bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilization of tissue ploidy level variation inde novotranscriptome assembly ofPinus sylvestris
Authors: Ojeda Dario I. , Mattila Tiina , Ruttink Tom , Kujala Sonja , Kärkkäinen Katri , Verta Jukka-Pekka , Pyhäjärvi Tanja 
Published: December 2018

AbstractCompared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use ofde novoassembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies, including the utility of haploid (megagametophyte) tissue duringde novoassembly as single-allele guides, for six individuals and five different tissues inPinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as risk factors in a diverse hotspot plant genus
Authors: Dinnage Russell , Skeels Alex , Cardillo Marcel 
Published: December 2018

AbstractComparative models used to predict species threat status often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genusHakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology, and spatial data, to calculate latent extinction risk (potential for non-threatened species to become threatened), and estimate the most important drivers of risk for individual species. This could be of value for proactive conservation decision-making that targets species of concern before they become threatened.
An evidence-based training and support course for caregivers of children with foetal alcohol spectrum disorder (FASD) in New Zealand
Authors: Gibbs Anita 
Published: December 2018

PurposeThe purpose of this paper is to outline the development of an evidence-based training and support course for caregivers of children with foetal alcohol spectrum disorder (FASD) in New Zealand, and a brief evaluation undertaken. The seven-week caregiver training course takes an empowerment and advocacy orientation, and the aim is to assist caregivers who are caring for children with, or suspected to have FASD, develop greater resilience and strategies to help their families live successfully with impairments in a disabling society.Design/methodology/approachA total of 13 parents and caregivers received a seven times two-hour weekly group programme of talks, exercises and case study discussions focused on the following objectives: an increased knowledge of FASD; an increased knowledge of successful strategies and interventions that can be used to help families; and having an opportunity to foster strong peer-support relationships with others who share the lived experience of FASD. A brief interview-based evaluation was undertaken to ascertain caregivers’ views of the course, its benefits and limitations.FindingsCaregivers valued both the content and process of the training course. They highlighted that strength of the training was the delivery by experienced, professionally trained caregivers of children with FASD. They valued the opportunity to spend time with peers in similar circumstances who understood the challenges of parenting a child with FASD.Originality/valueA short evidence-based specialist training course for parents and caregivers with an empowerment and peer-support orientation is beneficial to parenting children with FASD.
Lattice Boltzmann simulation of free convection’s hydrothermal aspects in a finned/multi-pipe cavity filled with CuO-water nanofluid
Authors: Rahimi Alireza , Azarikhah Pouria , Kasaeipoor Abbas , Hasani Malekshah Emad , Kolsi Lioua 
Published: December 2018

PurposeThis paper aims to investigate the natural convection fluid flow and heat transfer in a finned/multi-pipe cavity.Design/methodology/approachThe cavity is filled with the CuO-water nanofluid. The Koo–Kleinstreuer–Li model is used to estimate the dynamic viscosity and consider Brownian motion. On the other hand, the effect of the shapes of nanoparticles on the thermal conductivity and related heat transfer rate is presented.FindingsIn the present investigation, the governing parameters are Rayleigh number, CuO nanoparticle concentration in pure water and the thermal arrangements of internal active fins and solid bodies. Impacts of these parameters on the nanofluid flow, heat transfer rate, total/local entropy generation and heatlines are presented. It is concluded that adding nanoparticles to the pure fluid has a significant positive influence on the heat transfer performance. In addition, the average Nusselt number and total entropy generation have direct a relationship with the Rayleigh number. The thermal arrangement of the internal bodies and fins is a good controlling tool to determine the desired magnitude of heat transfer rate.Originality/valueThe originality of this paper is to use the lattice Boltzmann method in simulating the nanofluid flow and heat transfer within a cavity included with internal active bodies and fins.
A new framework to support Lean Six Sigma deployment in SMEs
Authors: Moya Carlos Abraham , Galvez Daniel , Muller Laurent , Camargo Mauricio 
Published: December 2018

Purpose
The purpose of this paper is to propose an assessment approach to evaluate the organizational capabilities to deploy a Lean Six Sigma (LSS) strategy.

Design/methodology/approach
Based on a comprehensive literature review, critical success factors required to deploy LSS were defined. These key factors are evaluated by a questionnaire based on maturity grids and structured as a multi-criteria model to compute a potential LSS performance indicator. This approach is illustrated through two case studies.

Findings
To promote a successful implementation of LSS in SMEs, it is necessary to consider five main critical factors. The evaluation of these factors could be achieved thanks to a multi-criterion-based maturity indicator for the LSS implementation. The case studies show that this approach allows SMEs to understand their strengths and weaknesses and thus better prepare the implementation of LSS.

Research limitations/implications
The proposed tool identifies characteristics of companies leading to successful LSS implementation; but is not yet able to provide a detailed strategy to improve them. The case studies were applied to manufacturing companies; therefore, there is no evidence of conclusions in the context of services.

Practical implications
The proposed methodology will help managers and practitioners to evaluate the readiness level of a company to implement LSS. Then, they could estimate the effort required to achieve the LSS deployment.

Originality/value
This paper proposes a new metric of the capacity to implement the LSS successfully in SMEs: the Lean Six Sigma Global Index. This indicator is based on a survey completed by managers and supported by observable phenomena to establish a tailored diagnosis before the LSS implementation.
The dual roles of the government in cloud computing assimilation: an empirical study in China
Authors: Wang Nianxin , Xue Yajiong , Liang Huigang , Wang Zhining , Ge Shilun 
Published: December 2018

PurposeThe purpose of this paper is to investigate the government roles in cloud computing assimilation along two dimensions: government regulation and government support.Design/methodology/approachA research model was developed to depict the dual roles of government regulation and government support in cloud computing assimilation as well as the mediating effect of top management support (TMS). Using survey data collected from 376 Chinese firms that have already adopted cloud services, the authors tested the research model.FindingsThe impacts of both government regulation and government support on cloud computing assimilation are partially mediated by TMS. Government support exerts stronger impacts on TMS than government regulation.Research limitations/implicationsThis study extends the current information systems literature by highlighting the specific mechanisms through which governments influence firms’ assimilation of cloud computing.Practical implicationsGovernments in developing countries could actively allocate funds or enact policies to effectively encourage cloud computing assimilation.Originality/valueThis study would complement previous findings about government regulation, and develop a more holistic understanding about the dual roles of governments in information technology innovation assimilation.
Social enterprising informing our concept; exploring informal micro social enterprise
Authors: Anderson Alistair R. , Younis Sohail , Hashim Hina , Air Carol 
Published: December 2018

Purpose
The paper investigates an unusual form of social enterprising located in a poor region of Pakistan. The purpose of this paper is to examine a novel form of micro social enterprise. Their form and functions are considered, examining how they conform to what is expected of a social enterprise. The extreme cases are analysed to reflect on what constitutes the explanatory characteristics of a social enterprise.

Design/methodology/approach
Information on examples of micro social entrepreneurship was collected from the troubled context of Khyber Pakhtunkhwa, a very poor region of Pakistan. Using the constant comparison method, explanatory themes of structure and practice are drawn out.

Findings
These enterprising social agents were engaged in opening up an opportunity space for those disadvantaged by the context. Driven by a strong sense of community responsibility, they drew upon limited, but culturally available resources. Relevance, embeddedness and informality were identified as structural characteristics, and bricolage and effectuation, frugality and social responsibility emerged as practices. Not only did context shape what they did and how they did it, but the purpose of these enterprises was also to help reshape context. From this analysis, it is argued that conceptual concerns should be directed towards behaviours; it should be asked how are enterprises agents of social change, and how are they enterprising?

Research limitations/implications
It is argued that a robust indicator for social enterprise is not what they are, but what they do. Consequently, for understanding and theorising, it is suggested that the focus remain on enterprising. This study was limited to unusual cases which may be atypical and ungeneralisable. Nonetheless, the concept – enterprising – may have theoretical applications.

Social implications
In reviewing the analysis and findings, it is noted that the proposals in the paper may comprise the early stages of a theory of social entrepreneurship practice. There may be considerable explanatory power in examining the interplays between the agency of social enterprises and the structures that are constituted in the formal and informal institutions with whom they interact.

Originality/value
Descriptively, the account draws attention to a possibly neglected phenomenon. Moreover, the extreme cases draw out the significance of a localised practice. Conceptually, there may be value in prioritising practice in social enterprise rather than form and structure.
Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov
Authors: Kutsuna Ryo , Miyoshi‐Akiyama Tohru , Mori Koji , Hayashi Masahiro , Tomida Junko , Morita Yuji , Tanaka Kaori , Kawamura Yoshiaki 
Published: December 2018

AbstractTaxonomic studies of strain PAGU 1678T, an obligately anaerobic, gram‐positive, spore‐forming bacterium isolated from biobreeding rat feces, were performed. This strain has been demonstrated to have the ability to exacerbate pathosis in a mouse model of dextran sulfate sodium‐induced ulcerative colitis. Phylogenetic analysis based on the 16S rRNA gene showed high homology with Paraclostridium bifermentans. To clarify the correct taxonomic position of strain PAGU 1678T, a comparative taxonomic study using P. bifermentans PAGU 2008T (═JCM 1386T) and the closely related bacterial species P. benzoelyticum PAGU 2068T (═LMG 28745T) was carried out. Despite the close similarity of 16S rRNA gene sequences, DNA‐DNA hybridization between strain PAGU 1678T and P. bifermentans PAGU 2008T was 60.03% on average, average nucleotide identity was 96.17%, and it was shown to have different genomic sequences. Biochemically, strain PAGU 1678T could be differentiated from P. bifermentans PAGU 2008T by H2S production. Furthermore, strain PAGU 1678T was characterized by the presence of two phospholipids with different polarity on polar lipid analysis. In addition, strain PAGU 1678T differed from P. bifermentans PAGU 2008T in findings on whole‐cell protein analysis and matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry. On the basis of these biochemical and genetic characteristics, a novel subspecies of P. bifermentans with the name Paraclostridium bifermentans subsp. muricolitidis subsp. nov. is here proposed, with PAGU 1678T (═CCUG 72489T ═NBRC 113386T) as the type strain, which automatically creates P. bifermentans subsp. bifermentans subsp. nov. JCM 1386T (═ATCC 638T ═DSM 14991T).
Identification of a germline‐expression promoter for genome editing in Bombyx mori
Authors: Xu Jun , Chen Rong‐Mei , Chen Shu‐Qing , Chen Kai , Tang Lin‐Meng , Yang De‐Hong , Yang Xu , Zhang Yong , Song Hong‐Sheng , Huang Yong‐Ping 
Published: December 2018

AbstractIdentification of stage‐ and tissue‐specific cis‐regulatory elements will enable more precise genomic editing. In previous studies of the silkworm Bombyx mori, we identified and characterized several tissue‐ and sex‐specific cis‐regulatory elements using transgenic technology, including a female‐ and fat body‐specific promoter, vitellogenin, testis‐specific promoters, Radial spoke head 1 (BmR1) and beta‐tubulin 4 (Bmβ4). Here we report a cis‐regulatory element specific for a somatic and germ cell‐expressed promoter, nanos (Bmnos). We investigated activities of three truncated promoter sequences upstream of the transcriptional initiation site sequences of Bmnos in vitro (nos‐0.6kb, nos‐1kb and nos‐2kb) and in vivo (nos‐2kb). In BmN cultured cells, all three lengths drove expression of the gene encoding enhanced green fluorescence protein (EGFP), although nos‐2kb had the highest fluorescence activity. In transgenic silkworms, nos‐2kb drove EGFP expression at the early embryonic stage, and fluorescence was concentrated in the gonads at later embryonic stages. In addition, this cis‐regulatory element was not sex differentiated. The fluorescence intensity gradually weakened following the larval developmental stage in the gonads and were broadly expressed in the whole body. The nos‐2kb promoter drove the Cas9 system with efficiency comparable to that of the broad‐spectrum strong IE1 promoter. These results indicate that Bmnos is an effective endogenous cis‐regulatory element in the early embryo and in the gonad that can be used in applications involving the clustered, regularly interspaced, short palindromic repeats (CRISPR)/Cas9 system.
Cetuximab‐radiotherapy combination in the management of locally advanced cutaneous squamous cell carcinoma
Authors: Joseph Kurian , Alkaabi Khalifa , Warkentin Heather , Ghosh Sunita , Jha Naresh , Smylie Michael , Walker John 
Published: December 2018

AbstractIntroductionWe report the outcomes of using a combination of cetuximab with radiation therapy (Cetux‐RT) to treat a selected group of patients with locally advanced (unresectable) cutaneous squamous cell carcinoma (LA‐cSCC). This study presents two‐year efficacy and safety data for 8 patients with LA‐cSCC treated within a single institution.MethodsBetween 2014 and 2017 a total of eight patients (seven males, one female) with LA‐cSCC received curative intent treatment with Cetux‐RT. All patients received an initial loading dose of cetuximab at 400 mg/m2 seven days prior to radiotherapy, followed by weekly treatment with 250 mg/m2, continuing through the end of radiotherapy. Radiation doses were 6600 cGy/30 fr (n = 2), 6300 cGy/30fr (n = 2) and 5500 cGy/22 fr (n = 4).ResultsThe median age was 81 years (range, 55–87). The ECOG performance status of all patients was between 0 and 2. With a median duration of follow‐up of 25 months (range 10–48 months), five patients remain in a complete response. After a partial response, another patient has relapsed and is receiving palliative chemotherapy, while two patients have died during the period of follow up (one of whom died following progression of disease, the other of an unrelated cause). Treatment in this group of patients was well tolerated, with most toxicities ≤ grade 2, and no toxicities of grade 4/5 reported.ConclusionsCetux‐RT was well tolerated and provided durable disease control within this patient sample. Our data support the use of the Cetux‐RT regimen for selected patients with inoperable LA‐cSCC and adequate performance status.
Comparison of methods for measuring antibiotic consumption in an intensive care unit
Authors: Olsen Markus Harboe , Anhøj Jacob , Knudsen Jenny Dahl , Frimodt‐Møller Niels , Møller Kirsten 
Published: December 2018

Hospitals worldwide are working on minimizing unnecessary use of antimicrobials. To assess actual changes of antimicrobial usage, correct and precise measurements are necessary. This study aimed to compare data on the purchase of antibiotics from the pharmacy and the administration of antibiotics to patients, respectively, in an intensive care unit (ICU). Data were obtained from the Neurointensive Care Unit (NICU) at Rigshospitalet, Denmark. During a 23‐month period, comprising 10 770 bed‐days (BD), the ward purchased 16 908 defined daily doses (DDD) of antibiotics from the pharmacy, and 15 130 DDD and 41 304 individual doses were administered. Intraclass correlation coefficients (ICCs) were calculated; control and runcharts and a Bland–Altman plot were constructed. Pharmacy sales and drug administration data showed no systematic variation over time with a monthly overestimation of pharmacy sales data of 10% (95% confidence interval (CI), 6.20–14.3%) for all antibiotics, and 7% (95% CI: 1.81–11.1%) for broad‐spectrum antibiotics. The antibiotic consumption, without bed‐days, has a clinically acceptable ICC of >0.70 and no systematic difference is suggested by the Bland–Altman plot. In this study of a large NICU, whose antibiotic consumption varied at random, pharmacy sales data were an acceptable approximation of the actual summarized drug consumption.
Clinical effectiveness and safety of erythropoietin‐stimulating agents for the treatment of low‐ and intermediate‐1−risk myelodysplastic syndrome: a systematic literature review
Authors: Park Sophie , Greenberg Peter , Yucel Aylin , Farmer Caroline , O'Neill Frank , De Oliveira Brandao Cisio , Fenaux Pierre 
Published: December 2018

SummaryMany patients with lower‐risk myelodysplastic syndrome (MDS) experience anaemia, which has negative consequences. Erythropoiesis‐stimulating agents (ESAs) and their biosimilars are used to treat anaemia in MDS and, currently, epoetin alfa and darbepoetin alfa are commonly used and recommended by clinical guidelines. To better understand the evidence available on the use of ESAs for anaemia in lower‐risk MDS, we conducted a systematic literature review to identify randomized and nonrandomized prospective studies reporting on clinical efficacy/effectiveness, patient‐reported quality of life (QoL), and safety. We extended our review to include retrospective studies for darbepoetin alfa specifically and to ascertain the feasibility of completing an indirect network meta‐analysis comparing epoetin and darbepoetin alfa. Overall, 53 articles reporting on 35 studies were included. The studies indicated a clinical benefit of ESAs, with benefits observed across key clinical outcomes. ESAs showed consistent improvement in erythroid response rates (ESA‐naïve, 45–73%; previous ESA exposure, 25–75%) and duration of response. Comparative studies demonstrated similar progression to acute myeloid leukaemia and several showed improved overall survival and QoL. Limited safety concerns were identified. This analysis confirmed ESA therapy should be the foremost first‐line treatment of anaemia in most patients with lower‐risk MDS who lack the 5q deletion.
Initial evaluation of PET/CT with 18F‐FSU‐880 targeting prostate‐specific membrane antigen in prostate cancer patients
Authors: Saga Tsuneo , Nakamoto Yuji , Ishimori Takayoshi , Inoue Takahiro , Shimizu Yoichi , Kimura Hiroyuki , Akamatsu Shusuke , Goto Takayuki , Watanabe Hiroyuki , Kitaguchi Kosuke , Watanabe Masao , Ono Masahiro , Saji Hideo , Ogawa Osamu , Togashi Kaori 
Published: December 2018

This first‐in‐man study was carried out to evaluate the safety, whole‐body distribution, dose estimation, and lesion accumulation of 18F‐FSU‐880, a newly developed probe targeting prostate‐specific membrane antigen. Six prostate cancer patients with known metastatic lesions underwent serial whole‐body PET/computed tomography (CT) with 18F‐FSU‐880. Blood and urine were analyzed before and after PET/CT. Accumulation of 18F‐FSU‐880 in organs and metastatic lesions in serial PET images were evaluated by measuring the standardized uptake values. From the biodistribution data, the organ doses and whole‐body effective dose were calculated using OLINDA/EXM software was developed by Dr. Michael Stabin of Vanderbilt University, Nashville, Tennessee, USA. 18F‐FSU‐880 PET/CT could be carried out without significant adverse effects. High physiological uptake was observed in the salivary/lachrymal glands and kidneys. The effective dose was calculated to be 0.921 × 10−2 mSv/MBq. Known metastatic lesions were clearly visualized with high image contrast that increased with time, except in 1 patient, whose bone metastases were well‐controlled and inactive. The PET/CT with 18F‐FSU‐880 could be carried out safely and could clearly visualize active metastatic lesions. The present results warrant further clinical studies with a larger number of cases to verify the clinical utility of 18F‐FSU‐880 PET/CT in the management of prostate cancer patients.