bluuebunny/crossref_metadata_2025_split huggingface dataset:
The build-up of the red sequence in the Hercules cluster
Authors: Agulli I. , Aguerri J. A. L. , Dominguez Palmero L. , Diaferio A. 
Published: May 2016

Abstract
We present the study of the colour–magnitude diagram of the cluster Abell 2151 (A 2151), with a particular focus on the low-mass end. The deep spectroscopy with AF2/WYFFOS@WHT and the caustic method enable us to obtain 360 members within 1.3 R200 and absolute magnitude $M_r \lesssim M_r^{\ast }+6$. This nearby cluster shows a well defined red sequence up to Mr ∼ −18.5; at fainter magnitudes only 36 per cent of the galaxies lie on the extrapolation of the red sequence. We compare the red sequences of A 2151 and Abell 85, which is another nearby cluster with similar spectroscopic data, but with different mass and dynamical state. Both clusters show similar red sequences at the bright end (Mr ≤ −19.5), whereas large differences appear at the faint end. This result suggests that the reddening of bright galaxies is independent of environment, unlike the dwarf population (Mr ≥ −18.0).
Disseminated Talaromyces marneffei and Mycobacterium abscessus in a Patient With Anti-Interferon-γ Autoantibodies
Authors: Pruetpongpun Nattapol , Khawcharoenporn Thana , Damronglerd Pansachee , Suthiwartnarueput Worapop , Apisarnthanarak Anucha , Rujanavej Sasinuch , Suwantarat Nuntra 
Published: May 2016

Abstract
Anti-interferon (IFN)-γ autoantibodies are increasingly recognized as a cause of adult-onset immunodeficiency and increased risk for infections with intracellular pathogens. We report on disseminated Talaromyces (Penicillium) marneffei and Mycobacterium abscessus infection in a 72-year-old, human immunodeficiency virus noninfected, Thai man with anti-IFN-γ autoantibody. The patient was successfully treated with antimicrobial therapy and rituximab to control B cell-derived autoantibodies.
Antimicrobial defence and persistent infection in insects revisited
Authors: Makarova Olga , Rodriguez-Rojas Alex , Eravci Murat , Weise Chris , Dobson Adam , Johnston Paul , Rolff Jens 
Published: May 2016

Insects show long-lasting antimicrobial immune responses that follow the initial fast-acting cellular processes. These immune responses are discussed to provide a form of phrophylaxis and/or to serve as a safety measure against persisting infections. The duration and components of such long-lasting responses have rarely been studied in detail, a necessary prerequisite to understand their adaptive value. Here, we present a 21 day proteomic time course of the mealworm beetleTenebrio molitorimmune-challenged with heat-killedStaphylococcus aureus. The most upregulated peptides are antimicrobial peptides (AMPs), many of which are still highly abundant 21 days after infection. The identified AMPs included toll and imd-mediated AMPs, a significant number of which have no known function againstS. aureusor other Gram-positive bacteria. The proteome reflects the selective arena for bacterial infections. The results also corroborate the notion of synergistic interactionsin vivothat are difficult to modelin vitro.This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Analytical considerations for comparative transcriptomics of wild organisms
Authors: Krabbenhoft Trevor J. , Turner Thomas F. 
Published: May 2016

AbstractComparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. However, important data handling and quality control challenges remain, particularly when working with non-model species outside of a controlled laboratory environment. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present computational solutions for processing, annotating and summarizing comparative transcriptome data for assessing genome-environment interactions across species. The resulting bioinformatics pipeline addresses the following points: (1) the potential importance of “essential genes”, (2) the influence of microbiomes and other exogenous DNA, (3) potentially novel, species-specific genes, and (4) genomic rearrangements (e.g., whole genome duplication). Quantitative consideration of these points contributes to a firmer foundation for future comparative work across distantly related taxa for a variety of sub-disciplines, including stress and immune response, community ecology, ecotoxicology, and climate change.
HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads
Authors: Mangul Serghei , Yang Harry (Taegyun) , Hormozdiari Farhad , Tseng Elizabeth , Zelikovsky Alex , Eskin Eleazar 
Published: May 2016

AbstractSequencing of RNA provides the possibility to study an individual’s transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms. In this paper, we present HapIso (Haplotype-specific Isoform Reconstruction), a method able to tolerate the relatively high error-rate of the single-molecule platform and partition the isoform reads into the parental alleles. Phasing the reads according to the allele of origin allows our method to efficiently distinguish between the read errors and the true biological mutations. HapIso uses a k-means clustering algorithm aiming to group the reads into two meaningful clusters maximizing the similarity of the reads within cluster and minimizing the similarity of the reads from different clusters. Each cluster corresponds to a parental haplotype. We use family pedigree information to evaluate our approach. Experimental validation suggests that HapIso is able to tolerate the relatively high error-rate and accurately partition the reads into the parental alleles of the isoform transcripts. Furthermore, our method is the first method able to reconstruct the haplotype-specific isoforms from long single-molecule reads.The open source Python implementation of HapIso is freely available for download at https://github.com/smangul1/HapIso/
From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterning
Authors: McDowell Gary S. , Rajadurai Suvithan , Levin Michael 
Published: May 2016

AbstractConsistent left-right asymmetry is a fundamental aspect of the bodyplan across phyla, and errors of laterality form an important class of human birth defects. Its molecular underpinning was first discovered as a sequential pathway of left-and right-sided gene expression that controlled positioning of the heart and visceral organs. Recent data have revised this picture in two important ways. First, the physical origin of chirality has been identified; cytoskeletal dynamics underlie the asymmetry of single cell behavior and of patterning of the left-right axis. Second, the pathway is not linear: early disruptions that alter the normal sidedness of upstream asymmetric genes do not necessarily induce defects in the laterality of the downstream genes or in organsitus. Thus, the LR pathway is a unique example of two fascinating aspects of biology: the interplay of physics and genetics in establishing large-scale anatomy, and regulative (shape-homeostatic) pathways that correct errors of patterning over time. Here, we review aspects of asymmetry from its intracellular, cytoplasmic origins to the recently-uncovered ability of the LR control circuitry to achieve correct gene expression and morphology despite reversals of key “determinant” genes. We provide novel functional data, inXenopus laevis, on conserved elements of the cytoskeleton that drive asymmetry, and repair of downstream gene expression anomalies over developmental time. LR patterning can thus serve as a paradigm of how subcellular physics and gene expression cooperate to achieve developmental robustness of a body axis.
myCircos: Facilitating the Creation and Use of Circos Plots Online
Authors: Labelle Caroline , Boucher Geneviève , Lemieux Sébastien 
Published: May 2016

AbstractCircos plots were designed to display large amounts of processed genomic information on a single graphical representation. The creation of such plots remains challenging for less technical users as the leading tool requires command-line proficiency. Here, we introduce myCircos, a web application that facilitates the generation of Circos plots by providing an intuitive user interface, adding interactive functionalities to the representation and providing persistence of previous requests. myCircos is available at:http://mycircos.iric.ca. Non registered users can explore the application through the Guest user. Source code (for local server installation) is available upon request.
Should the international accounting standards board have responsibility for human rights?
Authors: McPhail Ken , Macdonald Kate , Ferguson John 
Published: May 2016

Purpose– The purpose of this paper is to explore the basis for, and ramifications of, applying relevant human rights norms – such as the United Nations Guiding Principles on Business and Human Rights – to the International Accounting Standards Board (IASB). In doing so, the paper seeks to contribute to scholarship on the political legitimisation of the IASB’s structure and activities under prevailing global governance conditions.Design/methodology/approach– The paper explores three distinct argumentative logics regarding responsibilities for justice and human rightsvis-à-visthe IASB. First, the authors explore the basis for applying human rights responsibilities to the IASB through reasoning based on the analysis of “public power” (Macdonald, 2008) and public authorisation. Second, the authors develop the reasoning with reference to recent attempts by legal scholars and practitioners to apply human rights obligations to other non-state and transnational institutions. Finally, the authors develop reasoning based on Thomas Pogge’s (1992b) ideas about institutional harms and corresponding responsibilities.Findings– The three distinct argumentative logic rest on differing assumptions – the goal is not to reconcile or synthesise these approaches, but to propose that these approaches offer alternative and in some ways complementary insights, each of which contributes to answering questions about how human rights obligations of the IASB should be defined, and how such a responsibility could be “actually proceduralised”.Originality/value– The analysis provides an important starting point for beginning to think about how responsibilities for human rights might be applied to the operation of the IASB.
Rana Plaza collapse aftermath: are CSR compliance and auditing pressures effective?
Authors: Sinkovics Noemi , Hoque Samia Ferdous , Sinkovics Rudolf R. 
Published: May 2016

Purpose
– The purpose of this paper is to investigate the intended and unintended consequences of compliance and auditing pressures in the Bangladeshi garment industry. To explore this issue the authors draw on three medium-sized suppliers. The institutional changes that followed the Rana Plaza accident in April 2013 make Bangladesh in general and the garment industry in particular an interesting and suitable research setting for standards compliance.

Design/methodology/approach
– The study adopts a multiple case study approach. Face-to-face interviews have been conducted with the owners of three Bangladeshi garment manufacturing firms and several workers. Additionally, organisational documents and local newspaper articles had been collected wherever possible.

Findings
– The results indicate that the pressure for compliance has led the case companies to prioritise the implementation of measurable standards over the socially grounded needs and priorities of workers. As a consequence certain initiatives instead of adding new social value in fact destroyed previously existing social value. Furthermore, the pressure for compliance created the necessity to find ways to cover the sizable cost of compliance. This prompted firms to pursue process upgrading through technological advancements and increased work pressures on the labour force. These initiatives led to an increased power imbalance and the exclusion of unskilled workers from the job market.

Research limitations/implications
– The paper contributes to the understanding of the human rights implications of compliance and auditing pressures and initiatives. Furthermore, in order to further enrich existing knowledge in the critical accounting literature, the study draws on insights from the global value chains (GVC) and international business (IB) literatures.

Originality/value
– The paper contributes to the understanding of the human rights implications of compliance and auditing pressures and initiatives. Furthermore, in order to further enrich existing knowledge in the critical accounting literature, the study draws on insights from the GVC and IB literatures.
The use of imagery in the campaign speeches of Barack Hussein Obama and John McCain during the 2008 US Presidential Election
Authors: McGuire David , Garavan Thomas N. , Cunningham James , Duffy Greg 
Published: May 2016

Purpose– The use of imagery in leadership speeches is becoming increasingly important in shaping the beliefs and actions of followers. The purpose of this paper is to investigate the use of speech imagery and linguistic features employed during the 2008 US Presidential Election campaign.Design/methodology/approach– The authors analysed a total of 264 speeches (160 speeches from Obama and 104 speeches from McCain) delivered throughout the 2008 US Presidential Election and identified 15 speech images used by the two candidates. Both descriptive coding and axial coding approaches were applied to the data and speech images common to both candidates were further subjected to Pennebakeret al.(2003) linguistic inquiry methodology.Findings– The analysis revealed a number of important differences with Obama using inclusive language and nurturing communitarian values, whereas McCain focusing on personal actions and strict, conservative individualistic values. The use of more inclusive language by Obama was found to be significant in three of the five speech images common to both candidates.Research limitations/implications– The research acknowledges the difficulty of measuring the effectiveness of speech images without taking into account wider factors such as tone of voice, facial expression and level of conviction. It also recognises the heavy use of speechwriters by presidential candidates whilst on the campaign trail, but argues that candidates still exert a strong influence through instructions to speechwriters and that speeches should reflect the candidate’s values and beliefs.Originality/value– The research findings contribute to the emerging stream of leadership research that addresses language content issues surrounding and embedded in the leadership process. The research argues that leaders’ speeches provide a fertile ground for conducting research and for examining the evolving relationship between leaders and followers.
What helps successful community groups (involving peers support workers) to develop?
Authors: Deering Kris , Fieldhouse Jon , Parmenter Vanessa 
Published: May 2016

Purpose
– The purpose of this paper is to explore features of successful peer supported community support groups hosted by St Mungo’s and partners.

Design/methodology/approach
– Literature review and theme construction.

Findings
– Overall the review confirmed existing findings that successful support groups foster mutually supportive, reciprocal relationships capable of inspiring hope among group members. This paper will concentrate on findings that co-production was indicative of successful groups in terms of shared aims, negotiated agendas, clear communication, and engagement with the wider community.

Research limitations/implications
– A group’s success was seen in terms of growth in members’ self-esteem, empowerment, and optimism, which this paper proposes could become part of a conceptual framework of a learning organisational culture.

Originality/value
– Developing understanding of a rapidly growing phenomenon in community-based mental health care and presenting this in terms of a particular organisational culture.
Repeated fires trap Amazonian blackwater floodplains in an open vegetation state
Authors: Flores Bernardo M. , Fagoaga Raquel , Nelson Bruce W. , Holmgren Milena 
Published: May 2016

Summary

Climate change may increase the occurrence of droughts and fires in the Amazon. Most of our understanding on how fire affects tropical ecosystems is based on studies of non‐flooded forest–savanna ecotones. Nonetheless, tropical floodplain forests in the Amazon can burn severely during extreme droughts. The mechanisms slowing down forest regeneration in these ecosystems remain poorly understood and have never been assessed in the field.

We studied the recovery of Amazonian blackwater floodplain forests after one and two fire events. We used Landsat images to map fire history and conducted field surveys to measure forest structure, tree species richness, tree seed bank and post‐fire invasion of herbaceous plants.

Sites burnt once had on average 0% trees, 6% tree seed abundance, 23% tree seed species richness and 8% root mat thickness compared to unburnt forests. In contrast, herbaceous cover increased from 0 to 72%. Nonetheless, forest structure and diversity recovered slowly towards pre‐burn levels, except for tree seed banks that remained depleted even 15 years after fire.

Sites burnt twice had on average 0% trees, 1% tree seed abundance, 3% tree seed species richness and 1% root mat thickness compared to unburnt forests. Herbaceous cover increased to 100%. Mean recovery of tree basal area was 50% slower and of root mat thickness 93% slower compared to recovery in sites burnt once. Tree seed banks did not recover at all, and herbaceous cover persisted close to 100% for more than 20 years after the second fire.

Synthesis and applications. Our results indicate that after a second fire event, Amazonian blackwater floodplain forests lose their recovery capacity, and persist in a non‐forested state dominated by herbaceous vegetation. Such fragility implies that preventing human ignited fires during drought episodes is a particularly important conservation strategy for these ecosystems.
Status Incentives and Corporate Giving: Evidence From China's Political Reform On Private Enterprises
Authors: Chen Zhao , Zhang Jipeng 
Published: May 2016

AbstractIn this paper, we estimate the effect of status incentives on charitable giving by exploiting a natural experiment during China's political reform in 2002 that significantly improved the status of private entrepreneurs and their enterprises. We find that exogenous changes in social, political and economic status of private entrepreneurs led to a significant increase in the corporate giving of their privately owned firms. The findings are robust when we use different samples of the data and when we control for a large set of entrepreneurs and firm characteristics in the regression analysis.
Evaluation and establishment of a ward‐based geriatric liaison service for older urological surgical patients: Proactive care of Older People undergoing Surgery (POPS)‐Urology
Authors: Braude Philip , Goodman Anna , Elias Tania , Babic‐Illman Gordana , Challacombe Ben , Harari Danielle , Dhesi Jugdeep K. 
Published: May 2016

ObjectiveTo assess the impact of introducing and embedding a structured geriatric liaison service, Proactive care of Older People undergoing Surgery (POPS)‐Urology, using comprehensive geriatric assessment methodology, on an inpatient urology ward.Patients and MethodsA phased quality improvement project was undertaken using stepwise interventions. Phase 1 was a before‐and‐after study with initiation of a daily board round, weekly multidisciplinary meeting, and targeted geriatrician‐led ward rounds for elective and emergency urology patients aged ≥65 years admitted over two 1‐month periods. Outcomes were recorded from medical records and discharge documentation, including length of inpatient stay, medical and surgical complications, and 30‐day readmission and mortality rates. Phase 2 was a quality improvement project involving Plan‐Do‐Study‐Act cycles and qualitative staff surveys in order to create a Geriatric Surgical Checklist (GSCL) to standardize the intervention in Phase 1, improve equity of care by extending it to all ages, improve team‐working and streamline handovers for multidisciplinary staff.ResultsPhase 1 included 112 patients in the control month and 130 in the intervention month. The length of inpatient stay was reduced by 19% (mean 4.9 vs 4.0 days; P = 0.01), total postoperative complications were lower (risk ratio 0.24 [95% confidence interval 0.10, 0.54]; P = 0.001). A non‐significant trend was seen towards fewer cancellations of surgery (10 vs 5%; P = 0.12) and 30‐day readmissions (8 vs 3%; P = 0.07). In Phase 2, the GSCL was created and incrementally improved. Questionnaires repeated at intervals showed that the GSCL helped staff to understand their role better in multidisciplinary meetings, improved their confidence to raise issues, reduced duplication of handovers and standardized identification of geriatric issues. Equity of care was improved by providing the intervention to patients of all ages, despite which the time taken for the daily board round did not lengthen.ConclusionThis is the first known paper describing the benefits of daily proactive geriatric intervention in elective and emergency urological surgery. The results suggest that using a multidisciplinary team board round helps to facilitate collaborative working between surgical and geriatric medicine teams. The GSCL enables systematic identification of patients who require a focused comprehensive geriatric assessment. There is potential to transfer the GSCL package to other surgical specialties and hospitals to improve postoperative outcomes.