bluuebunny/crossref_metadata_2025_split huggingface dataset:
BiTrinA—multiscale binarization and trinarization with quality analysis
Authors: Müssel Christoph , Schmid Florian , Blätte Tamara J. , Hopfensitz Martin , Lausser Ludwig , Kestler Hans A. 
Published: October 2015

Abstract
Motivation: When processing gene expression profiles or other biological data, it is often required to assign measurements to distinct categories (e.g. ‘high’ and ‘low’ and possibly ‘intermediate’). Subsequent analyses strongly depend on the results of this quantization. Poor quantization will have potentially misleading effects on further investigations. We propose the BiTrinA package that integrates different multiscale algorithms for binarization and for trinarization of one-dimensional data with methods for quality assessment and visualization of the results. By identifying measurements that show large variations over different time points or conditions, this quality assessment can determine candidates that are related to the specific experimental setting.
Availability and implementation: BiTrinA is freely available on CRAN.
Contact: hans.kestler@leibniz-fli.de or hans.kestler@uni-ulm.de
Supplementary information: Supplementary data are available at Bioinformatics online.
First discovery of a magnetic field in a main-sequence δ Scuti star: the Kepler star HD 188774
Authors: Neiner C. , Lampens P. 
Published: October 2015

Abstract
The Kepler space mission provided a wealth of δ Sct–γ Dor hybrid candidates. While some may be genuine hybrids, others might be misclassified due to the presence of a binary companion or to rotational modulation caused by magnetism and related surface inhomogeneities. In particular, the Kepler δ Sct–γ Dor hybrid candidate HD 188774 shows a few low frequencies in its light and radial velocity curves, whose origin is unclear. In this work, we check for the presence of a magnetic field in HD 188774. We obtained two spectropolarimetric measurements with an Echelle SpectroPolarimetric Device for the Observation of Stars (ESPaDOnS) at Canada–France–Hawaii Telescope. The data were analysed with the least-squares deconvolution (LSD) method. We detected a clear magnetic signature in the Stokes V LSD profiles. The origin of the low frequencies detected in HD 188774 is therefore most probably the rotational modulation of surface spots possibly related to the presence of a magnetic field. Consequently, HD 188774 is not a genuine hybrid δ Sct–γ Dor star, but the first known magnetic main-sequence δ Sct star. This makes it a prime target for future asteroseismic and spot modelling. This result casts new light on the interpretation of the Kepler results for other δ Sct–γ Dor hybrid candidates.
Immune reconstitution inflammatory syndrome due to Mycobacterium genavense in an HIV-infected patient: Impact of rapid species identification by rpoB sequencing on clinical management
Authors: Andre Emmanuel , Belkhir Leila , Goeminne Léonie , Colmant Alexandre , Sottiaux Jean-Yves , Yildiz Halil , Ruelle Jean , Delmee Michel , Vandercam Bernard , Defour Jean-Philippe 
Published: October 2015

Introduction:
Diagnosis of infections due to Mycobacterium tuberculosis has been recently facilitated with the worldwide implementation of rapid molecular tests. However, the diagnosis of non-TB mycobacteria (NTM) remains a major challenge for laboratories, as this group of bacteria contains over 150 different species with highly variable bacteriological properties. The development and implementation in clinical practice of techniques allowing rapid identification of NTM at the species level is, therefore, important for clinical laboratories. We report the case of an HIV-1 positive patient presenting with severe NTM infection who benefited from a novel rapid diagnostic technique, based on the direct sequencing of the rpoB gene from smear-positive clinical samples.

Case Presentation:
A 43-year-old HIV-1 positive woman was hospitalized for bicytopenia in the presence of an inflamed supraclavicular lymph node. The diagnosis of disseminated Mycobacterium genavense infection, which involved the bone marrow and several lymph nodes, was missed by conventional mycobacteriological techniques. Identification was obtained by performing direct sequencing of the rpoB gene.

Conclusion:
We describe a novel technique that allows the rapid diagnosis of NTM infections directly from biological samples. This technique is now implemented in our routine workflow for smear and culture-positive samples, after the exclusion of TB, by rapid molecular assays.
An Effective Model of HL-60 Differentiation
Authors: Tasseff Ryan , Jensen Holly A. , Congleton Johanna , Yen Andrew , Varner Jeffrey D. 
Published: October 2015

AbstractWe present an effective model All-Trans Retinoic Acid (ATRA)-induced differentiation of HL-60 cells. The model describes a key architectural feature of ATRA-induced differentiation, positive feedback between an ATRA-inducible signalsome complex involving many proteins including Vav1, a guanine nucleotide exchange factor, and the activation of the mitogen activated protein kinase (MAPK) cascade. The model, which was developed by integrating logical rules with kinetic modeling, was significantly smaller than previous models. However, despite its simplicity, it captured key features of ATRA induced differentiation of HL-60 cells. We identified an ensemble of effective model parameters using measurements taken from ATRA-induced HL-60 cells. Using these parameters, model analysis predicted that MAPK activation was bistable as a function of ATRA exposure. Conformational experiments supported ATRA-induced bistability. These findings, combined with other literature evidence, suggest that positive feedback is central to a diversity of cell fate programs.Index Terms—Mathematical modeling, systems biology
Sex and Ageing: The Role of Sexual Recombination in Longevity
Authors: Smith Phillip R. 
Published: October 2015

1AbstractI use a set of machines based on the concept of nested rule systems built on the a modified version of the Wolfram elemental cellular automata to investigate the role of recombination in providing resistance to ageing. Class III and class IV machines are observed to respond differently to recombination. Class IV machines show recombinational centring in their neutral networks whereas class III machines respond negatively to recombination. Rule 110 shows a unusual response to recombination. Recombination selects for resistance to recombination, the population moves to regions of genome space with high redundancy, this results in organisms with highly robust genomes, more likely to complete development and to be long lived. The increase in longevity may be sufficient to compensate for the costs of sex, including the two fold cost of sex, through increased reproductive potential in long lived organisms requiring long maturation times. Large complex species should therefore be resistant to invasion by asexual mutants whereas small simple organisms with early maturation should be vulnerable to invasion by asexual forms.
Transcriptome Analysis of Cortical Tissue Reveals Shared Sets of Down-Regulated Genes in Autism and Schizophrenia
Authors: Ellis Shannon E. , Panitch Rebecca , West Andrew B. , Arking Dan E. 
Published: October 2015

ABSTRACTAutism (AUT), Schizophrenia (SCZ), and bipolar disorder (BPD) are three highly heritable neuropsychiatric conditions. Clinical similarities and genetic overlap between the three disorders have been reported; however, the causes and the downstream effects of this overlap remain elusive. By analyzing transcriptomic RNA-Sequencing data generated from post-mortem cortical brain tissues from AUT, SCZ, BPD and control subjects, we have begun to characterize the extent of gene expression overlap between these disorders. We report that the AUT and SCZ transcriptomes are significantly correlated (p<0.001), while the other two cross disorder comparisons (AUT-BPD, SCZ-BPD) are not. Among AUT and SCZ, we find that the genes differentially expressed across disorders are involved in neurotransmission and synapse regulation. Despite lack of global transcriptomic overlap across all three disorders, we highlight two genes, IQSEC3 and COPS7A, which are significantly down-regulated compared to controls across all three disorders, suggesting either shared etiology or compensatory changes across these neuropsychiatric conditions. Finally, we tested for enrichment of genes differentially expressed across disorders in genetic association signals in AUT, SCZ or BPD, reporting lack of signal in any of the previously published GWAS. Together, these studies highlight the importance of examining gene expression from the primary tissue involved in neuropsychiatric conditions, cortical brain. We identify a shared role for altered neurotransmission and synapse regulation in AUT and SCZ, in addition to two genes that may more generally contribute to neurodevelopmental and neuropsychiatric conditions.
Propagation of risks and their impact on performance in fresh food retail
Authors: Srivastava Samir K , Chaudhuri Atanu , Srivastava Rajiv K. 
Published: October 2015

Purpose
– The purpose of this paper is to carry out structural analysis of potential supply chain risks and performance measures in fresh food retail by applying interpretive structural modeling (ISM).

Design/methodology/approach
– Inputs were taken from industry experts in identifying and understanding interdependencies among food retail supply chain risks on different levels (sourcing and logistics outside the retail stores; storage and customer interface at the stores). Interdependencies among risks and their impact on performance measures are structured into a hierarchy in order to derive subsystems of interdependent elements to derive useful insights for theory and practice.

Findings
– Using the ISM approach the risks and performance measures were clustered according to their driving power and dependence power. Change in/inadequate government regulations’ are at the bottom level of the hierarchy implying highest driving power and require higher attention and focussed mitigation strategies. Risks like lack of traceability, transport delays/breakdowns and temperature abuse, cross-contamination in transport and storage have medium driver and dependence powers.

Research limitations/implications
– The approach is focussed on food retail supply chains in the Indian context and thereby limits the ability to generalize the findings. The academics and experts were selected on convenience and availability.

Practical implications
– It gives managers a better understanding of the risks and performance measures that have most influence on others (driving performance measures) and those measures which are most influenced by others (dependent performance measures) in fresh food retail and also a tool to prioritize them. This kind of information is strategic for managers who can use it to identify which performance measures they should concentrate on managing the trade-offs between measures. The findings and the applicability for practical use have been validated by both experts and practicing managers in food retail supply chains.

Originality/value
– The work is perhaps the first to link supply chain risks with performance and explains the propagation of risks in food retail supply chains. It contributes to theory by addressing a few research gaps and provides relevant managerial insights for practitioners.
Supply chain relationships as a context for learning leading to innovation
Authors: Knoppen Desirée , Johnston David , Sáenz María  Jesús 
Published: October 2015

Purpose
– The purpose of this paper is to integrate the literature on learning in the context of boundary spanning innovation in supply chains. A two-dimensional framework is proposed: the learning stage (exploration, assimilation, exploitation) and the learning facet (structural, cultural, psychological and policy). Supply chain management (SCM) practices are examined in light of this framework and propositions for further empirical research are developed.

Design/methodology/approach
– In total, 60 empirical papers from the major journals on supply chain relationships published over an 11-year time span (2000-2010) were systematically analyzed.

Findings
– The paper reveals a comprehensive set of best practices and identifies four gaps for future research. First, assimilation and exploitation are largely ignored as mediating learning stages between exploration and performance. Second, knowledge brokers and reputation management are key mechanisms that foster assimilation. Third, the iteration from exploitation back to exploration is critical though underdeveloped in efficiency seeking supply chains. Fourth, the literature stresses structural mechanisms of learning, at the expense of a more holistic view of structural, cultural, psychological and policy mechanisms.

Research limitations/implications
– The search could be extended to other journals that report on joint learning and innovation.

Practical implications
– The framework provides guidelines for practitioners to develop learning capabilities and leverage the knowledge from supply chain partners in order to continuously or radically improve boundary spanning processes and products.

Originality/value
– The study is multi-disciplinary; it applies a model developed by learning scholars to the field of SCM.
Coordinating a supply chain with a heterogeneous vehicle fleet under greenhouse gas emissions
Authors: Glock Christoph H , Kim Taebok 
Published: October 2015

Purpose– This paper studies a supply chain consisting of multiple suppliers and a single buyer. It considers the case where a set of heterogeneous trucks is used for transporting products, and develops a mathematical model that coordinates the supply chain. The purpose of this paper is to minimise the costs of producing and delivering a product as well as carbon emissions resulting from transportation. In addition, the authors analyse how imposing a tax on carbon emissions impacts the delivery of products from the suppliers to the buyer.Design/methodology/approach– It is assumed that heterogeneous vehicles are used for transporting products, which have different performance and cost attributes. A mathematical model that considers both operating costs and carbon emissions from transportation is developed. The impact of vehicle attributes on lot sizing and routing decisions is studied with the help of numerical examples and a sensitivity analysis.Findings– The analysis shows that considering carbon emissions in coordinating a supply chain leads to changes in the routing of vehicles. It is further shown that if carbon emissions lead to costs, routes are changed in such a way that vehicles travel long distances empty or with a low vehicle load to reduce fuel consumption and therewith emissions.Research limitations/implications– Several areas for future work are highlighted. The study of alternative supply chain structures, for example structures which include logistics service providers, or the investigation of different functional relationships between vehicle load and emission generation offer possibilities for extending the model.Originality/value– The paper is one of the first to study the use of heterogeneous vehicles in an inventory model of a supply chain, and one of the few supply chain inventory models that consider ecological aspects.
Living apart together
Authors: de Vries Walter Timo , Laarakker Peter Marinus , Wouters Hendrikus Johannes 
Published: October 2015

Purpose
– Against the backdrop of European eGovernment (eGov) and new public management strategies, public sector mergers are the ultimate transformation after collaboration and integration. The land administration domain is useful to evaluate how and why mergers occur or not. The domain usually comprises two types of organizations, cadastres and land registries. There are both national and international calls to merge these two types, yet some countries have opted to merge these, while others persist in maintaining two separate ones. How and why this occurs is the key question.

Design/methodology/approach
– This study applies a mixed-methods approach of data collection and a co-evolutionary perspective on organizational changes. Agencies change alongside perceptions of staff members and external stimuli of policies. These are exposed through narrated personal vignettes and international benchmarking surveys of land agencies.

Findings
– Decisions on mergers are primarily embedded in local organizational cultures, and follow non-linear paths and are historically path-dependent. Internal staff members tend to disfavour mergers. Contrastingly, external stimuli such as the benchmark surveys act as national and international stimuli which favour mergers. The common narrative of both perspectives is an increased relevance of “simplicity”, which does not however have an effect on merger decisions.

Research limitations/implications
– The land administration domain is perhaps idiosyncratic. It has a long history with discussions on merging collaborating organizations. Still, other domains affected by eGov strategies have so far only focused on operational interoperability and database integration, and less on the potential for institutional or organizational mergers. Therefore, experiences from land administration will be useful in the future.

Practical implications
– During the formulation of new eGov projects which foster further collaboration and integration in the public sector, it is necessary to take the merger experiences of land agencies into account. It is especially necessary to be aware of implicit norms which are fostered by positive feedback loops of social networks during mergers, which may influence discretionary decisions. In addition, international benchmarks and ranking need to reconsider their benchmarking criteria which currently only focus on efficiency measures.

Originality/value
– Mergers may not be a next logical step when collaborating and integrating. Instead, mergers need to be rooted in personal long-standing collaboration practices. Furthermore, individual staff members may only be willing to engage in the operational aspects of mergers if it significantly makes their own tasks simpler and the quality of their work better appreciated by external customers.
The ongoing quest for biomarkers in Ankylosing Spondylitis
Authors: Danve Abhijeet , O'Dell James 
Published: October 2015

AbstractAnkylosing Spondylitis poses significant challenges in terms of early diagnosis, assessment of disease activity, predicting response to the treatment and monitoring radiographic progression. With better understanding of underlying immunopathogenesis, effective targeted therapies are available which improve symptoms, quality of life and possibly slow the radiographic progression. There has been a growing interest in the discovery of biomarkers for defining various aspects of disease assessment and management in Ankylosing Spondylitis. The C‐reactive protein and HLA‐B27 are most commonly used biomarkers. This review describes many other newer biomarkers which have potential clinical applications in this chronic inflammatory disease.
Polarization and the Decline of the American Floating Voter
Authors: Smidt Corwin D. 
Published: October 2015

AbstractThe observed rate of Americans voting for a different party across successive presidential elections has never been lower. This trend is largely explained by the clarity of party differences reducing indecision and ambivalence and increasing reliability in presidential voting. American National Election Studies (ANES) Times Series study data show that recent independent, less engaged voters perceive candidate differences as clearly as partisan, engaged voters of past elections and with declining rates of ambivalence, being undecided, and floating. Analysis of ANES inter‐election panel studies shows the decline in switching is present among nonvoters too, as pure independents are as reliable in their party support as strong partisans of prior eras. These findings show parties benefit from the behavioral response of all Americans to polarization. By providing an ideological anchor to candidate evaluations, polarization produces a reliable base of party support that is less responsive to short‐term forces.
A 1 year retrospective audit of quality indicators of clinical pharmacological advice for personalized linezolid dosing: one stone for two birds?
Authors: Pea Federico , Cojutti Piergiorgio , Dose Lucia , Baraldo Massimo 
Published: October 2015

AimThis study explored the clinical and economic impact of clinical pharmacological advice (CPA) (based on therapeutic drug monitoring [TDM] results, and on patients' characteristics and co‐medications) on personalized linezolid therapy in a tertiary care hospital.MethodsA 1 year retrospective analysis of quality indicators of CPA (clinicians' adherence rate to CPA, pre‐post rate of linezolid trough concentrations within the desired range and cost balance analysis) was conducted.ResultsFive hundred and forty‐four CPAs were provided to clinicians during 2014 for personalizing linezolid therapy in 168 patients. Clinicians' adherence to CPAs was very high (94.7%). The pre‐post rate of linezolid Cmin distribution showed a favourable impact of CPA on patient care (pre‐post ratio of Cmin within the desired range + 23.4%, pre, 51.2% vs. post, 74.6%). Overall, linezolid dosage was mainly reduced (56.9% of cases), whereas dose augmentation was needed only in a minority of cases (7.7%). Cost balance analysis showed that overall 1258 standard doses of linezolid (unitary dose 600 mg) were spared for treating 168 patients with a personalized dosage for a median duration of 11 days (range 3–128 days) with a cost saving of 60038.05 €.ConclusionActive computerized advice elaborated by the clinical pharmacologist on the basis of TDM results and of patient's pathophysiological data and co‐medications may be cost‐effective for personalizing linezolid treatment.
How Long Is a Normal Labor? Contemporary Patterns of Labor and Birth in a Low‐Risk Sample of 1,612 Women from Four Nordic Countries
Authors: Hildingsson Ingegerd , Blix Ellen , Hegaard Hanne , Huitfeldt Anette , Ingversen Karen , Ólafsdóttír Ólof Ásta , Lindgren Helena 
Published: October 2015

AbstractObjectiveNormal progress of labor is a subject for discussion among professionals. The aim of this study was to assess the duration of labor in women with a planned home birth and spontaneous onset who gave birth at home or in hospital after transfer.MethodsThis is a population‐based study of home births in four Nordic countries (Denmark, Iceland, Norway, and Sweden). All midwives assisting at a home birth from 2008 to 2013 were asked to provide information about home births using a questionnaire.ResultsBirth data from 1,612 women, from Denmark (n = 1,170), Norway (n = 263), Sweden (n = 138), and Iceland (n = 41) were included. The total median duration from onset of labor until the birth of the baby was approximately 14 hours for primiparas and 7.25 hours for multiparas. The duration of the different phases varied between countries. Blood loss more than 1,000 mL and perineal ruptures that needed suturing were associated with a longer pushing phase and the latter with country of residence, parity, single status, and the baby's weight.ConclusionIn this population of healthy women with a low prevalence of interventions, the total duration of labor was fairly similar to what is described in the literature for multiparas, but longer for primiparas. Although the duration of the phases of labor differed among countries, it was to a minor extent associated with severe outcomes.