bluuebunny/crossref_metadata_2025_split huggingface dataset:
sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors
Authors: Chen Wenhan , Robertson Alan J. , Ganesamoorthy Devika , Coin Lachlan J.M. 
Published: February 2016

AbstractAccurate identification of copy number alterations is an essential step in understanding the events driving tumor progression. While a variety of algorithms have been developed to use high-throughput sequencing data to profile copy number changes, no tool is able to reliably characterize ploidy and genotype absolute copy number from tumor samples which contain less than 40% tumor cells. To increase our power to resolve the copy number profile from low-cellularity tumor samples, we developed a novel approach which pre-phases heterozygote germline SNPs in order to replace the commonly used ‘B-allele frequency’ with a more powerful ‘parental-haplotype frequency’. We apply our tool - sCNAphase - to characterize the copy number and loss-of-heterozygosity profiles of four publicly available breast cancer cell-lines. Comparisons to previous spectral karyotyping and microarray studies revealed that sCNAphase reliably identified overall ploidy as well as the individual copy number mutations from each cell-line. Analysis of artificial cell-line mixtures demonstrated the capacity of this method to determine the level of tumor cellularity, consistently identify sCNAs and characterize ploidy in samples with as little as 10% tumor cells. This novel methodology has the potential to bring sCNA profiling to low-cellularity tumors, a form of cancer unable to be accurately studied by current methods.
Corporate response to climate change: language, power and symbolic construction
Authors: Ferguson John , Sales de Aguiar Thereza Raquel , Fearfull Anne 
Published: February 2016

Purpose– The purpose of this paper is to explore corporate communications related to climate change in both a voluntary and mandatory setting. Adopting a critical perspective, the paper examines how companies who participated in the voluntary UK Emissions Trading Scheme (UK ETS) and the UK Government’s mandatory Carbon Reduction Commitment (CRC) Energy Efficiency Scheme positioned themselves within the climate change debate. In particular, the analysis draws attention to how companies, through their communicative practice, helped to constitute and reproduce the structure of the field in which they operate.Design/methodology/approach– A context-sensitive discursive analysis of 99 stand-alone reports produced by companies participating in the UK ETS and CRC over a nine-year period. The analysis is informed by Thompson’s (1990) depth-hermeneutic framework, which mediates the connection between linguistic strategies and the institutional field.Findings– The analysis suggests that companies tended to adopt particular linguistic strategies in their communications related to climate change. For example, the strategy of “rationalisation” was employed in order to emphasise the organisational “opportunities” resulting from climate change; in this sense, companies sought to exploit climate crises in order to advance a doctrine that endorsed market-based solutions. A noteworthy finding was that in the mandatory CRC period, there was a notable shift towards the employment of the strategies that Thompson (1990) refers to as “differentiation” – whereby companies attempted to displace responsibility by presenting either government or suppliers as barriers to progress.Originality/value– This paper explores how disclosure on climate change evolved while organisations participate in voluntary and compulsory climate change initiatives. In this respect, the analysis is informed by the social and political context in which the disclosure was produced.
Outsourcing destination choices: the role of economic and cultural attributes
Authors: Livanis Grigorios , Robertson Christopher J. , Al-Shuaibi Khalid M. , Hussain Khalid 
Published: February 2016

Purpose– The purpose of this paper is to examine how country-of-origin (COO) perceptions of managers affect their provider selection for offshoring and offshore-outsourcing of services. In particular, it examines how economic and cultural attributes of the supplier’s host nation shape these choices and identifies whether these attributes have a substitutive, complementary, or competing relationship.Design/methodology/approach– A quantitative study was performed using data collected from 235 managers in Saudi Arabia, which has relatively homogeneous managerial population with a clear significant cultural attribute and so presents an ideal setting to study the theory developed in this paper. Data were analyzed using a repeated-measures analysis of variance and a repeated-measures and doubly multivariate analysis of variance.Findings– Building on signaling theory, it is shown that buyers from developing countries prefer suppliers from developed rather than culturally distant developing economies as stronger institutions in developed nations increase the credibility of firms. It is also shown that they prefer suppliers from developing countries that share a common cultural attribute such as religion over other developing countries, supporting social identification behavior and a substitutive relationship between cultural and economic attributes. Finally, they are indifferent between suppliers located in a developed and in a culturally similar developing country, even when the cost of obtaining the service is the same in both countries. In such cases, economic and cultural COO attributes have a competing relationship in provider selection.Research limitations/implications– It would be interesting to examine if the results of the current study extend to cultural attributes/cues other than religion that may shrink the social distance between buyers and suppliers.Practical implications– Service multinationals from developing countries may struggle to establish credibility in the eyes of potential customers, who consistently evaluate them lower than firms in developed markets or firms from developing countries that share a common social trait with the potential customers. They can compensate for this by adopting policies that enhance pre-contract trust, invest in homogeneity capital that decreases the social distance between the two firms, or by focussing their sales efforts on countries with which they share a social/cultural attribute.Originality/value– This paper contributes to the marketing and international business literatures by providing insights on how firms from developing countries can effectively compete in the global marketplace given COO effects. Overall, the results provide novel evidence of the importance of co-membership in transnational communities (for instance, religious groups across countries) in supplier selection and its relationship to economic attributes.
Cultural influences on expectations and evaluations of service quality in emerging markets
Authors: Guesalaga Rodrigo , Pierce Meghan , Scaraboto Daiane 
Published: February 2016

Purpose
– The purpose of this paper is to explore cultural sources of variation on consumers’ expectations and evaluations of service quality within local emerging markets.

Design/methodology/approach
– The authors employ a multi-method approach. The multi-method research design utilizes: first, netnography to examine foreign consumers’ blogs and online communities; second, interviews with local and foreign consumers to unveil critical incidents in service encounters; and third, an online survey of 139 foreign consumers living in Chile and 460 Chilean consumers to map differences in their expectations and evaluations of services.

Findings
– A general analysis of local and foreign consumers living in an emerging market reveals that these two groups do not differ significantly in their expectations of service quality. The authors also find that differences in expectations and evaluations of service quality within a local emergent market are only partially explained by aggregating consumers according to their country or region of origin. Finally, the findings demonstrate that examining cultural differences at the individual level generates a better understanding of how cultural factors impact consumer expectations and evaluations of service quality within emerging markets.

Research limitations/implications
– The research is limited to one emerging market (Chile) and focusses largely in one industry (banking). Further research should be conducted to examine the findings in other contexts, including developed markets, and to identify how other cultural differences (e.g. language mastery) within local markets may impact consumer expectations and evaluations of services.

Practical implications
– Service companies operating in emerging markets should account for cultural differences when determining service standards and protocols. These differences may cut across the local-foreign divide and suggest that profiling foreign customers depending on their country of origin is not the most adequate approach for providing excellence in service and enjoying the benefits that follow.

Social implications
– Foreign consumers living in a local market are frequently considered a homogeneous group distinct from local consumers, and are treated as such by public and private service providers. The study demonstrates that foreign consumers may be more or less similar to local consumers depending on their cultural values, and should not be considered as a uniform group.

Originality/value
– The findings extend research on consumer expectations and evaluations of service quality to account for cultural diversity within local emerging markets. The authors demonstrate that a cluster-approach to examining consumer expectations and evaluations of service quality better accounts for variations due to cultural values within local markets.
Destabilizing or stabilizing the identity of Slawek Magala?
Authors: Klamer Arjo 
Published: February 2016

Purpose
– The purpose of this paper is to demonstrate that Slawek Magala and the author have a great deal in common and that the author is putting the differences to an interesting use in the Erasmus Honors Program designed for the top students of all faculties of the Erasmus University in Rotterdam. The model of education gaining the upper hand in contemporary universities should be balanced with the more fundamental humanist upbringing of students-citizens.

Design/methodology/approach
– The paper has been written as an empirical report based on five years of participative observation, regular analysis and group discussion of student essays, and on the on-going application of qualitative techniques in designing a curriculum, running the program and joint evaluation of its intended effects with the main protagonist of the paper, namely the colleague Slawek Magala. The labels “traditionalist” and “postmodernist” have been codified according to the most frequent academic usage.

Findings
– If Slawek manifests himself as a typical post-modernist who does not believe in stable identities, the author will be then the neo-traditionalist, who tries to connect identities to value choices and value choices to stable philosophies of virtue and moral choices. Both of them have multiple identities. Slawek is a Pole who has adapted the Dutch nationality. The author is a born Dutch who also carries an American passport. What brings them together intellectually, the author thinks, is a conviction that they have to bring culture into the scientific pursuits.

Originality/value
– Very few academic studies pointed out that cultural repertoire of value qchoices involves an on-going cultural negotiation. The author has succeeded in legitimizing the concept of culture in the teaching and research. Other researchers may employ the notions of culture and value to develop a value-based approach to the economy. The paper helps to show that identities get stabilized, that people are in need of stabilizing their values, and with those their identities.
Analysis of the traveltime sensitivity kernels for an acoustic transversely isotropic medium with a vertical axis of symmetry
Authors: Djebbi Ramzi , Plessix René‐Édouard , Alkhalifah Tariq 
Published: February 2016

ABSTRACTIn anisotropic media, several parameters govern the propagation of the compressional waves. To correctly invert surface recorded seismic data in anisotropic media, a multi‐parameter inversion is required. However, a tradeoff between parameters exists because several models can explain the same dataset. To understand these tradeoffs, diffraction/reflection and transmission‐type sensitivity‐kernels analyses are carried out. Such analyses can help us to choose the appropriate parameterization for inversion. In tomography, the sensitivity kernels represent the effect of a parameter along the wave path between a source and a receiver. At a given illumination angle, similarities between sensitivity kernels highlight the tradeoff between the parameters. To discuss the parameterization choice in the context of finite‐frequency tomography, we compute the sensitivity kernels of the instantaneous traveltimes derived from the seismic data traces. We consider the transmission case with no encounter of an interface between a source and a receiver; with surface seismic data, this corresponds to a diving wave path. We also consider the diffraction/reflection case when the wave path is formed by two parts: one from the source to a sub‐surface point and the other from the sub‐surface point to the receiver. We illustrate the different parameter sensitivities for an acoustic transversely isotropic medium with a vertical axis of symmetry. The sensitivity kernels depend on the parameterization choice. By comparing different parameterizations, we explain why the parameterization with the normal moveout velocity, the anellipitic parameter η, and the δ parameter is attractive when we invert diving and reflected events recorded in an active surface seismic experiment.
Demography of the critically endangered Balearic shearwater: the impact of fisheries and time to extinction
Authors: Genovart Meritxell , Arcos José Manuel , Álvarez David , McMinn Miguel , Meier Rhiannon , B. Wynn Russell , Guilford Tim , Oro Daniel 
Published: February 2016

Summary

World‐wide, many seabirds are affected by fisheries in opposing ways: as a source of mortality from bycatch, but also by providing discards as a predictable and abundant food resource. This applies to the Balearic shearwater Puffinus mauretanicus, the most endangered European seabird, whose time to extinction was estimated at only ˜40 years a decade ago.

Since the previous assessment, new data and more sophisticated demographic modelling have become available, and new fishing policies from the European Union (Common Fisheries Policy, CFP) will apply, posing different scenarios for the viability of the species. Thus, there is both an urgent need and an opportunity for a more reliable update of the conservation status of the species.

Demographic data were collected between 1985 and 2014 at one of the world's largest colonies. Most demographic parameters were estimated using multievent capture–recapture modelling. Some parameters, such as bycatch rate, immature individual survival and recruitment, were estimated for the first time. We incorporated estimates into stochastic population models to forecast time to extinction and assess the viability under different management scenarios, accounting for upcoming fishing policies.

Adult survival was much lower than expected (0·809, SE: 0·013) and largely influenced by bycatch, which accounted for a minimum of 0·455 (SE: 0·230) of total mortality. Breeding success was positively correlated with discard availability. Recruitment started at low rates in 3‐year‐old birds (0·030, SE: 0·0455), increasing in following age classes and was almost complete at 6 years. Under the present scenario, we predict a time to extinction of 61 years (95% CI: 55–69).

Synthesis and applications. Population projections suggest that the actual impact of fisheries on Balearic shearwaters is unsustainable and the imminent discard ban under the new Common Fisheries Policy may accelerate the declining trend. This study demonstrates that reducing the bycatch rates of fisheries is an unavoidable and urgent conservation measure for avoiding the extinction of the species. We also advise setting up demographic long‐term studies, to allow researchers to diagnose, with reliability, the effectiveness of management actions. These actions will also benefit many other marine top‐predator species affected by this anthropogenic impact.
Candidate‐centred electoral systems and change in incumbent vote share: A cross‐national and longitudinal analysis
Authors: SÖDERLUND PETER 
Published: February 2016

AbstractThis study examines if prime minister's parties are punished or rewarded by voters to a lesser extent in candidate‐centred electoral systems compared to party‐centred systems. Candidate‐centred systems allow the voters greater choice in determining the fate of individual candidates at the district level and create incentives for candidates to cultivate a personal vote rather than pursuing a party vote. Voters in these systems are more likely to focus on individual candidates than on parties, thus fostering individual accountability at the expense of collective (party) accountability. Cross‐sectional time‐series data for 23 OECD countries between 1961 and 2014 were analysed. Two indices of intraparty efficiency (the Farrell–McAllister Index and the Shugart Index) were used to capture the candidate‐centredness of electoral systems. The analysis of aggregate‐level data with almost 300 observations showed that incumbent parties tend to win or lose fewer votes in candidate‐centred electoral systems. This effect has become stronger over time. Candidate‐centredness has a weak moderating impact on the state of the economy on the degree of public sanctioning of government parties.
Diabetes, hyperglycemia, and the burden of functional disability among older adults in a community‐based study
Authors: Godino Job G , Appel Lawrence J , Gross Alden L , Schrack Jennifer A , Parrinello Christina M , Kalyani Rita R , Windham Beverly Gwen , Pankow James S , Kritchevsky Stephen B , Bandeen‐Roche Karen , Selvin Elizabeth 
Published: February 2016

AbstractBackgroundThere is a need for continued surveillance of diabetes‐related functional disability. In the present study, we examined associations between diabetes, hyperglycemia, and the burden of functional disability in a community‐based population.MethodsA cross‐sectional analysis was conducted of 5035 participants who attended Visit 5 (2011–13) of the Atherosclerosis Risk in Communities study. Functional disability was dichotomously defined by any self‐reported difficulty performing 12 tasks essential to independent living grouped into four functional domains. Associations of diagnosed diabetes (via self‐report) and undiagnosed diabetes and prediabetes (via HbA1c) with functional disability were evaluated using Poisson regression.ResultsParticipants had a mean age of 75 years, 42 % were male, 22 % were Black, and 31 % had diagnosed diabetes. Those with diagnosed diabetes had a significantly greater burden of functional disability than those without diabetes, even after adjustment for demographics, health behaviors, and comorbidities: prevalence ratios (95 % confidence intervals) were 1.24 (1.15, 1.34) for lower extremity mobility, 1.14 (1.07, 1.21) for general physical activities, 1.33 (1.16, 1.52) for instrumental activities of daily living (ADL), and 1.46 (1.24, 1.73) for ADL (all P < 0.05). The associations of undiagnosed diabetes and prediabetes with disability were not statistically significant (all P > 0.05).ConclusionsAmong older adults, the burden of functional disability associated with diabetes was not entirely explained by known risk factors, including comorbidities. Hyperglycemia below the threshold for the diagnosis of diabetes was not associated with disability. Research into effective strategies for the prevention of functional disability among older adults with diabetes is needed.
Is deep neuromuscular block beneficial in laparoscopic surgery? No, probably not
Authors: Kopman Aaron F. , Naguib Mohamed 
Published: February 2016

BackgroundThere is currently a controversy regarding the need for and clinical benefit of maintaining deep neuromuscular block (post‐tetanic counts of 1 or 2) vs. moderate block (train‐of‐four counts of 1–3) for routine laparoscopic surgery. Two recent review articles on this subject arrived at rather different conclusions. This manuscript is part of Pro/Con debate from the authors of these two reviews.MethodsThe authors of the Pro and Con sides of the debate had the opportunity to read each other manuscripts and worked from the same basic database of references.ResultsThe present authors could find only one peer‐reviewed paper which presented objective evidence supporting the proposition that deep neuromuscular block provides superior operating conditions for the surgeon during laparoscopic surgery.ConclusionThere is not enough good evidence available to justify the routine use of deep neuromuscular block for laparoscopic surgery and the associated expense of high‐dose sugammadex.
Radiation recall pneumonitis induced by erlotinib after palliative thoracic radiotherapy for lung cancer: Case report and literature review
Authors: Awad Raef , Nott Louise 
Published: February 2016

AbstractRadiation lung injury usually develops 1–6 months after cessation of radiation therapy to the lung. Acute change in the previously irradiated lung after administration of antineoplastic agent is known as radiation recall pneumonitis. Erlotinib is a reversible epidemal growth factor receptor tyrosine kinase inhibitor, which is effective for patients with advanced lung cancer with epidermal growth factor receptor mutations. Here we report a rare case of radiation recall pneumonitis following treatment with erlotinib 4 months after palliative radiotherapy to the lung. A 76‐year‐old man with non–small cell lung cancer was treated with polychemotherapy, palliative thoracic irradiation (30 Gy in 12 fractions) and erlotinib thereafter. Two months after administration of erlotinib he developed of severe dyspnea, cough, anorexia and lack of energy. CT chest revealed extensive radiation pneumonitis. Erlotinib was ceased and high‐dose steroids were started. The symptoms ultimately resolved and erlotinib was resumed cautiously after 11 weeks. On dosimetric analysis, lung V20 and the mean lung dose were 20.33% and 10.7 Gy, respectively, and hence, the risk of radiation pneumonitis is very low. These data indicate that systemic administration of erlotinib after low‐dose palliative radiation therapy can be associated with unexpected toxicity when visceral organs are within the radiation field.