth in water demand is found in the region where water demand is already very high, which may cause serious water shortage and conflicts among water users.

Originality/value
The simple regression-based domestic water demand model proposed in the study can be used for rapid evaluation of possible changes in domestic water demand due to environmental changes to aid in adaptation and mitigation planning.