bluuebunny/crossref_metadata_2025_split huggingface dataset:
A snapshot of progenitor-derivative speciation in action inIberodes(Boraginaceae)
Authors: Otero Ana , Vargas Pablo , Valcárcel Virginia , Fernández-Mazuecos Mario , Jiménez-Mejías Pedro , Hipp Andrew L. 
Published: October 2019

SUMMARYTraditional classification of speciation modes has focused on physical barriers to gene flow. While allopatry has been viewed as the most common mechanism of speciation, parapatry and sympatry, both entail speciation in the face of ongoing gene flow and thus both are far more difficult to detect and demonstrate.Iberodes(Boraginaceae, NW Europe) with a small number of recently derived species (five) and contrasting morphological traits, habitats and distribution patterns constitutes an ideal system in which to study drivers of lineage divergence and differentiation.To reconstruct the evolutionary history of the genus, we undertook an integrative study entailing: (i) phylogenomics based on restriction-site associated DNA sequencing (RAD-seq), (ii) morphometrics, and (iii) climatic niche modelling.Key results revealed a history of repeated progenitor-derivative speciation, manifesting in paraphyletic pattern withinIberodes. Climatic niche analyses, together with the morphometric data and species distributions, suggest that ecological and geographical differentiation have interacted to shape the diversity of allopatric and parapatric distributions observed inIberodes.Our integrative study has enabled to overcome previous barriers to understanding parapatric speciation by demonstrating the recurrence of progenitor-derivative speciation in plants with gene flow and ecological differentiation, explaining observed parapatry and paraphyly.
Oxidized phosphatidylcholines induce multiple functional defects in airway epithelial cells
Authors: Pascoe Christopher D , Roy Neilloy , Turner-Brannen Emily , Schultz Alexander , Vaghasiya Jignesh , Ravandi Amir , Halayko Andrew J , West Adrian R 
Published: October 2019

ABSTRACTOxidative stress is a hallmark of numerous airway diseases, contributing to extensive cell and tissue damage. Cell membranes and the airway mucosal lining are rich in phospholipids that are particularly susceptible to oxidative attack, producing bioactive molecules including oxidized phosphatidylcholines (OxPC). With the recent discovery of elevated OxPC in asthmatic patients after allergen challenge, we hypothesized that OxPC directly contribute to disease by inducing airway epithelial cell dysfunction.We found that OxPC induced dose-dependent cell stress and loss of viability in BEAS-2B and Calu-3 cell lines and primary human epithelial cells. These responses corresponded with significant epithelial barrier dysfunction, which was further compounded when combining OxPC with an epithelial wound. OxPC inhibited DNA synthesis and migration required to re-establish barrier function, but cells recovered if OxPC were washed off soon after treatment. OxPC induced generation of reactive oxygen species, lipid peroxidation and mitochondrial dysfunction, raising the possibility that OxPC cause pathological lipid metabolism in a self-propagating cycle. The oxidative stress induced by OxPC could not be abrogated by putative OxPC receptor blockers, but partial recovery of barrier function, proliferation and lipid peroxidation could be achieved with the antioxidant n-acetyl cysteine.In summary, we have identified OxPC as a group of bioactive molecules that significantly impair multiple facets of epithelial cell function, consistent with pathological features of asthma. Further characterisation of the mechanisms by which OxPC affect epithelial cells could yield new insights into how oxidative stress contributes to the pathogenesis of airway disease.
Deficits in monitoring self-produced speech in Parkinson’s disease
Authors: Railo Henry , Nokelainen Niklas , Savolainen Saara , Kaasinen Valtteri 
Published: October 2019

AbstractObjectiveSpeech deficits are common in Parkinson’s disease, and behavioural findings suggest that the deficits may be due to impaired monitoring of self-produced speech. The neural mechanisms of speech deficits are not well understood. We examined a well-documented electrophysiological correlate of speech self-monitoring in patients with Parkinson’s disease and control participants.MethodsWe measured evoked electroencephalographic responses to self-produced and passively heard sounds (/a/ phonemes) in age-matched controls (N=18), and Parkinson’s disease patients who had minor speech impairment, but reported subjectively experiencing no speech deficits (N=17).ResultsDuring speaking, auditory evoked activity 100 ms after phonation (N1 wave) was less suppressed in Parkinson’s disease than controls when compared to the activity evoked by passively heard phonemes. This difference between the groups was driven by increased amplitudes to self-produced phonemes, and reduced amplitudes passively heard phonemes in Parkinson’s disease.ConclusionsThe finding indicates that auditory evoked activity is abnormally modulated during speech in Parkinson’s patients who do not subjectively notice speech impairment. This mechanism could play a role in producing speech deficits in as the disease progresses.
Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence
Authors: Olan Ioana , Parry Aled J. , Schoenfelder Stefan , Narita Masako , Ito Yoko , Chan Adelyne S.L. , Slater Guy St.C. , Bihary Dóra , Bando Masashige , Shirahige Katsuhiko , Kimura Hiroshi , Samarajiwa Shamith A. , Fraser Peter , Narita Masashi 
Published: October 2019

AbstractSenescence is a phenotypic state of stable proliferative arrest, typically occurring in lineage-committed cells and triggered by various stimuli. It is generally accompanied by activation of a secretory program (senescence-associated secretory phenotype, SASP), which modulates both local (tissue microenvironment) and systemic (ageing) homeostasis1,2. Enhancer-promoter interactions play a key role in gene regulation3–5, facilitated by chromatin loops, mostly formed via CCCTC binding factor (CTCF) and cohesin tethering6–8. The three-dimensional chromatin structure of senescent cells has been characterised9–11 mostly in terms of macro-domain structures, but its relevance in gene expression remains elusive. Here, we use Hi-C and capture Hi-C12,13 to show that oncogenic HRAS-induced senescence (RIS) in human diploid fibroblasts (HDFs) is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks at the 3’ end of a subset of active genes, reminiscent of the transcription-driven ‘cohesin islands’ recently discovered in mouse embryonic fibroblasts deficient in both CTCF and the cohesin release factor Wings apart-like (Wapl)14. RIS de novo cohesin peaks are also transcription-dependent and enriched for SASP genes, as exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Cytokine induction is associated with similar cohesin islands appearance and enhancer-promoter rewiring during the terminal differentiation of monocytes to macrophages15, but not upon acute TNFα treatment of HDFs16. These results suggest that RIS represents a fate-determined process in which gene expression is regulated beyond the cell type specific 3D chromatin framework, in part through cohesin redistribution.
Honey bee pollen foraging ecology across an urbanization gradient
Authors: Richardson Rodney T. , Eaton Tyler D. , Lin Chia-Hua , Cherry Garrett , Johnson Reed M. , Sponsler Douglas B. 
Published: October 2019

AbstractUnderstanding animal foraging ecology requires large samples sizes spanning broad environmental and temporal gradients. For pollinators, this has been hampered by the laborious nature of morphologically identifying pollen. Metagenetic pollen analysis is a solution to this issue, but the field has struggled with poor quantitative performance. Building upon prior laboratory and bioinformatic methods, we applied quantitative multi-locus metabarcoding to characterize the foraging ecology of honey bee colonies situated along an urban-agricultural gradient in central Ohio, USA. In cross-validating a subset of our metabarcoding results using microscopic palynology, we find strong concordance between the molecular and microscopic methods. Our results show that, relative to the agricultural environment, urban and suburban environments were associated with higher taxonomic diversity and temporal turnover of honey bee pollen forage. This is likely reflective of the fine-grain heterogeneity and high beta diversity of urban floral landscapes at the scale of honey bee foraging. Our work also demonstrates the power of honey bees as environmental samplers of floral community composition at large spatial scales, aiding in the distinction of taxa characteristically associated with urban or agricultural land use from those distributed ubiquitously across our landscape gradient.
Synergism of gut microbiota to double-stranded RNAs in RNA interference of a leaf beetle
Authors: Xu Letian , Xu Shijing , Sun Liuwei , Zhang Yiqiu , Luo Jing , Bock Ralph , Zhang Jiang 
Published: October 2019

AbstractRNA interference (RNAi) has emerged as an efficient tool to control insect pests. When lethal double-stranded RNAs (dsRNAs) were ingested by the insects, strong gene silencing and mortality can be induced. To exert their function, dsRNA molecules must pass through insect’s gut and enter epithelial cells and/or the hemolymph. Gut bacteria are known to inhabit on the epithelial surface to confer host new capabilities to counter both biotic and abiotic stress. Whether there is a crosstalk between gut bacteria and dsRNAs and the effects of the microbiome on RNAi efficiency remains unknown. Here, using a leaf beetle-gut microbiota system, we investigated whether and how gut bacteria interact with dsRNA molecules and its effects on host insects. We firstly showed that the leaf beetlePlagiodera versicolora(Coleoptera) is highly susceptible to RNAi. Then, we found that ingestion of dsRNAs by non-axenicP. versicoloralarvae results in (i) significantly accelerated mortality compared to axenic larvae, and (ii) over-growth and dysbiosis of the gut microbiota. The latter is mainly caused by the bacterial utilization of the dsRNA degraded products initiated by the host insect. Furthermore, we found thatPseudomonas putida, a gut bacterium ofP. versicolora, was a main commensal-to-pathogen strain that accelerated the death ofP. versicoloralarvae. Taken together, our findings reveal a synergistic role of gut microbiota to dsRNA-induced mortality of pest insects, which provides new insights in the ecological functions of insect gut bacteria, and also contributes to a better understanding of the RNAi mechanisms in insects.
Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling
Authors: Ros-Freixedes Roger , Whalen Andrew , Gorjanc Gregor , Mileham Alan J , Hickey John M 
Published: October 2019

AbstractBackgroundFor assembling large whole-genome sequence datasets to be used routinely in research and breeding, the sequencing strategy should be adapted to the methods that will later be used for variant discovery and imputation. In this study we used simulation to explore the impact that the sequencing strategy and level of sequencing investment have on the overall accuracy of imputation using hybrid peeling, a pedigree-based imputation method well-suited for large livestock populations.MethodsWe simulated marker array and whole-genome sequence data for fifteen populations with simulated or real pedigrees that had different structures. In these populations we evaluated the effect on imputation accuracy of seven methods for selecting which individuals to sequence, the generation of the pedigree to which the sequenced individuals belonged, the use of variable or uniform coverage, and the trade-off between the number of sequenced individuals and their sequencing coverage. For each population we considered four levels of investment in sequencing that were proportional to the size of the population.ResultsImputation accuracy largely depended on pedigree depth. The distribution of the sequenced individuals across the generations of the pedigree underlay the performance of the different methods used to select individuals to sequence. Additionally, it was critical to balance high imputation accuracy in early generations as well as in late generations. Imputation accuracy was highest with a uniform coverage across the sequenced individuals of around 2x rather than variable coverage. An investment equivalent to the cost of sequencing 2% of the population at 2x provided high imputation accuracy. The gain in imputation accuracy from additional investment diminished with larger populations and larger levels of investment. However, to achieve the same imputation accuracy, a proportionally greater investment must be used in the smaller populations compared to the larger ones.ConclusionsSuitable sequencing strategies for subsequent imputation with hybrid peeling involve sequencing around 2% of the population at a uniform coverage around 2x, distributed preferably from the third generation of the pedigree onwards. Such sequencing strategies are beneficial for generating whole-genome sequence data in populations with deep pedigrees of closely related individuals.
Co-inhibition of BCL-XL and MCL-1 with BCL-2 selective inhibitors A1331852 and S63845 enhances cytotoxicity of cervical cancer cell lines
Authors: Rahman Siti Fairus Abdul , Muniandy Kalaivani , Soo Yong Kit , Tiew Elvin Yu Huai , Tan Ke Xin , Bates Timothy E. , Mohana-Kumaran Nethia 
Published: October 2019

AbstractA combination of the BCL-2 inhibitors ABT-263 and A-1210477 inhibited cell proliferation in the HeLa, C33A, SiHa and CaSki human cervical cancer cell lines. Drug sensitivity was initially tested using 2-dimensional (2D) cell culture models. As ABT-263 binds to both BCL-2 and BCL-XL at high affinity, it was unclear whether the synergism of the drug combination was driven either by singly inhibiting BCL-2 or BCL-XL, or inhibition of both. Therefore, we used the BCL-2 selective inhibitor ABT-199 and the BCL-XL selective inhibitor A1331852 to resolved the individual antitumor activities of ABT-263 into BCL-2 and BCL-XL dependent mechanisms. A-1210477 was substituted with the orally bioavailable S63845. The SiHa, C33A and CaSki cell lines were resistant to single agent treatment of all three drugs, suggesting that none of these anti-apoptotic proteins singly mediate survival of the cells. HeLa cells were resistant to single agent treatment of ABT-199 and A1331852 but were sensitive to S63845 indicating that they depend on MCL-1 for survival. Co-inhibition of BCL-XL and MCL-1 with A1331852 and S63845 significantly inhibited cell proliferation of all four cell lines. Similar data were obtained with 3-dimensional spheroid cell culture models generated from two cervical cancer cell linesin vitro. Treatment with a combination of A1331852 and S63845 resulted in inhibition of growth and invasion of the 3D spheroids. Co-inhibition of BCL-2 and MCL-1 with ABT-199 and S63845, also inhibited cell proliferation of all cancer cell lines, except SiHa. However, the effect of the combination was not as pronounced as combination of A1331852 and S63845. Collectively, our data demonstrate that the combination of MCL-1-selective inhibitors with either selective inhibitors of either BCL-XL or BCL-2 may be potentially useful as treatment strategies for the management of cervical cancer.
Shaping accountability at an NGO: a Bourdieusian perspective
Authors: Kuruppu Sanjaya Chinthana , Lodhia Sumit 
Published: October 2019

Purpose
The purpose of this paper is to examine the concept of accountability as it relates to a non-governmental organisation (NGO) evolving through a period of considerable change in Sri Lanka.

Design/methodology/approach
An in-depth single case study of a large NGO working in Sri Lanka is presented. Data collection involved conducting semi-structured interviews with a range of NGO employees and stakeholders, undertaking participant and non-participant observation and document analysis.

Findings
This paper shows how accountability is a contested notion that is shaped by struggles among stakeholders within a field. The authors explore how the “widespread field” consisting of the aid context in Sri Lanka and internationally is rapidly shifting. This creates unique pressures within the “restricted field” of the case NGO and its constituents. These pressures are manifested in the contest between the different capitals held by various stakeholders to shape the NGO. The nature of access to these capitals is important in the way that the NGO is shaped by external forces, and also by the individuals within it.

Research limitations/implications
This study adds fresh perspective to the growing body of work in NGO accountability. The paper highlights the tensions NGOs face through a holistic application of a Bourdieusian conceptual framework. The authors show how the habitus of the organisation is shaped in such a way that conceptions of accountability were captured by powerful external and internal constituencies. Ultimately, the nature of an organisation’s agency is questioned.

Practical implications
The authors present a more nuanced understanding of forces which shape accountability in an NGO setting which is of practical relevance to NGOs and their stakeholders. The authors highlight the struggle for an NGO to maintain its agency through resisting external forces that impact on its operations.

Originality/value
This study presents a comprehensive and holistic application of Bourdieu’s concepts and their interactions in an organisational setting. The struggle to harness various forms of capital in the field, shapes doxa and the habitus of NGO actors, illuminating the role of symbolic violence in the creation of an organisational identity.
Sensitivity model based PID controller for various high-order processes
Authors: Ghosh Sreya , Pan Somnath 
Published: October 2019

Purpose
This paper aims to propose a reference model based simple strategy for the design of proportional-integral-derivative (PID) controller using frequency response matching for high-order stable, integrating and unstable processes that may have time-delay and non-minimum phase zero.

Design/methodology/approach
The reference sensitivity model is designed fulfilling stability conditions of the control system responses such as set-point response, load-disturbance response and noise response along with transient response criteria. The analytical controller thus designed is approximated to a PID controller using a simple formula based on a model-matching technique at low frequency.

Findings
PID controllers are designed for examples with varied dynamics taken from the literature, and the performances of the designed control systems are compared with some methods prevalent in the literature to show the efficacy of the proposed work. Overall, the method gives satisfactory set-point, as well as load-disturbance responses and controller-outputs in all the cases considered.

Originality/value
The method is applicable to high-order processes of various monotonic or oscillating dynamics without requiring process reduction. The PID controller designed considering a reference model with suitable criteria ensuring stability and a modified model matching technique, which provides a stable control system for all these high-order processes.
Diffusion of management accounting innovations: a virus perspective
Authors: Johanson Daniel , Madsen Dag Øivind 
Published: October 2019

PurposeThe diffusion of management accounting innovations (MAIs) is the focus of much debate in the management accounting research community. Extant contributions have drawn on a large of number of theories, including innovation diffusion theory and various sociologically inspired theories such as management fashion. The purpose of this paper is to examine and develop Røvik’s virus theory in the context of how MAIs diffuse. The paper further evaluates and elaborates on the potential usefulness of the virus perspective to empirical research on MAIs.Design/methodology/approachThe paper uses a conceptual and explorative research approach. The paper introduces the virus perspective and compares this perspective with several other theoretical perspectives often used in studies of the diffusion of MAIs. This enables the identification of characteristics specific to the virus perspective. The paper also re-examines a number of prior studies of MAIs and identifies different virus characteristics implicit in these studies.FindingsThe findings of the paper imply that the virus perspective is a useful basis for empirical research on MAIs. The virus perspective differs from other theoretical perspectives in several respects and is particularly suited for longitudinal studies of both MAIs and organizational change. However, the perspective could be used at other levels of analysis as well. The extant studies reviewed in this paper provide support for the viral characteristics of MAIs. The paper also identifies and discusses avenues for future research using the virus perspective as a theoretical lens.Originality/valueThe virus perspective has been given little attention in research on MAIs, as well as more generally within accounting research. This research paper demonstrates that the virus perspective offers a rich and valuable conceptual framework for studying how demand-side organizations are affected by MAIs over extensive periods of time. The paper also discusses the implications of the virus perspective with respect to the research method.
Bridging the data divide between practitioners and academics
Authors: Benoit Sabine , Klose Sonja , Wirtz Jochen , Andreassen Tor Wallin , Keiningham Timothy L. 
Published: October 2019

PurposeOrganizations (data gatherers in the context) drown in data while at the same time seeking managerially relevant insights. Academics (data hunters) have to deal with decreasing respondent participation and escalating costs of data collection while at the same time seeking to increase the managerial relevance of their research. The purpose of this paper is to provide a framework on how, managers and academics can collaborate better to leverage each other’s resources.Design/methodology/approachThis research synthesizes the academic and the managerial literature on the realities and priorities of practitioners and academics with regard to data. Based on the literature, reflections from the world’s leading service research centers, and the authors’ own experiences, the authors develop recommendations on how to collaborate in research.FindingsFour dimensions of different data realities and priorities were identified: research problem, research resources, research process and research outcome. In total, 26 recommendations are presented that aim to equip academics to leverage the potential of corporate data for research purposes and to help managers to leverage research results for their business.Research limitations/implicationsThis paper argues that both practitioners and academics have a lot to gain from collaborating by exchanging corporate data for scientific approaches and insights. However, the gap between different realities and priorities needs to be bridged when doing so. The paper first identifies data realities and priorities and then develops recommendations on how to best collaborate given these differences.Practical implicationsThis research has the potential to contribute to managerial practice by informing academics on how to better collaborate with the managerial world and thereby facilitate collaboration and the dissemination of academic research for the benefit of both parties.Originality/valueWhereas the previous literature has primarily examined practitioner–academic collaboration in general, this study is the first to focus specifically on the aspects related to sharing corporate data and to elaborate on academic and corporate objectives with regard to data and insights.