bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Gastrostomy Placement With Concurrent Fundoplication Increase the Risk of Gastrostomy‐related Complications?
Authors: Thomas Christine , Forrest Alison , Klingberg Hannah , Moore David , Abu‐Assi Rammy , Barry Simon C. , Khurana Sanjeev 
Published: December 2015

ABSTRACTObjective:To compare the incidence of complications with a primary gastrostomy versus gastrostomy with concurrent fundoplication and evaluating the impact of the method of gastrostomy tube placement. Neurologically impaired children were compared with neurologically normal children. Two low profile devices were compared for longevity.Methods:Ninety‐eight patients (58 boys, mean age 4.66 years) with 107 gastrostomies inserted between April 2004 and May 2008 were included in this retrospective, single institution audit. Minimum follow‐up period was 1 year. Specific complications reviewed were tube and site related. Logistic regression analysis examined the relationship between complications, type of procedure, method of placement, and neurological status. Survival analysis with log‐rank test was used to compare the duration of the low‐profile devices.Results:There were 63 primary gastrostomies and 44 with concurrent fundoplication, 71 children were neurologically impaired. Mean (±SD) follow‐up time was 35.6 ± 1.4 months. There was a significant association between concurrent gastrostomy insertion with fundoplication and incidence of infection (odds ratio = 2.4, 95% confidence interval (CI) 1.02–5.56, P = 0.02) and excoriation (odds ratio = 2.5, 95% CI 1.09–5.71, P = 0.015). There were no associations between the complications with gastrostomy placement and neurological status. Failure rate of the balloon device was significantly greater than the fixed bolster device with a Hazard Ratio for survival of 3.2 (95% CI 2.2–4.6).Conclusions:Gastrostomy site‐related problems were more common than generally reported. There was a higher incidence of site infection and skin excoriation for gastrostomy placement with concurrent fundoplication. There was no significant difference in complications between the method of gastrostomy placement or neurological status. Balloon devices were changed 3 times more often than bolster retention devices.
Combating the scientific decline effect with confidence (intervals)
Authors: Groppe David M. 
Published: December 2015

ABSTRACTA symptom of the need for greater reproducibility in scientific practice is the “decline effect,” the fact that the size of many experimental effects decline with subsequent study or fail to replicate entirely. A simple way to combat this problem is for scientists to more routinely use confidence intervals (CIs) in their work. CIs provide frequentist bounds on the true size of an effect and can reveal when a statistically significant effect is possibly too small to be reliable or when a large effect might have been missed due to insufficient statistical power. CIs are often lacking in psychophysiological reports, likely due to the large number of dependent variables, which complicates deriving and visualizing CIs. In this article, I explain the value of CIs and show how to compute them for analyses involving multiple variables in various ways that adjust the intervals for the greater uncertainty induced by multiple statistical comparisons. The methods are illustrated using a basic visual oddball event-related potential (ERP) dataset and freely available Matlab software.
Ritornello: High fidelity control-free chip-seq peak calling
Authors: Stanton Kelly Patrick , Jin Jiaqi , Weissman Sherman , Kluger Yuval 
Published: December 2015

AbstractWith the advent of next generation high-throughput DNA sequencing technologies, omics experiments have become the mainstay for studying diverse biological effects on a genome wide scale. ChIP-seq is the omics technique that enables genome wide localization of transcription factor binding or epigenetic modification events. Since the inception of ChIP-seq in 2007, many methods have been developed to infer ChIP target binding loci from the resultant reads after mapping them to a reference genome. However, interpreting these data has proven challenging, and as such these algorithms have several shortcomings, including susceptibility to false positives due to artifactual peaks, poor localization of binding sites, and the requirement for a total DNA input control which increases the cost of performing these experiments. We present Ritornello, a new approach with roots in digital signal processing (DSP) that addresses all of these problems. We show that Ritornello generally performs equally or better than the peak callers tested and recommended by the ENCODE consortium, but in contrast, Ritornello does not require a matched total DNA input control to avoid false positives, effectively decreasing the sequencing cost to perform ChIP-seq.
LEAFY COTYLEDON1-CASEIN KINASE I-TCP15-PHYTOCHROME INTERACTING FACTOR4 Network Regulates Somatic Embryogenesis by Regulating Auxin Homeostasis
Authors: Min Ling , Hu Qin , Li Yaoyao , Xu Jiao , Ma Yizan , Zhu Longfu , Yang Xiyan , Zhang Xianlong 
Published: December 2015

AbstractSomatic embryogenesis (SE) is an efficient tool for the propagation of plant species and also, a useful model for studying the regulatory networks in embryo development. However, the regulatory networks underlying the transition from nonembryogenic callus to somatic embryos during SE remain poorly understood. Here, we describe an upland cotton (Gossypium hirsutum) CASEIN KINASE I gene, GhCKI, which is a unique key regulatory factor that strongly affects SE. Overexpressing GhCKI halted the formation of embryoids and plant regeneration because of a block in the transition from nonembryogenic callus to somatic embryos. In contrast, defective GhCKI in plants facilitated SE. To better understand the mechanism by which GhCKI regulates SE, the regulatory network was analyzed. A direct upstream negative regulator protein, cotton LEAFY COTYLEDON1, was identified to be targeted to a cis-element, CTTTTC, in the promoter of GhCKI. Moreover, GhCKI interacted with and phosphorylated cotton CINCINNATA-like TEOSINTE BRANCHED1-CYCLOIDEA-PCF transcription factor15 by coordinately regulating the expression of cotton PHYTOCHROME INTERACTING FACTOR4, finally disrupting auxin homeostasis, which led to increased cell proliferation and aborted somatic embryo formation in GhCKI-overexpressing somatic cells. Our results show a complex process of SE that is negatively regulated by GhCKI through a complex regulatory network.
Preparing a framework for two-stage target-cost arrangement formulation
Authors: Lahdenperä Pertti 
Published: December 2015

Purpose
– Early involvement of the project team with the construction resources seems to be gaining popularity as it aims to improve the cost efficiency of a project as there is significantly more potential to influence the project solution at that point in time. The missing price during early involvement/selection and the principal-agent setting, however, tend to leave the project owner in doubt of the reasonableness of pricing when it is fixed only later after the joint design phase involving the service provider and the owner. The purpose of this paper is to find a solution for this challenge.

Design/methodology/approach
– A two-stage target-cost (2STC) arrangement has been proposed as the solution. In this model the service provider earns a bonus by suggesting a lower target cost than the reference set at the time of the involvement of the provider. The amount of bonus also impacts the cost over-run risk transferred to the service provider to avoid overly optimistic promises. The proposition encompassed just the basic idea, and did not really delve into actual model formulations and their functioning under practical realities. Therefore, the required work is presented here in the form of a conceptual, discursive study focusing on relevant theories and empirical findings from major investment projects.

Findings
– The study produces a requirement framework for the 2STC model to allow functioning models to be formulated and tested. The framework incorporates numerous requirements, constraints and a suggested path forward. For instance, while the model may not be manipulatable, it must incentivise the service provider to seek more cost-effective project solutions, be feasible also from the view of the project owner and adapt to various project risk profiles and ranges of efficiency improvements.

Research limitations/implications
– The study suggests more concrete model formulations to be provided under the guidance of the presented framework.

Originality/value
– The 2STC model is a unique concept and no comparable construct is known to exist. Besides the requirement framework, the study also strengthens the foundation of and need for the 2STC model by a thorough survey of its theoretical linkages. Accordingly, the study presented in this paper forms the second stage in the overall 2STC development process focused on benefiting project owners and the industry.
Formularising two-stage target-cost arrangements for use in practice
Authors: Lahdenperä Pertti 
Published: December 2015

Purpose
– Early involvement of the project team with the construction resources seems to be gaining popularity as it aims to improve the cost efficiency of a project as there is significantly more potential to influence the project solution at that point in time. The missing price during early involvement/selection and the principal-agent setting, however, tend to leave the project owner in doubt of the reasonableness of pricing when it is fixed only later after the joint design phase involving the service provider and the owner. The purpose of this paper is to find a solution for this challenge.

Design/methodology/approach
– A two-stage target-cost (2STC) arrangement has been proposed as the solution. In this model the service provider earns a bonus by suggesting a lower target cost than the reference set at the time of the involvement of the provider. The amount of bonus also impacts the cost over-run risk transferred to the service provider to avoid overly optimistic promises. Besides the initial conceptualisation of the idea, earlier research has also produced a framework for developing and assessing alternative formulations of the 2STC model. By means of mathematical modelling and optimisation and critical review the work seeks to provide formulations that meet the set requirements.

Findings
– The study establishes concrete formulations that are believed to function as intended with certain reservations. Two potential mechanisms, the constant and variable share models, are generated and presented, and recommendations are given for their use in practice. In the former, the extent of cost efficiency improvement in the development phase has no impact on percentage shares, but in the latter the service provider’s relative development bonus and share of cost over-runs are the bigger, the bigger the improvement.

Research limitations/implications
– The study suggests piloting the formulations in carefully selected projects in order to discover their practical feasibility.

Originality/value
– The 2STC model is a unique concept and no comparable construct is known to exist. The study produced concrete formulations for a 2STC construct while ensuring and illustrating their functioning to avoid surprises in their use. The study presented in this paper forms the third stage in the overall 2STC development process focussed on benefiting project owners and the industry.
Cognitive, affective and behavioural responses in mall experience
Authors: Lucia-Palacios Laura , Pérez-López Raúl , Polo-Redondo Yolanda 
Published: December 2015

Purpose
– The purpose of this paper is to identify specific cognitive and affective responses in mall experience, as well as their antecedents, moderators and behavioural outcomes.

Design/methodology/approach
– The paper is based on content analysis technique. Data were obtained through in-depth interviews conducted from February 2013 to January 2014.

Findings
– The study reports the identification of efficiency and confusion as cognitive responses, as well as frustration, stress, peacefulness and excitement as affective responses experienced during the shopping trip. These responses lead to behavioural outcomes that are time spent, buying intentions and repatronage intentions. Furthermore, the paper identifies the main antecedents of these responses and the moderators of their relationships.

Research limitations/implications
– The findings provide insights into the study of psychological responses in retailing and avenues for further research.

Practical implications
– This research offers practical implications for managers, related to the manipulation of mall characteristics in order to encourage positive cognitive and affective responses and avoid negative ones.

Originality/value
– Based on content analysis technique, the present paper proposes a theoretical framework to conceptualize mall experience, detecting specific cognitive and affective responses and their specific behavioural outcomes as well as moderators.
Exploring logistics-related environmental sustainability in large retailers
Authors: Björklund Maria , Forslund Helena , Persdotter Isaksson Maria 
Published: December 2015

Purpose– The purpose of this paper is to explore and illustrate ways in which the world’s largest retailers describe their logistics-related environmental considerations, their environmental indicators applied to measure the effects of these considerations and their environmental consciousness in their CSR reports.Design/methodology/approach– Classification models are developed via a literature review on logistics-related environmental considerations, indicators and consciousness. A content analysis approach is then applied to examine CSR reports from 12 of the world’s largest retailers.Findings– Few retailers show environmental considerations in all logistics activities, but purchasing is especially well described. Even if many retailers claim to use the Global Reporting Initiative (GRI) framework, no one uses is completely. Judging consciousness from CSR reports raised a number of questions.Research limitations/implications– A contribution to theory is the development of two classification models. The first provides a description structure for environmental considerations related to logistics activities. The second expands the GRI indicator framework by incorporating a structure for logistics activities.Practical implications– The classification models developed can be an important mean for managers and also consumers to judge the environmental sustainability of retailers by their CSR reports.Social implications– The study makes a social contribution with its input on sustainability and especially environmental issues.Originality/value– Few studies have focused upon environmentally sustainable logistics in retail chains, and even fewer address how to measure environmental sustainability in this context.
Trust me: the keys to success in cooperative collections ventures
Authors: Jakubs Deborah Lynn 
Published: December 2015

Purpose
– Cooperation among research libraries is a venerable pursuit with a long history. The purpose of this paper is to examine three collaborative tools and programs ranging from the late 1970s to the present to identify the promise of each as well as the challenges, the factors that both facilitate and interfere with true cooperation, highlighting the lessons learned.

Design/methodology/approach
– The author analyzes the development and functions of the Conspectus of the Research Libraries Group, the Global Resources Program of the Association of Research Libraries, and the Triangle Research Libraries Network in the state of North Carolina, USA.

Findings
– While the goals of collaborative collections initiatives are laudable, it is often difficult to accomplish true, balanced, and lasting cooperation that results in both expanded access and financial reallocation.

Originality/value
– The study is a first-hand, inside look at the methods and mechanisms of cooperative collection development that offers suggestions for future partnerships on either a small or a large scale.
Bacterial predation: 75 years and counting!
Authors: Pérez Juana , Moraleda‐Muñoz Aurelio , Marcos‐Torres Francisco Javier , Muñoz‐Dorado José 
Published: December 2015

SummaryThe first documented study on bacterial predation was carried out using myxobacteria three quarters of a century ago. Since then, many predatory strains, diverse hunting strategies, environmental consequences and potential applications have been reported by groups all over the world. Now we know that predatory bacteria are distributed in a wide variety of environments and that interactions between predatory and non‐predatory populations seem to be the most important factor in bacterial selection and mortality in some ecosystems. Bacterial predation has now been proposed as an evolutionary driving force. The structure and diversity of the predatory bacterial community is beginning to be recognized as an important factor in biodiversity due to its potential role in controlling and modelling bacterial populations in the environment. In this paper, we review the current understanding of bacterial predation, going over the strategies used by the main predatory bacteria to kill their prey. We have also reviewed and integrated the accumulated advances of the last 75 years with the interesting new insights that are provided by the analyses of genomes, predatomes, predatosomes and other comparative genomics studies, focusing on potential applications that derive from all of these areas of study.
Intergenerational Transmission of Aggression: Physiological Regulatory Processes
Authors: Margolin Gayla , Ramos Michelle C. , Timmons Adela C. , Miller Kelly F. , Han Sohyun C. 
Published: December 2015

AbstractChildren who grow up in aggressive households are at risk of having problems with physiological regulation, but researchers have not investigated physiology as a mechanism in the intergenerational transmission of aggression. In this article, we posit that physiological regulation, particularly during stressful interpersonal interactions, may shed light on sensitivity to conflict. It can also inform our understanding of associations between childhood exposure to aggression in families of origin and aggression against partners in adolescence or adulthood. In support of this model, we highlight findings showing that childhood exposure to family aggression relates to physiological regulation across the life span, and that reactions to physiological stress concurrently relate to aggression against intimate partners. Emerging evidence from research on biological processes during stressful interpersonal interactions raises questions about what is adaptive for individuals from aggressive families, particularly as past family experiences intersect with the challenges of new relationships.
Thyroid dysfunction and anaemia in a large population‐based study
Authors: M'Rabet‐Bensalah Khadija , Aubert Carole E. , Coslovsky Michael , Collet Tinh‐Hai , Baumgartner Christine , den Elzen Wendy P. J. , Luben Robert , Angelillo‐Scherrer Anne , Aujesky Drahomir , Khaw Kay‐Tee , Rodondi Nicolas 
Published: December 2015

SummaryObjective and backgroundAnaemia and thyroid dysfunction are common and often co‐occur. Current guidelines recommend the assessment of thyroid function in the work‐up of anaemia, although evidence on this association is scarce.Patients and methodsIn the ‘European Prospective Investigation of Cancer’ (EPIC)‐Norfolk population‐based cohort, we aimed to examine the prevalence and type of anaemia (defined as haemoglobin <13 g/dl for men and <12 g/dl for women) according to different thyroid function groups.ResultsThe mean age of the 8791 participants was 59·4 (SD 9·1) years and 55·2% were women. Thyroid dysfunction was present in 437 (5·0%) and anaemia in 517 (5·9%) participants. After excluding 121 participants with three most common causes of anaemia (chronic kidney disease, inflammation, iron deficiency), anaemia was found in 4·7% of euthyroid participants. Compared with the euthyroid group, the prevalence of anaemia was significantly higher in overt hyperthyroidism (14·6%, P < 0·01), higher with borderline significance in overt hypothyroidism (7·7%, P = 0·05) and not increased in subclinical thyroid dysfunction (5·0% in subclinical hypothyroidism, 3·3% in subclinical hyperthyroidism). Anaemia associated with thyroid dysfunction was mainly normocytic (94·0%), and rarely macrocytic (6·0%).ConclusionThe prevalence of anaemia was higher in overt hyperthyroidism, but not increased in subclinical thyroid dysfunction. Systematic measurement of thyroid‐stimulating hormone in anaemic patients is likely to be useful only after excluding common causes of anaemia.
Daily salivary cortisol patterns in midlife women with hot flashes
Authors: Reed S.D. , Newton K.M. , Larson J.C. , Booth‐LaForce C. , Woods N.F. , Landis C.A. , Tolentino E. , Carpenter J.S. , Freeman E.W. , Joffe H. , Anawalt B.D. , Guthrie K.A. 
Published: December 2015

SummaryObjectiveDiurnal salivary cortisol patterns in healthy adults are well established but have not been studied in midlife women with hot flashes. We hypothesized that frequent hot flashes are associated with aberrant cortisol patterns similar to sleep‐deficient individuals.DesignCross‐sectional.ParticipantsA total of 306 women, ages 40–62, randomized to a behavioural intervention for hot flashes.MeasurementsBaseline comparisons of cortisol geometric means (nmol/l) from four daily time points averaged over two consecutive days plus other calculated cortisol measures were made between groups defined by baseline: (i) mean daily hot flash frequency tertile (≤5·5, N = 103; >5·5–8·8, N = 103; >8·8, N = 100) and (ii) selected characteristics. Repeated‐measures linear regression models of log‐transformed cortisol evaluated group differences, adjusting for covariates.ResultsWomen were 67% White and 24% African American, with 7·6 (SD 3·9) hot flashes per day. Salivary cortisol geometric means (nmol/l) among all women were as follows: 75·0 (SD 44·8) total, 8·6 (SD 5·6) wake, 10·0 (SD 7·5) wake +30 min, 3·7 (SD 3·3) early afternoon and 1·6 (SD 1·8) bedtime. Wake + 30‐minute values showed an 18% median rise from wake values (interquartile range −24 to 96%), and means varied by hot flash frequency tertile, from lowest to highest: 11·4(SD 7·3), 10·3 (SD 6·5) and 8·6 (SD 7·8), respectively, P = 0·003. Beside the early afternoon value (P = 0·02), cortisol values did not vary by hot flash frequency.ConclusionTaken together, these findings suggest that high frequency of moderate‐to‐severe hot flashes may be associated with subtle abnormalities in cortisol concentrations – a pattern consistent with chronic sleep disturbance.