bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust approach for identifying differentially abundant features in metagenomic samples
Authors: Sohn Michael B. , Du Ruofei , An Lingling 
Published: March 2015

AbstractMotivation: The analysis of differential abundance for features (e.g. species or genes) can provide us with a better understanding of microbial communities, thus increasing our comprehension and understanding of the behaviors of microbial communities. However, it could also mislead us about the characteristics of microbial communities if the abundances or counts of features on different scales are not properly normalized within and between communities, prior to the analysis of differential abundance. Normalization methods used in the differential analysis typically try to adjust counts on different scales to a common scale using the total sum, mean or median of representative features across all samples. These methods often yield undesirable results when the difference in total counts of differentially abundant features (DAFs) across different conditions is large.Results: We develop a novel method, Ratio Approach for Identifying Differential Abundance (RAIDA), which utilizes the ratio between features in a modified zero-inflated lognormal model. RAIDA removes possible problems associated with counts on different scales within and between conditions. As a result, its performance is not affected by the amount of difference in total abundances of DAFs across different conditions. Through comprehensive simulation studies, the performance of our method is consistently powerful, and under some situations, RAIDA greatly surpasses other existing methods. We also apply RAIDA on real datasets of type II diabetes and find interesting results consistent with previous reports.Availability and implementation: An R package for RAIDA can be accessed from http://cals.arizona.edu/%7Eanling/sbg/software.htm.Contact: anling@email.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Biodiversity baseline for large marine ecosystems: an example from the Barents Sea
Authors: Certain Grégoire , Planque Benjamin 
Published: March 2015

Abstract
Biodiversity is an increasingly important issue for the management of marine ecosystems. However, the proliferation of biodiversity indices and difficulties associated with their interpretation have resulted in a lack of clearly defined framework for quantifying biodiversity and biodiversity changes in marine ecosystems for assessment purpose. Recent theoretical and numerical developments in biodiversity statistics have established clear algebraic relationships between most of the diversity measures commonly used, and have highlighted those that most directly relates to the concept of biological diversity, terming them “true” diversity measures. In this study, we implement the calculation of these “true” diversity measures at the scale of a large-marine ecosystem, the Barents Sea. We applied hierarchical partitioning of biodiversity to an extensive dataset encompassing 10 years of trawl-surveys for both pelagic and demersal fish community. We quantify biodiversity and biodiversity changes for these two communities across the whole continental shelf of the Barents Sea at various spatial and temporal scales, explicitly identifying areas where fish communities are stable and variable. The method is used to disentangle areas where community composition is subject to random fluctuations from areas where the fish community is drifting over time. We discuss how our results can serve as a spatio-temporal biodiversity baseline against which new biodiversity estimates, derived from sea surveys, can be evaluated.
Percutaneous Kyphoplasty for the Treatment of Osteoporotic Vertebral Fractures With Intravertebral Fluid or Air
Authors: Niu Junjie , Song Dawei , Zhou Haifei , Meng Qian , Meng Bin , Yang Huilin 
Published: March 2015

Study Design:
A retrospective comparative study.

Objective:
To compare the characteristics of osteoporotic vertebral fractures (OVFs) with intravertebral fluid (IVF) and those with intravertebral air (IVA), and the efficacy of percutaneous balloon kyphoplasty (PKP) in treating OVFs with these 2 different intravertebral components.

Summary of Background Data:
Previous studies have focused on the efficacy of percutaneous vertebroplasty (PVP) and PKP in treating OVFs with intravertebral cleft. However, no prior studies investigated the impact of the different components of cleft on the therapeutic effect of PVP or PKP.

Methods:
On the basis of the presence of IVF or IVA signal on preoperative MR images, 22 patients were classified into IVF group and 13 patients into IVA group. The characteristics of patients with IVF and those with IVA were compared. The anterior and middle heights of the involved vertebrae, the kyphotic angles, the Visual Analogue Scale (VAS), and Oswestry Disability Index (ODI) scores were recorded preoperatively, 1 day after surgery, and at last follow-up.

Results:
Severe collapse of involved vertebrae (P=0.024) and the gap appearance of clefts (P=0.004) were significantly more common in IVA group than in IVF group. The vertebral heights, the local kyphotic angles, the VAS, and ODI scores were all significantly improved after PKP in both groups. However, the vertebral height restoration and kyphotic deformity correction were more significant in IVF group than in IVA group (P<0.001). No significant differences regarding VAS and ODI scores were detected between the 2 groups at each follow-up time.

Conclusions:
PKP is an effective treatment strategy for both OVFs with IVF and with IVA, whereas vertebral height restoration and kyphotic deformity correction are much more significant in vertebrae with IVF. Presence of IVA without fluid filling-in on MR images may indicate an advanced stage of intravertebral osteonecrosis.
Mapping the Conformational Landscape of a Dynamic Enzyme by Multitemperature and XFEL Crystallography
Authors: Keedy Daniel A. , Kenner Lillian R. , Warkentin Matthew , Woldeyes Rahel A. , Hopkins Jesse B. , Thompson Michael C. , Brewster Aaron S. , Van Benschoten Andrew H. , Baxter Elizabeth L. , Uervirojnangkoorn Monarin , McPhillps Scott E. , Song Jinhu , Alonso-Mori Roberto , Holton James M. , Weis William I. , Brunger Axel T. , Michael Soltis S. , Lemke Henrik , Gonzalez Ana , Sauter Nicholas K. , Cohen Aina E. , den Bedem Henry van , Thorne Robert E. , Fraser James S. 
Published: March 2015

AbstractDetermining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free electron laser (XFEL) crystallography. The “diffraction-before-destruction” nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states for a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function.
Is China transmuting to fast overtake the USA in innovation?
Authors: Li Weibao , Wu Weiwei , Yu Bo , Foo Check-Teck 
Published: March 2015

Purpose– This paper aims to argue for a China transmuting to fast overtake USA in innovation based on the extrapolation of past statistical trend. Case studies in self and co-innovation are provided so that the documentation of the dynamics of knowledge flows and a brain-linguistic explanation is given as to why, in the future, the Chinese are likely to lead in innovation.Design/methodology/approach– This paper illustrates a multi-method approach in research forChinese Management Studies. First, the sociological background of China is highlighted (Mao Zedong’s aphorism). Second, insights from OECD patent database are utilized. Third, the use of comparative research and development case-studies: self-innovation (Chinese) and co-innovation (contrasting Japanese versus French cooperation with Chinese). Fourth, is the inter-disciplinarily approach wherein the assimilating of knowledge is related to recent advances in brain research. Fifth, emphasizing the different levels in organizing for innovation: national (China), organizational (SOE), group processes and person-to-person, synapses within individual brains.Findings– Statistical trend suggests that China is transforming and is on the path toward overtaking the USA in innovation. When will this happen? Using extrapolation as an indication, China may surpass the USA by the 50 per cent mark within the next decade. Insights into the processes of self-innovation and co-innovation are provided. Authors argue for a brain-linguistic explanation (Hebb, 1949) for further understanding why China will eventually leadceteris paribusinnovation, a function of the human brain.Originality/value– This paper highlights on the basis of statistical trends (using OECD database) a rising, innovative China that is poised to overtake the USA in the near future. A major contribution is in providing insights of interactional processes required to foster innovation: self and co-innovation (comparing Japanese and French). The critical brain-linguistic role as the rationale as to why the Chinese are given a greater, more developed brain power that will eventually surpass the West in innovation.
Association between leadership style and decision making style in Indian organisations
Authors: Verma Neha , Bhat Aruna B. , Rangnekar S. , Barua M. K. 
Published: March 2015

Purpose– The purpose of this paper is to study the leadership style (LS) and decision-making style (DMS) of Indian manufacturing executives, and to explore the association between the LS and DMS.Design/methodology/approach– For this study the sample was drawn from Indian manufacturing organisations’ executives from both public and private sectors. The respondents were lower, middle and senior levels executives involved in leadership and decision-making functions. Correlation, regression and ANOVA were used to pursue the research questions.Findings– Indian manufacturing executives have shown highest rational and least avoidant in their DMSs. Transformational (TFM) leaders are found rational, while the transactional (TSL) leaders are observed to be rational and dependent. Laissez faire style has correlation with avoidant decision making and interactive dependent and avoidant styles.Research limitations/implications– The study is a cross sectional research with limitations of self-serving bias and common method variance. However, this limitation has been dealt with a statistical test.Practical implications– The study bears significant implications for Indian executives who are working on LSs and decision making. It also provides the details of decision-making behaviours of the manufacturing executives thereby suggesting the associated benefits and drawbacks of particular styles.Originality/value– This paper contributes to leadership and decision-making literature. In the recent times, no such study in Indian manufacturing context have been reported. Moreover there are few contrasting and contributing findings in this research.
Imagining what underlies corporate sustainability
Authors: Ahern Geoffrey Maurice 
Published: March 2015

Purpose– The purpose of this paper is to draw attention to the range and depth of sustainability issues at their points of impact with company experience, and to pilot an illustration of how they could be imaginatively yet critically approached for management development purposes.Design/methodology/approach– Citing and making sense of a variety of seminal or otherwise relevant sources in order to illustrate an imaginative yet critical approach to sustainability. This is a pilot demonstration to stimulate discussion and to help individuals develop their own sense making.Findings– The need to allow space and time for reflection on the depth and breadth of sustainability approaches in order to enable personal understanding leading to wise action.Research limitations/implications– This paper discusses planetary sustainability yet is confined to mainly Anglophone sources. Some of the latent environmental thought forms discussed, e.g. doom, may be largely restricted to them.Practical implications– Divergent evaluations of trans-disciplinary, critical sustainability approaches are necessary for the longer-term development of motivation within companies.Originality/value– This appears to be the first attempted trans-disciplinary yet critical business studies approach to sustainability at its points of impact with corporate operations. It aims to contribute to a new kind of management development path.
The contribution of academic scholarship to management development
Authors: Ross Catharine Mary , Robinson Laurie , Francis-Smythe Jan 
Published: March 2015

Purpose– The purpose of this paper is to explore the impact of academic scholarship on the development and practice of experienced managers.Design/methodology/approach– Semi-structured interviews with experienced managers, modelled on the critical incident technique. “Intertextuality” and framework analysis technique are used to examine whether the use of academic scholarship is a sub-conscious phenomenon.Findings– Experienced managers make little direct use of academic scholarship, using it only occasionally to provide retrospective confirmation of decisions or a technique they can apply. However, academic scholarship informs their practice in an indirect way, their understanding of the “gist” of scholarship comprising one of many sources which they synthesise and evaluate as part of their development process.Practical implications– Managers and management development practitioners should focus upon developing skills of synthesising the “gist” of academic scholarship with other sources of data, rather than upon the detailed remembering, understanding and application of specific scholarship, and upon finding/providing the time and space for that “gisting” and synthesis to take place.Originality/value– The paper addresses contemporary concerns about the appropriateness of the material delivered on management education programmes for management development. It is original in doing this from the perspective of experienced managers, and in using intertextual analysis to reveal not only the direct but also the indirect uses of they make of such scholarship. The finding of the importance of understanding the “gist” rather than the detail of academic scholarship represents a key conceptual innovation.
The role of power conceptions when choosing a host city
Authors: Gherra Sandrine , Lassalle Frédéric 
Published: March 2015

Purpose– International sport competitions continue to attract a high number of spectators and the potential political, community building and financial payoffs are such that the competition to become a host city is often fierce. France has several attractive cities with all of the resources required to host these events, but they have repeatedly failed (Summer Olympic Games 2008 and 2012, Winter Olympic Games 2018, etc.). Most of the studies that have explored these failures have done so from a resource-based view. But when a city has all the required resources, what other factors may have been decisive? Could a misfit in the conception of power during the negotiation process explain it? The paper aims to discuss these issues.Design/methodology/approach– We looked at the specific failure of Marseille to host the 2007 America’s Cup and focused particularly on the conceptions of power held, respectively by Marseille representatives and the committee in charge of choosing the host city. In line with French qualitative methods we performed a single case study based on discourse analysis (23 interviews with the involved parties and 22 outside experts) to analyze the sources of power that Marseille and America’s Cup Management (ACM) had.Findings– The authors found that Marseille and ACM had different sources of power. According to Weber’s categories, Marseille had an “Organization” source of power: “it’s is a structure and an organization that implies specific rules” and ACM had a “Property” source of power: “it’s a commercial structure that has ownership rights to this very special event.” Analysis of the interviews reveals that points of disagreement reflected differing conceptions of power, which suggests new perspectives for future research in the context of failed negotiations in sports.Originality/value– Analyzing failure from another angle that the classical resource-based view: having the right resources is no longer enough; cities have to have the winning strategy.
Radiation‐induced skin ulcer and rib fractures following percutaneous coronary intervention (PCI): A case of right back skin ulcer and adjacent rib fractures after single PCI
Authors: Yasukochi Yumi , Nakahara Takeshi , Koike Akihiro , Ichikawa Ryutaro , Koga Tetsuya , Furue Masutaka 
Published: March 2015

AbstractWe experienced a 75‐year‐old male patient with a refractory and severely painful skin ulcer on the right back. He had suffered from ischemic heart disease and undergone percutaneous coronary intervention 5 months prior to the consultation with us. The characteristic clinical appearance, location of the lesion and his past medical history led us to the diagnosis of radiation‐induced skin ulcer. Magnetic resonance imaging, computed tomography as well as bone scintigraphy showed fractures of the right back rib adjacent to the ulcer, which was thought to be attributable to bone damage due to X‐ray radiation and/or persistent secondary inflammation of the chronic ulcer. In the published work, there are no other reports of bone fractures associated with radiation dermatitis after coronary interventional radiology.
Olfactory response of Anastrepha striata (Diptera: Tephritidae) to guava and sweet orange volatiles
Authors: Diaz‐Santiz Edvin , Rojas Julio C. , Cruz‐López Leopoldo , Hernández Emilio , Malo Edi A. 
Published: March 2015

AbstractThe behavioral responses of virgin and mated female Anastrepha striata Schiner (Diptera: Tephritidae) to guava (Psidium guajava L.) or sweet orange (Citrus sinensis L.) were evaluated separately using multilure traps in two‐choice tests in field cages. The results showed that flies were more attracted to guava and sweet orange volatiles than to control (unbaited trap). The physiological state (virgin or mated) of females did not affect their attraction to the fruit volatiles. Combined analysis of gas chromatography coupled with electroantennography (GC‐EAD) of volatile extracts of both fruits showed that 1 and 6 compounds from orange and guava, respectively elicited repeatable antennal responses from mated females. The EAD active compounds in guava volatile extracts were identified by gas chromatography‐mass spectrometry (GC‐MS) as ethyl butyrate, (Z)‐3‐hexenol, hexanol, ethyl hexanoate, hexyl acetate, and ethyl octanoate. Linalool was identified as the only antennal active compound in sweet orange extracts. In field cage tests, there were no significant differences between the number of mated flies captured by the traps baited with guava extracts and the number caught by traps baited with the 6‐component blend that was formulated according to the relative proportions in the guava extracts. Similar results occurred when synthetic linalool was evaluated against orange extracts. From a practical point of view, the compounds identified in this study could be used for monitoring A. striata populations.
Development of a Nutrition Care Process implementation package for hospital dietetic departments
Authors: Porter Jane M. , Devine Amanda , Vivanti Angela , Ferguson Maree , O'Sullivan Therese A. 
Published: March 2015

AbstractAimThe Academy of Nutrition and Dietetics has led the development and dissemination of the Nutrition Care Process (NCP), incorporating the Nutrition Care Process Terminology as the standardised language. This research investigates and compares the views of Australian dietitians pre and post NCP implementation to inform development of an NCP implementation package.MethodsDietitians from two hospitals that had undergone informal NCP implementation (post‐implementers, n = 35) and three hospitals yet to implement NCP (pre‐implementers, n = 35) completed an online questionnaire (ASK NCP) surveying demographics and constructs relating to knowledge, familiarity, confidence, support, value, barriers, training and NCP education.ResultsPost‐implementers had higher knowledge scores (P < 0.05), were more familiar with NCP (P < 0.01), confident to implement (P < 0.01) and supported to use NCP (P < 0.01) than pre‐implementers. Lack of knowledge, support, training and resources was identified as a barrier by pre‐implementers. Busy workloads and work status were identified as barriers by post‐implementers. Pre‐implementers felt they had insufficient NCP training; however, if further training and support were to be provided, almost all reported they would be more confident to implement. Keys to successful implementation included allocated time to practice and regular tutorials; support and leadership from their management and NCP department leader; and professional growth through understanding how change could benefit practice.ConclusionsThe results of the study were used to inform the development of an NCP implementation package. Kotter's eight stages of change were identified as the most appropriate change management model with the framework incorporated into the package development.
Primary extranodal natural killer/T‐cell lymphoma of bronchus and lung: A case report and review of literature
Authors: Chien Chu‐Chun , Lee Herng‐Sheng , Lin Min‐Hsi , Hsieh Pin‐Pen 
Published: March 2015

AbstractPrimary pulmonary non‐Hodgkin's lymphoma (NHL) is very rare. It represents less than 1% of all NHL, and 0.5–1% of all primary pulmonary malignancies. Almost all cases of primary pulmonary NHL originate from B‐cell lineage. We present a case of a 53‐year‐old man with primary extranodal NK/T‐cell lymphoma of the bronchus and lung, presented progressive dyspnea caused by right lower lung consolidation, and pleural effusion. Initial chest computed tomography suggested advanced lung cancer. Bronchofiberscopy showed a polypoid tumor on which a biopsy was performed. Histologically, the diffusely infiltrative atypical cells were positive for cytoplasmic CD3, CD56, granzyme B, and negative for cytokeratin, CD20 immunostains, suggesting NK/T cell lineages. In situ hybridization for Epstein‐Barr virus encoded ribonucleic acid (EBER) was positive. Herein, we discuss the clinicopathological features of this case and review the literature on primary extranodal NK/T‐cell lymphoma of the lung. Compared with other patients, who died after the first cycle of chemotherapy and/or within three months, our patient had longer survival under aggressive chemotherapy and auto‐peripheral blood stem cell transplantation.