bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational signatures reveal the role of RAD52 in p53-independent p21 driven genomic instability
Authors: Galanos Panagiotis , Pappas George , Polyzos Alexander , Kotsinas Athanassios , Svolaki Ioanna , Giakoumakis Nikos N , Glytsou Christina , Pateras Ioannis S , Swain Umakanta , Souliotis Vassilis , Georgakilas Alexander , Geacintov Nicholas , Scorrano Luca , Lukas Claudia , Lukas Jiri , Livneh Zvi , Lygerou Zoi , Sørensen Claus Storgaard , Bartek Jiri , Gorgoulis Vassilis G. 
Published: September 2017

AbstractBackgroundGenomic instability promotes evolution and heterogeneity of tumors. Unraveling its mechanistic basis is essential to design appropriate therapeutic strategies. In a recent study we reported an unexpected oncogenic property of p21WAF1/Cip1showing that its chronic expression, in a p53-deficient environment, causes genomic instability by deregulating the replication licensing machinery.ResultsExtending on this work we now demonstrate that p21WAF1/Cip1can further fuel genomic instability by suppressing the repair capacity of low and high fidelity pathways that deal with nucleotide abnormalities. Consequently, fewer single nucleotide substitutions (SNSs) occur, while formation of highly deleterious DNA double-strand breaks (DSBs) is enhanced, crafting a characteristic mutational signature landscape. Guided by the mutational signatures formed, we found at the mechanistic level that the DSBs were repaired by Rad52-dependent Break-Induced Replication (BIR) and Single-Strand Annealing (SSA). Conversely, the error-free synthesis-dependent strand annealing (SDSA) repair route was deficient. Surprisingly, Rad52 was activated transcriptionally in an E2F1-dependent manner, rather than post-translationally as is common for DNA repair factor activation.ConclusionsOur results signify the importance of mutational signatures as guides to disclose the “repair history” leading to genomic instability. In this vein, following this approach we unveiled how chronic p21WAF1/Cip1expression rewires the repair process, identifying Rad52 as a source of genomic instability and a candidate therapeutic target.
Impact of spatial organization on a novel auxotrophic interaction among soil microbes
Authors: Jiang Xue , Zerfaß Christian , Eichmann Ruth , Asally Munehiro , Schäfer Patrick , Soyer Orkun S 
Published: September 2017

AbstractA key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environment requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a specific defined system to study the metabolic interactions in a spatial context among a plant-beneficial endophytic fungusSerendipita indica,and the soil-dwelling model bacteriumBacillus subtilis. Focusing on the growth dynamics ofS. indicaunder defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found thatS. indicagrowth is restored in thiamine-free media, when co-cultured withB. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact ofB. subtiliswas only visible when its inoculation was separated from that ofS. indicaeither in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant-seed treatments and for vertical farming under defined conditions.
Force dependence of filopodia adhesion: involvement of myosin II and formins
Authors: Alieva N. O. , Efremov A. K. , Hu S. , Oh D. , Chen Z. , Natarajan M. , Ong H. T. , Jégou A. , Romet-Lemonne G. , Groves J. T. , Sheetz M. P. , Yan J. , Bershadsky A. D. 
Published: September 2017

AbstractFilopodia are dynamic membrane protrusions driven by polymerization of an actin filament core, mediated by formin molecules at the filopodia tips. Filopodia can adhere to the extracellular matrix and experience both external and cell generated pulling forces. The role of such forces in filopodia adhesion is however insufficiently understood. Here, we induced sustained growth of filopodia by applying pulling force to their tips via attached fibronectin-coated beads trapped by optical tweezers. Strikingly, pharmacological inhibition or knockdown of myosin IIA, which localized to the base of filopodia, resulted in weakening of filopodia adherence strength. Inhibition of formins, which caused detachment of actin filaments from formin molecules, produced similar effect. Thus, myosin IIA-generated centripetal force transmitted to the filopodia tips through interactions between formins and actin filaments are required for filopodia adhesion. Force-dependent adhesion led to preferential attachment of filopodia to rigid versus fluid substrates, which may underlie cell orientation and polarization.
Acute condensin depletion causes genome decompaction without altering the level of global gene expression inSaccharomyces cerevisiae
Authors: Paul Matthew Robert , Markowitz Tovah Elise , Hochwagen Andreas , Ercan Sevinç 
Published: September 2017

AbstractCondensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeastSaccharomyces cerevisiae. Spike-in-controlled 3C-seq analysis revealed that acute condensin inactivation leads to a global decrease in close-range chromosomal interactions as well as more specific losses of homotypic tRNA gene clustering. In addition, a condensin-rich topologically associated domain between the ribosomal DNA and the centromere on chromosome XII is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture are not associated with global changes in transcript levels as determined by spike-in-controlled mRNA-seq analysis. Our data suggest that the global transcriptional program ofS. cerevisiaeis resistant to condensin inactivation and the associated profound changes in genome organization.Significance StatementGene expression occurs in the context of higher-order chromatin organization, which helps compact the genome within the spatial constraints of the nucleus. To what extent higher-order chromatin compaction affects gene expression remains unknown. Here, we show that gene expression and genome compaction can be uncoupled in the single-celled model eukaryoteSaccharomyces cerevisiae. Inactivation of the conserved condensin complex, which also organizes the human genome, leads to broad genome decompaction in this organism. Unexpectedly, this reorganization has no immediate effect on the transcriptome. These findings indicate that the global gene expression program is robust to large-scale changes in genome architecture in yeast, shedding important new light on the evolution and function of genome organization in gene regulation.
Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes
Authors: Carvalho Daniel S. , Schnable James C. , Almeida Ana Maria R. 
Published: September 2017

AbstractThe study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide more robust assessments of gene family evolution.
EWS-FLI-1 creates a cell surface microenvironment conducive to IGF signaling by inducing pappalysin-1
Authors: Jayabal Panneerselvam , Houghton Peter J. , Shiio Yuzuru 
Published: September 2017

AbstractEwing sarcoma is an aggressive cancer of bone and soft tissue in children with poor prognosis. It is characterized by the chromosomal translocation between EWS and an Ets family transcription factor, most commonly FLI-1. EWS-FLI-1 fusion accounts for 85% of Ewing sarcoma cases. EWS-FLI-1 regulates the expression of a number of genes important for sarcomagenesis, can transform NIH3T3 and C3H10T1/2 cells, and is necessary for proliferation and tumorigenicity of Ewing sarcoma cells, suggesting that EWS-FLI-1 is the causative oncoprotein.Here we report that EWS-FLI-1 induces the expression of pappalysin-1 (PAPPA), a cell surface protease that degrades IGF binding proteins (IGFBPs) and increases the bioavailability of IGF. EWS-FLI-1 binds to the pappalysin-1 gene promoter and stimulates the expression of pappalysin-1, leading to degradation of IGFBPs and enhanced IGF signaling. Silencing of pappalysin-1 strongly inhibited anchorage-dependent and anchorage-independent growth as well as xenograft tumorigenicity of Ewing sarcoma cells. These results suggest that EWS-FLI-1 creates a cell surface microenvironment conducive to IGF signaling by inducing pappalysin-1, which emerged as a novel target to inhibit IGF signaling in Ewing sarcoma.
Travelers’ preferences for peer-to-peer (P2P) accommodations and hotels
Authors: Young Cheri A. , Corsun David L. , Xie Karen L. 
Published: September 2017

Purpose
The purpose of this study was to investigate travelers’ preferences for peer-to-peer (P2P) accommodations or hotels when traveling for leisure or business purposes given the rise of P2P accommodations in the form of Airbnb, Vacation Rentals by Owners (VRBO) One Fine Stay, etc.

Design/methodology/approach
VRBO hosts in Denver, Colorado, USA provided contact information for 788 travelers who stayed with them over the prior three years. These travelers received an email survey and the opportunity to be entered in a drawing for one of three US$250 gift cards.

Findings
P2P usage was driven by leisure travel. The most influential factors in the choice of P2P over hotel were price, location, party size, dwelling size and trip length. When choosing a hotel for business travel, the influential factors were location, safety and security, price and knowing what one will receive in the way of facility and services.

Research limitations/implications
The external validity of the findings is limited as the study was conducted in one US city using travelers of only one P2P accommodations platform.

Practical implications
Hotels may want to leverage their loyalty programs and stress the importance of safety and security when traveling as a means of competing with P2P accommodations.

Originality/value
Given limited empirical research on P2P accommodations, this study provides an informative first look at the preferences and behaviors of travelers using P2P accommodations and points to a growing loyalty to P2P accommodations versus hotels in the leisure segment.
Patients’ perspectives of emergency care quality and priorities for care improvement
Authors: Yarney Lily , Atinga Roger Ayimbillah 
Published: September 2017

Purpose
Studies have examined strategies implemented to strengthen quality of emergency care in healthcare provider institutions in Ghana. But few studies have focused on what determines quality of emergency care from the patient’s perspective. The purpose of this paper is to fill that gap by examining factors salient to gauging quality of emergency care and priority areas for care improvement.

Design/methodology/approach
Cross-sectional data were collected from patients admitted in emergency units of public hospitals in two regions: Greater Accra and Central Regions. A structured questionnaire designed with inputs from emergency medicine physicians and patients was used to collect data from 381 patients. Principal component analysis (PCA) and logistic regression models were computed to respectively determine salient measures of emergency care quality and their association with patient overall perceived quality of emergency care.

Findings
Using the PCA, four factors (social and relational care, attentive prehospitalised care, ward quality and privacy and medical supplies) were derived as salient measures of emergency care quality. All the factors derived had statistically significant association with patient overall perception of quality.

Originality/value
Emergency care quality improvement strategies that incorporate the dimensions identified can produce effective therapeutic outcomes.
Internal coordination to enable high load factor
Authors: Rogerson Sara , Sallnäs Uni 
Published: September 2017

Purpose
The purpose of this paper is to clarify how activities may be coordinated within shippers’ organisations to enable high load factor (a key aspect of transport efficiency).

Design/methodology/approach
A multiple-case study involving three shippers was conducted, in which the logistics or transport managers of each company were interviewed. The cases were analysed according to which activities were coordinated to achieve high load factor, interdependencies between the activities, and the coordination mechanisms that shippers adopted.

Findings
A matrix is developed to show the differences in applying various coordination mechanisms in eight categories, according to intrafunctional or interfunctional coordination, sequential or reciprocal interdependencies, and the number of activities (dyadic or multiple). For example, coordination mechanisms aimed at exerting control are more suitable for intrafunctional than interfunctional interaction; interfunctional coordination relies more on mechanisms that aim to increase the understanding of transport-related issues among non-logistics activities.

Research limitations/implications
The study is based on data from three Swedish companies.

Practical implications
Managers are provided with suggestions for coordinating activities when their goal is to improve load factor. These findings are of interest for reducing costs and emissions.

Originality/value
In response to suggestions in the earlier literature that shippers could improve their internal coordination to improve their load factor, this paper articulates several mechanisms for performing such coordination in eight situations.
Supply network resilience: a systematic literature review and future research
Authors: Datta P. 
Published: September 2017

PurposeThe purpose of this paper is to investigate the knowledge existing in the literature on supply chain resilience for identifying the supply chain practices adopted for securing resilience in given uncertain event.Design/methodology/approachA systematic literature review is conducted to identify 84 conceptual and empirical studies. The research findings are synthesized in categories of uncertain events, supply chain practices and outcomes.FindingsA set of propositions linking the uncertain events, mechanisms and supply chain resilience improvement is developed. It was found that the sufficient conditions for resilience under unexpected disasters are substantially different from those required for resilience against disruptions caused by internal practices or complexity.Originality/valuePractitioners can benefit from the knowledge of interventions and mechanisms to improve their supply chain resilience in the face of different unpredictable situations. The contribution of this paper is twofold: first, it develops an actionable theory of supply chain resilience by developing testable propositions in the context of supply chains exposed to uncertainties resulting from unexpected disruptions, complexity of supply chains and adoption of certain internal practice; second, the paper highlights the key shortcomings of existing literature and provides opportunities for further research and improvement.
Key factors for truly sustainable supply chain management
Authors: Wu Jei-Zheng , Santoso Caroline Himadewi , Roan Jinshyang 
Published: September 2017

Purpose
The purpose of this paper is to explore key factors or criteria of sustainable supply chain management (SSCM) influencing Indonesian coal companies, using “adoption, implementation, and performance” (A-I-P) of SSCM, thru three means: first, to investigate which criteria have higher weight to achieve SSCM in Indonesia; second, to see whether there are any differences between the Indonesia case and existing literature of SSCM; third, to highlight any causal relationships between the Indonesia case and the SSCM theory.

Design/methodology/approach
DEMATEL-based analytic network process (DANP) questionnaire survey with a theoretical SSCM model is applied to conduct an empirical test for the coal production and supply chain companies in Indonesia.

Findings
The “performance” dimension out of the A-I-P of the SSCM is the most important one, while the “adoption” dimension is the least. Out of the 12 criteria under the three dimensions, the “operational, economic, environmental, and social” factors under the category of the performance dimension and the “ISO 14001 certification” criteria belonging to the dimension of “implementation” are the top five key factors in the SSCM.

Research limitations/implications
There are some limitations in this study. First and foremost is the relatively small sample size with a limited geographic area, although they are unavoidable owing to one country case study.

Practical implications
The test results are helpful to draw guidance for sustainable supply chain managers in implementing efficient SSCM in the wave of tough competition and changing marketplace.

Originality/value
This study contributes first to developing a theoretical framework for SSCM under the A-I-P model and second, to applying DANP to an empirical case of SSCM of the coal industry in Indonesia. As a result, the authors draw helpful guidelines and policy implications for SSCM of the coal industry, referring to the A-I-P dimension as drivers and enablers for the SSCM performances of the industry.
An examination of drivers and barriers to reducing carbon emissions in China’s manufacturing sector
Authors: Subramanian Nachiappan , Abdulrahman Muhammad 
Published: September 2017

Purpose
Carbon Efficient Practices (CEPs) are gaining momentum due to the serious consequences of climate change. While past studies have focused on the effects of either drivers or barriers to green practices especially in the context of developed countries, relatively little attention has been devoted to the simultaneous effects of drivers and barriers on product redesign, particularly in the context of China. The paper aims to discuss these issues.

Design/methodology/approach
Using a blend of the Contextual Interaction Theory and Newton’s second law of motion, this paper proposes a conceptual model that simultaneously examines the impact of CEP drivers and barriers on product redesign and performance.

Findings
Structural Equation Modeling (SEM) analysis on a sample of 239 Chinese manufacturing firms indicated that drivers had substantially higher effects on product redesign and performance compared to the influence of other barriers.

Originality/value
Use of Newton’s second law of motion as a theoretical framework for understanding the adoption of CEPs in the context of China is novel. Implications of this pattern of results on academic theory building and practice are offered.
A quantitative risk assessment methodology and evaluation of food supply chain
Authors: Rathore Rishabh , Thakkar Jitesh J. , Jha Jitendra Kumar 
Published: September 2017

Purpose
The food supply chain is exposed to severe environmental and social issues with serious economic consequences. The identification and assessment of risk involved in the food supply chain can help to overcome these challenges. In response, the purpose of this paper is to develop a risk assessment framework for a typical food supply chain.

Design/methodology/approach
An integrated methodology of grey analytical hierarchy process and grey technique for order preference by similarity to the ideal solution is proposed for developing a comprehensive risk index. The opinion of the experts is used to illustrate an application of the proposed methodology for the risk assessment of the food supply chain in India.

Findings
Valuable insights and recommendations are drawn from the results, which are helpful to the practitioners working at strategic and tactical levels in the food supply chain for minimising the supply chain disruptions.

Research limitations/implications
The risk quantification for the case organisation is primarily based on inputs collected from the experts working for Indian food supply chain, and so the generalisation of the results is limited to the context of developing countries. However, the generalisability of the proposed risk quantification methodology and key insights developed in the food supply chain will assist practitioners in policy making.

Practical implications
The risk priorities established by this research would enable an implementation of systematic risk mitigation strategies and deployment of necessary resources for leveraging the efficiency of food supply chain.

Originality/value
Specifically, this research has delivered a risk quantification framework and strengthened the inquiry of risk management for the food supply chain.
Role of power in supply chain performance: evidence from agribusiness SMEs in Uganda
Authors: Odongo Walter , Dora Manoj Kumar , Molnar Adrienn , Ongeng Duncan , Gellynck Xavier 
Published: September 2017

PurposeThe purpose of this paper is to examine the role of power on supply chain performance (SCP) in the context of small and medium sized agribusiness enterprises (SMEs). Contrary to most of previous studies, which collect and analyze data from one side of a relationship dyad using a focal firm approach, a matched triad approach was employed in data collection and analysis.Design/methodology/approachEmpirical data was collected from 150 agribusiness supply chain members from the maize supply chain in Uganda. Analysis was done using multi-group analysis and structural equations modeling.FindingsResults highlight the differences in the perception of power use and how it influences SCP. The differences in perception suggest the existence of power asymmetry amongst supply chain members. This work contributes to the ongoing debate concerning the use of triad as a unit of analysis as opposed to a firm or a dyad.Research limitations/implicationsThis study only focused on one commodity chain in one country, which can limit the broad application of the findings.Originality/valueThe novelty of this work lies in fact that the authors assess perception of power amongst supply chain members in a triadic context, a perspective that has not been adequately tested in agribusiness supply chain management studies before.