bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida albicans
Authors: Erb Downward John R. , Falkowski Nicole R. , Mason Katie L. , Muraglia Ryan , Huffnagle Gary B. 
Published: July 2013

AbstractThe introduction of Candida albicans into cefoperazone-treated mice results in changes in bacterial community reassembly. Our objective was to use high-throughput sequencing to characterize at much greater depth the specific changes in the bacterial microbiome. The colonization of C. albicans significantly altered bacterial community reassembly that was evident at multiple taxonomic levels of resolution. There were marked changes in the levels of Bacteriodetes and Lactobacillaceae. Lachnospiraceae and Ruminococcaceae, the two most abundant bacterial families, did not change in relative proportions after antibiotics, but there were marked genera-level shifts within these two bacterial families. The microbiome shifts occurred in the absence of overt intestinal inflammation. Overall, these experiments demonstrate that the introduction of a single new microbe in numerically inferior numbers into the bacterial microbiome during a broad community disturbance has the potential to significantly alter the subsequent reassembly of the bacterial community as it recovers from that disturbance.
Extracellular matrix of secondary lymphoid organs impacts on B-cell fate and survival
Authors: Song Jian , Lokmic Zerina , Lämmermann Tim , Rolf Julia , Wu Chuan , Zhang Xueli , Hallmann Rupert , Hannocks Melanie-Jane , Horn Nathalie , Ruegg Markus A. , Sonnenberg Arnoud , Georges-Labouesse Elisabeth , Winkler Thomas H. , Kearney John F. , Cardell Susanna , Sorokin Lydia 
Published: July 2013

Significance
We describe a unique extracellular matrix (ECM) niche in the spleen, the marginal zone (MZ), that supports a specialized population of MZ B lymphocytes that respond rapidly to blood-borne antigens and are therefore crucial for the first line of immune defense. We show, for the first time, that both the novel 3D structure and the biochemical composition of the ECM impacts on B-cell fate and survival. Similar pericellular ECM networks occur in thymus, bone marrow, and lymph node; hence, our data are likely to have broader ramifications to the fate and survival of other immune cells.
pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling
Authors: Gil Víctor A. , Guallar Víctor 
Published: July 2013

Abstract
Summary: We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms.
Availability: The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section.
Contact: victor.guallar@bsc.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Modeling nucleosome position distributions from experimental nucleosome positioning maps
Authors: Schöpflin Robert , Teif Vladimir B. , Müller Oliver , Weinberg Christin , Rippe Karsten , Wedemann Gero 
Published: July 2013

Abstract
Motivation: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average.
Results: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain.
Availability: Source code, precompiled binaries, test data and a web-based test installation are freely available at http://bioinformatics.fh-stralsund.de/nucpos/
Contact: gero.wedemann@fh-stralsund.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Reducing heart failure admission rates in England 2004–2011 are not related to changes in primary care quality: national observational study
Authors: Brettell Rachel , Soljak Michael , Cecil Elizabeth , Cowie Martin R. , Tuppin Philippe , Majeed Azeem 
Published: July 2013

AimsHeart failure (HF) is an important clinical problem. Expert consensus has defined HF as a primary care‐sensitive condition for which the risk of unplanned admissions may be reduced by high quality primary care, but there is little supporting evidence. We analysed time trends in HF admission rates in England and risk and protective factors for admission.Methods and resultsWe used Hospital Episodes Statistics to produce indirectly standardized HF admission counts by general practice for 2004–2011. Clustered negative binomial regression analysis produced admission risk ratios and assessed the significance of potential explanatory covariates. These included population factors (deprivation; HF, coronary heart disease, and smoking prevalence), primary care resourcing [access; general practitioner (GP) supply], and primary care quality (‘Quality and Outcomes Framework’ indicator.) There were 327 756 HF admissions of patients registered with 8405 practices over the study period. There was a significant reduction in admissions over time, from 6.96/100 000 in 2004 to 5.60/100 000 in 2010 (P < 0.001). Deprivation and HF prevalence were risk factors for admission. GP supply and access protected against admission. However, these effects were small and did not explain the large and highly significant annual trend in falling admission rates.ConclusionsThe observed fall in admissions over time cannot be explained by the primary care covariates we included. This analysis suggests that the potential for further significant reduction in emergency HF admissions by improving clinical quality of primary care (as currently measured) may be limited. Further work is required to identify the reasons for the reduction in admissions.
Cyclosporine-inhibitable Blood–Brain Barrier Drug Transport Influences Clinical Morphine Pharmacodynamics
Authors: Meissner Konrad , Avram Michael J. , Yermolenka Viktar , Francis Amber M. , Blood Jane , Kharasch Evan D. 
Published: July 2013

Abstract

Background:
The blood–brain barrier is richly populated by active influx and efflux transporters influencing brain drug concentrations. Morphine, a drug with delayed clinical onset, is a substrate for the efflux transporter P-glycoprotein in vitro and in animals. This investigation tested whether morphine is a transporter substrate in humans.

Methods:
Fourteen healthy volunteers received morphine (0.1 mg/kg, 1-h IV infusion) in a crossover study without (control) or with the infusion of validated P-glycoprotein inhibitor cyclosporine (5 mg/kg, 2-h infusion). Plasma and urine morphine and morphine glucuronide metabolite concentrations were measured by mass spectrometry. Morphine effects were measured by miosis and analgesia.

Results:
Cyclosporine minimally altered morphine disposition, increasing the area under the plasma morphine concentration versus time curve to 100 ± 21 versus 85 ± 24 ng/ml·h (P < 0.05) without changing maximum plasma concentration. Cyclosporine enhanced (3.2 ± 0.9 vs. 2.5 ± 1.0 mm peak) and prolonged miosis, and increased the area under the miosis–time curve (18 ± 9 vs. 11 ± 5 mm·h), plasma effect-site transfer rate constant (ke0, median 0.27 vs. 0.17 h−1), and maximum calculated effect-site morphine concentration (11.5 ± 3.7 vs. 7.6 ± 2.9 ng/ml; all P < 0.05). Analgesia testing was confounded by cyclosporine-related pain.

Conclusions:
Morphine is a transporter substrate at the human blood–brain barrier. Results suggest a role for P-glycoprotein or other efflux transporters in brain morphine access, although the magnitude of the effect is small, and unlikely to be a major determinant of morphine clinical effects. Efflux may explain some variability in clinical morphine effects.
Assessment of Abdominal Pain Through Global Outcomes and Recent FDA Recommendations in Children
Authors: Mohammad Saeed , Di Lorenzo Carlo , Youssef Nader N. , Miranda Adrian , Nurko Samuel , Hyman Paul , Saps Miguel 
Published: July 2013

ABSTRACTObjectives:Irritable bowel syndrome is a multisymptom construct, with abdominal pain (AP) acting as the driving symptom of patient‐reported severity. The Food and Drug Administration considers a >30% decrease in AP as satisfactory improvement, but this has not been validated in children. We investigated the correspondence of 2 measures for AP assessment, ≥30% improvement in AP and global assessment of improvement.Methods:Secondary analysis of data from 72 children who completed a randomized clinical trial for abdominal pain–associated functional gastrointestinal disorders. Children completed daily assessment of AP intensity, functional disability inventory (FDI), question regarding pain's interference with activities, and 2 global assessment questions. We measured the extent to which ≥30% improvement of AP and global assessment questions correlated with each other and with disability.Results:The global questions correlated with each other (r = 0.74; P < 0.0001) and with a ≥30% improvement in AP (P < 0.01). Global outcomes were satisfaction with treatment was inversely related to the child's report of interference with activities (P < 0.01) and symptom relief was positively associated with ≥30% improvement in FDI scores (P < 0.009). A 30% change in FDI scores was associated with global questions of symptom relief (P = 0.009) but not with satisfaction with treatment (P = 0.07). The association of AP improvement with interference with activities (P = 0.14) or change in FDI scores (P = 0.27) did not reach significance.Conclusions:Currently used global assessments are significantly associated with decreased pain intensity, decreased interference with daily activities, and a ≥30% change in FDI scores, whereas recommended 30% improvement in pain intensity is not as comprehensive.
Chromosome Aberrations and Gene Mutations in Patients With Esophageal Atresia
Authors: Bednarczyk Damian , Sasiadek Maria M. , Smigiel Robert 
Published: July 2013

ABSTRACTEsophageal atresia (EA) is one of the most frequent congenital malformations of the gastrointestinal tract. Many genetic alterations in patients with EA have been described in the literature. It is thought that the etiology of EA is heterogeneous. This review of the literature provides detailed information about chromosomal aberrations, gene mutations, and clinical features of neonates with EA, and serves as an excellent source to compare newly diagnosed patients with those described in the literature.
Collaboration networks and innovation: does corporate lobbying matter?
Authors: Ozer Mine , Demirkan Irem , Gokalp Omer N. 
Published: July 2013

PurposeThis study aims to investigate how corporate lobbying affects the relationship between collaboration networks and innovation.Design/methodology/approachThe study incorporates insights from the corporate political strategy perspective into the social network research to examine how firms utilize non‐market mechanisms as a way to manage uncertainty. In particular, using data from 291 US pharmaceutical firms, the authors study the moderating effects of corporate lobbying on the relationship between collaboration networks and firm innovativeness.FindingsThe results show that corporate lobbying moderates the relationship between network centrality, structural holes, and network size, and firm innovativeness.Originality/valueThe study integrates social network and corporate political strategy research in the case of collaboration networks. Integrating social network and corporate political strategy literatures provides us with new insights into what determines success of firm innovativeness. The study shows that in addition to network structures, firms must consider other variables such as government regulation in fostering their innovativeness.
Advisors’ role in cross‐border acquisitions: new challenges and opportunities
Authors: Caiazza Rosa 
Published: July 2013

PurposeCurrent events have led academics and practitioners to rethink cross‐border M&A challenges in a tumultuous global business environment and the role of advisors in supporting the deals. The article aims to discuss current trend in M&A and presents some cases to evidence the relevance of advisors’ role in cross‐border M&A.Design/methodology/approachExploratory field interviews were conducted with M&A advisors, as well as a diligent scanning of local and international articles to evidence advisors’ roles in cross‐border M&AFindingsThis article evidences new direction in cross‐border M&A research for reinterpreting advisors’ role in facing them.
A new model of strategic thinking competency
Authors: Nuntamanop Polboon , Kauranen Ilkka , Igel Barbara 
Published: July 2013

PurposeThis paper seeks to present new insights into strategic thinking, proposing a model of strategic thinking competency.Design/methodology/approachTo find new knowledge, the research applies the Straussian grounded theory research method using multiple sources and techniques of data inquiry: in‐depth interviews, observations, literature review, and related published documents. The sample cases are business leaders of leading high growth companies in their respective markets, representing eleven different industries in Thailand.FindingsAmong many new knowledge, the study found seven characteristics of strategic thinking that impacts strategy formulation, strategic actions, and business performance: conceptual thinking ability, visionary thinking, analytical thinking ability, synthesizing ability, objectivity, creativity, and learning ability. This set of abilities and skilled are termed “strategic thinking competency”.Research limitations/implicationsIn‐depth interview data inquiry method has potential bias towards positive information. Although the study covers many industries, the small number of sample cases limits degree of generalization. A constraint of qualitative research method in interpretation of the results is reduced by comparing empirical results to the literature.Practical implicationsThe “strategic thinking competency” model offers a framework for developing strategic thinking of business leaders and managers which contributes to better strategy and better business performance. Human resource developers may apply the model for designing training programs to develop better strategic thinkers.Social implicationsBetter strategic thinking could help improving efficiency and effectiveness of business and general management.Originality/valueThe study introduces a model of “Strategic Thinking Competency” with seven characteristics, proposing a new way of defining strategic thinking.
Translating strategy into practice: the role of communities of practice
Authors: Macpherson Allan , Antonacopoulou Elena 
Published: July 2013

PurposeThis empirical paper aims to show how communities of practice have been used as a tractable management tool to operationalize strategy in practice. The analysis shows how CoPs can be used in business to find traction in order to achieve strategic goals.Design/methodology/approachA two‐year longitudinal case study approach was adopted employing semi‐structured interviews, participant observations and document analysis for data collection. The findings were verified with the participants in the study during feedback events organised for that purpose.FindingsThe study provides in‐depth insights into the challenges of translating strategy into practice in complex work settings. In this case, uneven outcomes were attributed to three critical contributing factors: the leadership and governance structures, the meaningful ways in which members can participate and interact with others; and their identity and sense of belonging.Research limitations/implicationsAlthough a single case study only provides indications of potential generalisations, it does give access to issues that cannot be identified without an in‐depth analysis.Practical implicationsThe authors encourage executives to consider concepts of identity, participation and governance as useful heuristics for the analysis of practices of communities. Potential inconsistencies in community practices could have implications for the way strategy is translated into action.Originality/valueUnlike most community of practice studies, which focus on the community aspect of the concept, this study analyses the practices of communities. In doing so, it adds value to our understanding of the forces that shape social interactions embedded in the implementation of strategy in practice.
Managing access to the internet in public libraries
Authors: Pautz Hartwig 
Published: July 2013

PurposeThe purpose of this paper is to discuss the management of internet access in the public library. It stresses how important professional access management is, addresses practical and ethical challenges and dilemmas with regard to managing access, highlights management strategies and emphasises the librarian's enduring ethical principles in the “internet age”.Design/methodology/approachThe paper is based on a critical literature review.FindingsFirst, there is not necessarily a difference between managing internet access and “traditional” stock selection. Second, managing internet access must not be understood as synonymous with limiting the information that is accessible through it. Third, the librarian must be aware of the risks that filters and other “technological fixes” pose to the library and the librarian's principles. Fourth, a number of strategies exist which protect these principles and allow information literacy and user independence to develop.Practical implicationsThe paper highlights practical challenges to a librarian's everyday work and provides a discussion that is relevant to public librarians everywhere. It raises awareness of the potentials and pitfalls of a number of internet access management tools and assures the librarian of their important position as an enabler to information access and its use.Originality/valueThe paper raises awareness of important issues pertaining to internet access and its management in the public library. It asks pertinent and timely questions of relevance to the practical work of the librarian.
3D printing and the library
Authors: Massis Bruce E. 
Published: July 2013

PurposeThe purpose of this column is to examine the current environment of 3D printing and its suitability for use in the library.Design/methodology/approachLiterature review and commentary on this topic that has been addressed by professionals, researchers and practitioners.FindingsThe library is more than its collection. As 3D printing joins the technology selections available in the library, it offers patrons the opportunity to create and further develop their skills, in order to explore and potentially innovate, in a welcoming environment of intellectual stimulation and experimentation.Originality/valueThe value in addressing this issue is to present the basic details around this new technology and suggest that it has value for its inclusion into the current array of library services.
Aligning planning with outcomes
Authors: Sayed Ellen N. 
Published: July 2013

PurposeThis paper aims to describe the process of identifying, applying and assessing the balanced scorecard model on a five‐year, strategic plan in an academic, medical library two years into the five‐year period. The existing strategic plan consisted of eight inter‐connected pathways with multiple goals and objectives, generating a high volume of data, which made it difficult to track the implementation of the plan.Design/methodology/approachA research query seeking an alternative to the current strategic plan framework was developed and researched. This process identified the balanced scorecard as a possible successful alternative to the eight inter‐connected pathways in place. After the application of the balanced scorecard, a second query, with assessment criteria, was developed to determine if the balanced scorecard did, in fact, provide a better framework than the original plan.FindingsThe balanced scorecard restructured the eight pathways into four perspectives to create an aligned, cause‐and‐effect strategy. The original plan had too many themes to manage and lacked a cohesive strategy. Performance measures proved more meaningful and manageable in measuring the success of the strategic plan than the high volume of project management data. It was concluded that the balanced scorecard met the assessment criteria as a better framework for the strategic plan.Practical implicationsAligning goals and objectives to form strategy simplified the implementation of the strategic plan. Performance measures focus on the performance of the organization, creating a process of continuous improvement.Originality/valueWhile the balanced scorecard has been applied in academic libraries, this project successfully applied the model on a strategic plan two years after its implementation.
A strategic approach to making sense of the “wicked” problem of ERM
Authors: McLeod Julie , Childs Sue 
Published: July 2013

PurposeThe purpose of this paper is to provide an approach to viewing the “wicked” problem of electronic records management (ERM), using the Cynefin framework, a sense‐making tool. It re‐conceptualises the ERM challenge by understanding the nature of the people issues. This supports decision making about the most appropriate tactics to adopt to effect positive change.Design/methodology/approachCynefin was used to synthesise qualitative data from an empirical research project that investigated strategies and tactics for improving ERM.FindingsERM may be thought of as a dynamic, complex challenge but, viewed through the Cynefin framework, many issues are not complex; they are simple or complicated and can be addressed using best or good practice. The truly complex issues need a different approach, described as emergent practice. Cynefin provides a different lens through which to view, make sense of and re‐perceive the ERM challenge and offers a strategic approach to accelerating change.Research limitations/implicationsSince Cynefin has been applied to one data set, the findings are transferrable not generalisable. They, and/or the approach, can be used to further test the propositions.Practical implicationsThe resultant ERM framework provides a practical example for information and records managers to exploit or use as a starting point to explore the situation in particular organisational contexts. It could also be used in other practical, teaching and/or research‐related records contexts.Originality/valueThis paper provides a new strategic approach to addressing the wicked problem of ERM, which is applicable for any organisational context.