bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced de-novo mutation in survival outliers of glioblastoma
Authors: Hwang Taeyoung , Mathios Dimitrios , McDonald Kerrie L , Daris Irene , Park Sung-Hye , Burger Peter C , Kim Sojin , Dho Yun-Sik , Carolyn Hruban , Bettegowda Chetan , Shin Joo Heon , Lim Michael , Park Chul-Kee 
Published: April 2018

AbstractThe study of survival outliers of glioblastoma (GBM) can have important implications on gliomagenesis as well as in the identification of ways to alter clinical course on this almost uniformly lethal cancer type. However, current studied epigenetic and genetic signatures of the GBM outliers have failed to identify unifying criteria to characterize this unique group of patients. In this study, we profiled the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma and performed comprehensive enrichment analyses with genomic and epigenomic signatures. We found that the genome of long-term survivors in glioblastoma is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. The hypomethylation pattern at the region distant from CGI is associated with lower rates of de novo mutations while the hypermethylation at CGIs correlates with transcriptional downregulation of genes involved in cancer progression pathways. These results extend our understanding of DNA methylation of survival outliers in glioblastoma in a genome-wide level, and provide insight on the potential impact of DNA hypomethylation in cancer genome.
UROPA GUI: A web platform for genomic region annotation
Authors: Schultheis Hendrik , Preussner Jens , Fust Annika , Bentsen Mette , Kuenne Carsten , Looso Mario 
Published: April 2018

AbstractThe annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with considerable impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which improves upon the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive web-based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively.Availability and ImplementationThe open source UROPA GUI server was implemented in R Shiny and Python and is available from http://loosolab.mpi-bn.mpg.de. The source code of our App can be downloaded at https://github.molgen.mpg.de/loosolab/UROPA_GUI under the MIT license.
Timing Determines Tuning: a Rapid Spatiotemporal Transformation in Superior Colliculus Neurons During Reactive Gaze Shifts
Authors: Sadeh Morteza , Sajad Amirsaman , Wang Hongying , Yan Xiaogang , Crawford John Douglas 
Published: April 2018

AbstractGaze saccades –rapid shifts of the eyes and head toward a goal— have provided fundamental insights into the neural control of movement. For example, it has been shown that the superior colliculus (SC) transforms a visual target (T) code to future gaze (G) location commands after a memory delay. However, this transformation has not been observed in ‘reactive’ saccades made directly to a stimulus, so its contribution to normal gaze behavior is unclear. Here, we tested this using a quantitative measure of the spatial continuum between T and G coding based on variable gaze errors. We demonstrate that a rapid T-G transformation occurs between SC visual and motor responses during reactive saccades, evenwithinvisuomotor cells, with a continuous spatiotemporal shift in coding occurring in cell types (visual, visuomotor, motor). We further show that the primary determinant of this spatial code was not the intrinsic visual-motor index of different cells or populations, but rather thetimingof the response inallcells. These results suggest that the SC provides a rapid spatiotemporal transformation for normal gaze saccades, that its motor responses contribute to variable gaze errors, and that those errors arise from a noisy spatiotemporal transformation involving all SC neurons.Significance StatementOculomotor studies have demonstrated visuomotor transformations in structures like the superior colliculus with the use of trained behavioral manipulations, like the memory delay and antisaccades tasks, but it is not known how this happens during normal saccades. Here, using a spatiotemporal model fitting method based on endogenous gaze errors in ‘reactive’ gaze saccades, we show that the superior colliculus provides a rapid spatiotemporal transformation from target to gaze coding that involves visual, visuomotor, and motor neurons. This technique demonstrates that SC spatial codes are not fixed, and may provide a quantitative biomarker for assessing the health of sensorimotor transformations.
Evolutionary dynamics of multiple games
Authors: Venkateswaran Vandana R. , Gokhale Chaitanya S. 
Published: April 2018

AbstractEvolutionary game theory has been successful in describing phenomena from bacterial population dynamics to the evolution of social behavior. Interactions between individuals are usually captured by a single game. In reality, however, individuals take part in many interactions. Here, we include multiple games and analyze their individual and combined evolutionary dynamics. A typical assumption is that the evolutionary dynamics of individual behavior can be understood by constructing one big comprehensive interactions structure, a single big game. But if any one of the multiple games has more than two strategies, then the combined dynamics cannot be understood by looking only at individual games. Devising a method to study multiple games – where each game could have an arbitrary number of players and strategies – we provide a concise replicator equation, and analyze its resulting dynamics. Moreover, in the case of finite populations, we formulate and calculate a basic and useful property of stochasticity, fixation probability. Our results reveal that even when interactions become incredibly complex, their properties can be captured by relatively simple concepts of evolutionary game(s) theory.
The putative siderophore-interacting protein fromVibrio anguillarum: protein production, analysis, crystallization and X-ray crystallographic studies
Authors: Han Yu , Zang Kun , Liu Changshui , Li Yingjie , Ma Qingjun 
Published: April 2018

Siderophore-interacting proteins (SIPs) play an important role in iron acquisition in many bacteria. SIPs release iron from the internalized ferric siderophore complex by reducing ferric iron to ferrous iron, but how the iron is reduced is not well understood. Here, asipgene was identified in the genome ofVibrio anguillarum775. To further understand the catalytic mechanism of the protein, the SIP was overexpressed inEscherichia coliRosetta (DE3) cells, purified and crystallized for X-ray diffraction analysis. The crystal diffracted to 1.113 Å resolution and belonged to space groupP21, with unit-cell parametersa = 64.63,b= 58.47,c= 70.65 Å, β = 114.19°.
An accurate method for the dynamic behavior of tensegrity structures
Authors: He Dongdong , Gao Qiang , Zhong Wanxie 
Published: April 2018

Purpose
The purpose of this paper is to propose an accurate and efficient numerical method for determining the dynamic responses of a tensegrity structure consisting of bars, which can work under both compression and tension, and cables, which cannot work under compression.

Design/methodology/approach
An accurate time-domain solution is obtained by using the precise integration method when there is no cable slackening or tightening, and the Newton–Raphson scheme is used to determine the time at which the cables tighten or slacken.

Findings
Responses of a tensegrity structure under harmonic excitations are given to demonstrate the efficiency and accuracy of the proposed method. The validation shows that the proposed method has higher accuracy and computational efficiency than the Runge–Kutta method. Because the cables of the tensegrity structure might be tense or slack, its dynamic behaviors will exhibit stable periodicity, multi-periodicity, quasi-periodicity and chaos under different amplitudes and frequencies of excitation.

Originality/value
The steady state response of a tensegrity structure can be obtained efficiently and accurately by the proposed method. Based on bifurcation theory, the Poincaré section and phase space trajectory, multi-periodic vibration, quasi-periodic vibration and chaotic vibration of the tensegrity structures are predicted accurately.
Analysis of unsteady radial forces of multistage centrifugal pump with double volute
Authors: Cui Baoling , Li Xiaodi , Rao Kun , Jia Xiaoqi , Nie Xiaolin 
Published: April 2018

Purpose
Radial vibration of horizontal centrifugal pump has a close association with radial exciting forces. The purpose of this paper is to analyze the unsteady radial force in multistage centrifugal pump with double volute in detail and investigate the relevance of static pressure, radial force and radial vibration.

Design/methodology/approach
The unsteady numerical simulation with realizable k-ε turbulence model was carried out for a multistage centrifugal pump with double volute using computational fluid dynamics codes Fluent. The performance tests were conducted by use of a closed loop system and performance curves from numerical simulation agree with that of experiment. Vibration tests were carried out by vibration probes instrumented on the bearing cover of pump near no-driven end. Fast Fourier transform was used to obtain the frequency components of radial forces on the impellers from numerical simulation, which are compared with ones of radial vibration from experiment in Y and Z direction. And the static pressure distributions in the impeller were analyzed under different flow rates.

Findings
The symmetrical double volute can effectively balance radial forces. The maximum radial force and vibration velocity appear at 0.6 Q among the three flow rates 0.6 Q, Q and 1.2 Q. The frequencies corresponding to relatively large amplitude of vibration velocities and radial forces on the impellers in Y direction are blade passing frequency of the impellers. Blade passing frequency of first-stage impeller and shaft frequency are predominating in Z direction. It indicates that the radial vibration of centrifugal pump is closely related to the unsteady radial force.

Originality/value
The unsteady radial forces of the impeller in multistage centrifugal pump with double volute were comprehensively analyzed. The radial forces should be considered to balance during the design of multistage centrifugal pump.
Market basket analysis insights to support category management
Authors: Musalem Andres , Aburto Luis , Bosch Maximo 
Published: April 2018

Purpose
This paper aims to present an approach to detect interrelations among product categories, which are then used to produce a partition of a retailer’s business into subsets of categories. The methodology also yields a segmentation of shopping trips based on the composition of each shopping basket.

Design/methodology/approach
This work uses scanner data to uncover product category interdependencies. As the number of possible relationships among them can be very large, the authors introduce an approach that generates an intuitive graphical representation of these interrelationships by using data analysis techniques available in standard statistical packages, such as multidimensional scaling and clustering.

Findings
The methodology was validated using data from a supermarket store. The analysis for that particular store revealed four groups of products categories that are often jointly purchased. The study of each of these groups allowed us to conceive the retail store under study as a small set of sub-businesses. These conclusions reinforce the strategic need for proactive coordination of marketing activities across interrelated product categories.

Research limitations/implications
The approach is sufficiently general to be applied beyond the supermarket industry. However, the empirical findings are specific to the store under analysis. In addition, the proposed methodology identifies cross-category interrelations, but not their underlying sources (e.g. marketing or non-marketing interrelations).

Practical implications
The results suggest that retailers could potentially benefit if they transition from the traditional category management approach where retailers manage product categories in isolation into a customer management approach where retailers identify, acknowledge and leverage interrelations among product categories.

Originality/value
The authors present a fast and wide-range approach to study the shopping behavior of customers, detect cross-category interrelations and segment the retailer’s business and customers based on information about their shopping baskets. Compared to existing approaches, its simplicity should facilitate its implementation by practitioners.
Entrepreneurship and project management relationships
Authors: Fonrouge Cécile , Bredillet Christophe , Fouché Charles 
Published: April 2018

Purpose
Both project investments and entrepreneurial ventures are considered powerful catalysts of economic prosperity and social progress. But these ventures and investments come with their inherent challenges and risks. Observing this situation, academics have paid close attention to the fields of entrepreneurship and project management (E&PM). Thus, for over 30 years, the two fields have witnessed remarkable developments among management and organization studies. The historical perspective reveals that these two multidisciplinary fields were built in parallel, on very distinct mindsets and cultures. The purpose of this paper is to offer a wider dialogic conversation between two distinct perspectives and related propositions: E&PM should stay separated; and E&PM should converge.

Design/methodology/approach
In order to guide the investigation of these propositions, the authors call for Luhmann and a systemic-discursive perspective of both fields discourses. Ultimately, the purpose is to contribute to the debate surrounding the following questions: are E&PM fields so far from each other, and thus, irreconcilable? And, if so, is it so good?

Findings
Finally, the authors will suggest that E&PM may stay far from each other as they do not share similar discourses and codes. This may be a good state of affairs, however, as distance generates a fruitful creative tension between them.

Originality/value
While many researchers focus on linking E&PM, arguing that they largely agree as to their underlying goal, the paper aims to offer a wider dialogical conversation between the two distinct perspectives and their related propositions: E&PM should stay separate; and E&PM should converge. In order to do so, this paper calls for a Luhmannian and a systemic-discursive perspective.
Relationship between contractual flexibility and contractor’s cooperative behavior
Authors: Song Haoyang , Zhu Fangwei , Klakegg Ole Jonny , Wang Peng 
Published: April 2018

PurposeDue to the increasing risk and uncertainty of construction projects, contractual flexibility has been considered as an effective tool to cope with emergences and to promote cooperation between owners and contractors. However, in practice, owners often failed to build an efficient cooperative relationship via contracts, resulting in a lacking of appropriate justice. Furthermore, due to a lack of available empirical research, the influence of contractual flexibility on the cooperative behavior of contractors requires further investigation. The purpose of this paper is to fill this gap by conducting empirical research from the perspective of justice perception.Design/methodology/approachA theoretical model was developed and a series of hypotheses were proposed. Then, partial least squares structural equation modeling analyses were conducted on a sample of 188 respondents.FindingsThe results show that contractual content and executing flexibility both have a positive influence on the cooperative behavior of a contractor, which was partially mediated by distribution, procedural, and interactional justice perceptions. Moreover, content flexibility has a significant impact on all three types of justice perception, and the execution of flexibility has more impact on interactional justice compared to other justice perceptions.Originality/valueThe findings contribute to an improved understanding of how contractual flexibility affects the cooperative behavior of contractors, indicating that the owner could develop a fair exchange relationship through flexible contracting and motivation of the other party.
Procurement sustainability tensions: an integrative perspective
Authors: Fayezi Sajad , Zomorrodi Maryam , Bals Lydia 
Published: April 2018

PurposeThe purpose of this paper is to unpack tensions faced by procurement professionals as part of their triple bottom line (TBL) sustainability activities. The authors take an integrative perspective based on the procurement sustainability and organizational tensions literature, as well as stakeholder and institutional theory.Design/methodology/approachThe authors use a multiple case study approach. Data are collected through multiple interviews and archival data from eight case companies in Australia.FindingsThe authors identify supply chain and company procurement sustainability tensions (PSTs) and explain their multi-level nature. The analysis also dissects the multi-stakeholder and multi-institutional environments where PSTs operate. The authors discuss such environments in terms of various temporal and spatial legitimacy contexts (LCs) that, through their assessment of institutional distance, can characterize the manifestation of PSTs.Practical implicationsThe findings are instrumental for managers to make informed decisions when dealing with PSTs, and they pave the way for paradoxical leadership given the increasing importance of simultaneous development and balancing of TBL dimensions, as evidenced in this study.Originality/valueThis is one of the first studies to empirically investigate PSTs by drawing on an integrative approach to identify PSTs, and to discern various LCs that underpin stakeholder judgments of procurement’s TBL sustainability activities.
When to integrate strategic and tactical decisions? Introduction of an asset/inventory ratio guiding fit for purpose production planning
Authors: Asmussen Jesper Normann , Kristensen Jesper , Steger-Jensen Kenn , Wæhrens Brian Vejrum 
Published: April 2018

Purpose
Significant transitions in firms (e.g. outsourcing) may impact the relative importance of production and inventory assets, affecting the hierarchical separation of planning decisions. The purpose of this paper is to contribute to planning literature by investigating how the production system and the planning environment influence the performance difference between hierarchical and monolithic planning. Further, it seeks to reduce the prevailing theory-practice gap in tactical planning.

Design/methodology/approach
Through an action research study, a monolithic model integrating tactical production planning decisions, subject to upstream supply chain constraints, with strategic investments decisions was developed, tested and implemented in a global OEM. Using the developed model and a measure of the capital cost of production assets relative to the cost of holding inventory, it is numerically examined how the production system and planning environment influence the performance of hierarchical and monolithic planning.

Findings
The research demonstrates the potential of integrating decisions and reveals significant performance differences between hierarchical and monolithic planning for firms with low capital cost relative to inventory holding cost.

Research limitations/implications
The findings suggest a fit between planning processes, the production system and planning environment. Future research should empirically validate the findings and propositions.

Originality/value
The paper combine capital investments and production planning decisions, which usually transpire at different hierarchical levels and on different time-horizons, and investigates the consequences of hierarchical separation through a real-life validated case and numerical analysis.
Hepatitis C antibody reactivity among high-risk rural women: opportunities for services and treatment in the criminal justice system
Authors: Strickland Justin C. , Staton Michele , Leukefeld Carl G. , Oser Carrie B. , Webster J. Matthew 
Published: April 2018

Purpose
The purpose of this paper is to examine the drug use and criminal justice factors related to hepatitis C virus (HCV) antibody reactivity among rural women in the USA recruited from local jails.

Design/methodology/approach
Analyses included 277 women with a history of injection drug use from three rural jails in Kentucky. Participants completed health and drug use questionnaires and received antibody testing for HCV.

Findings
The majority of women tested reactive to the HCV antibody (69 percent). Reactivity was associated with risk factors, such as unsterile needle use. Criminal justice variables, including an increased likelihood of prison incarceration, an earlier age of first arrest, and a longer incarceration history, were associated with HCV reactive tests. Participants also endorsed several barriers to seeking healthcare before entering jail that were more prevalent in women testing HCV reactive regardless of HCV status awareness before entering jail.

Originality/value
Injection and high-risk sharing practices as well as criminal justice factors were significantly associated with HCV reactivity. Future research and practice could focus on opportunities for linkages to HCV treatment during incarceration as well as during community re-entry to help overcome real or perceived treatment barriers. The current study highlights the importance of the criminal justice system as a non-traditional, real-world setting to examine drug use and related health consequences such as HCV by describing the association of high-risk drug use and criminal justice consequences with HCV among rural women recruited from local jails.
The user experience (UX) in libraries
Authors: Massis Bruce 
Published: April 2018

Purpose
The purpose of this paper is to review the library’s expanded role into its engagement with the user experience (UX).

Design/methodology/approach
Literature review and commentary on this topic that has been addressed by professionals, researchers and practitioners.

Findings
Although UX is constantly expanding its focus, in actively paying close attention to its users’ unique and distinctive requirements, libraries can react more effectively in serving its patrons with a realistic and sensible set of options for the programs and services developed to satisfy the user’s changing needs and expectations.

Originality/value
The value in exploring this topic is to present a snapshot of several of the elements used by libraries in their efforts to understand and react to its patrons’ needs through its strategies deployed in support of the user experience.