bluuebunny/crossref_metadata_2025_split huggingface dataset:
FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies
Authors: Yao Jianchao , Zhang Kelvin Xi , Kramer Melissa , Pellegrini Matteo , McCombie W. Richard 
Published: January 2014

Abstract
Summary: FamAnn is an automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies. It can apply a different inheritance pattern or a de novo mutations discovery model to each family and select single nucleotide variants and small insertions and deletions segregating in each family or shared by multiple families. It also provides a variety of variant annotations and retains and annotates all transcripts hit by a single variant. Excel-compatible outputs including all annotated variants segregating in each family or shared by multiple families will be provided for users to prioritize variants based on their customized thresholds. A list of genes that harbor the segregating variants will be provided as well for possible pathway/network analyses. FamAnn uses the de facto community standard Variant Call Format as the input format and can be applied to whole exome, genome or targeted resequencing data.
Availability: https://sites.google.com/site/famannotation/home
Contact: jianchaoyao@gmail.com, kelvinzhang@mednet.ucla.edu, mccombie@cshl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Length-dependent processing of telomeres in the absence of telomerase
Authors: Fallet Emilie , Jolivet Pascale , Soudet Julien , Lisby Michael , Gilson Eric , Teixeira Maria Teresa 
Published: January 2014

Abstract
In the absence of telomerase, telomeres progressively shorten with every round of DNA replication, leading to replicative senescence. In telomerase-deficient Saccharomyces cerevisiae, the shortest telomere triggers the onset of senescence by activating the DNA damage checkpoint and recruiting homologous recombination (HR) factors. Yet, the molecular structures that trigger this checkpoint and the mechanisms of repair have remained elusive. By tracking individual telomeres, we show that telomeres are subjected to different pathways depending on their length. We first demonstrate a progressive accumulation of subtelomeric single-stranded DNA (ssDNA) through 5′-3′ resection as telomeres shorten. Thus, exposure of subtelomeric ssDNA could be the signal for cell cycle arrest in senescence. Strikingly, early after loss of telomerase, HR counteracts subtelomeric ssDNA accumulation rather than elongates telomeres. We then asked whether replication repair pathways contribute to this mechanism. We uncovered that Rad5, a DNA helicase/Ubiquitin ligase of the error-free branch of the DNA damage tolerance (DDT) pathway, associates with native telomeres and cooperates with HR in senescent cells. We propose that DDT acts in a length-independent manner, whereas an HR-based repair using the sister chromatid as a template buffers precocious 5′-3′ resection at the shortest telomeres.
Electrical Stimulation of the Ventral Tegmental Area Induces Reanimation from General Anesthesia
Authors: Solt Ken , Van Dort Christa J. , Chemali Jessica J. , Taylor Norman E. , Kenny Jonathan D. , Brown Emery N. 
Published: January 2014

Abstract

Background:
Methylphenidate or a D1 dopamine receptor agonist induces reanimation (active emergence) from general anesthesia. The authors tested whether electrical stimulation of dopaminergic nuclei also induces reanimation from general anesthesia.

Methods:
In adult rats, a bipolar insulated stainless steel electrode was placed in the ventral tegmental area (VTA, n = 5) or substantia nigra (n = 5). After a minimum 7-day recovery period, the isoflurane dose sufficient to maintain loss of righting was established. Electrical stimulation was initiated and increased in intensity every 3 min to a maximum of 120 µA. If stimulation restored the righting reflex, an additional experiment was performed at least 3 days later during continuous propofol anesthesia. Histological analysis was conducted to identify the location of the electrode tip. In separate experiments, stimulation was performed in the prone position during general anesthesia with isoflurane or propofol, and the electroencephalogram was recorded.

Results:
To maintain loss of righting, the dose of isoflurane was 0.9% ± 0.1 vol%, and the target plasma dose of propofol was 4.4 ± 1.1 µg/ml (mean ± SD). In all rats with VTA electrodes, electrical stimulation induced a graded arousal response including righting that increased with current intensity. VTA stimulation induced a shift in electroencephalogram peak power from δ (<4 Hz) to θ (4–8 Hz). In all rats with substantia nigra electrodes, stimulation did not elicit an arousal response or significant electroencephalogram changes.

Conclusions:
Electrical stimulation of the VTA, but not the substantia nigra, induces reanimation during general anesthesia with isoflurane or propofol. These results are consistent with the hypothesis that dopamine release by VTA neurons, but not substantia nigra neurons, induces reanimation from general anesthesia.
Acute Effects of the Glucagon‐Like Peptide 2 Analogue, Teduglutide, on Intestinal Adaptation in Short Bowel Syndrome
Authors: Thymann Thomas , Stoll Barbara , Mecklenburg Lars , Burrin Douglas G. , Vegge Andreas , Qvist Niels , Eriksen Thomas , Jeppesen Palle B. , Sangild Per T. 
Published: January 2014

ABSTRACTNeonatal short bowel syndrome following massive gut resection is associated with malabsorption of nutrients. The intestinotrophic factor glucagon‐like peptide 2 (GLP‐2) improves gut function in adult patients with short bowel syndrome, but its effect in pediatric patients remains unknown. Our objective was to test the efficacy of the long‐acting synthetic human GLP‐2 analogue, teduglutide (ALX‐0600), in a neonatal piglet jejunostomy model. Two‐day‐old pigs were subjected to resection of 50% of the small intestine (distal part), and the remnant intestine was exteriorized on the abdominal wall as a jejunostomy. All pigs were given total parenteral nutrition for 7 days and a single daily injection of the following doses of teduglutide: 0.01 (n = 6), 0.02 (n = 6), 0.1 (n = 5), or 0.2 mg · kg−1 · day−1 (n = 6), and compared with placebo (n = 9). Body weight increment was similar for all 4 teduglutide groups but higher than placebo (P < 0.05). There was a dose‐dependent increase in weight per length of the remnant intestine (P < 0.01) and fractional protein synthesis rate in the intestine was increased in the 0.2 mg · kg−1 · day−1 group versus placebo (P < 0.001); however, functional and structural endpoints including activity of digestive enzymes, absorption of enteral nutrients, and immunohistochemistry (Ki67, villin, FABP2, ChgA, and GLP‐2R) were not affected by the treatment. Teduglutide induces trophicity on the remnant intestine but has limited acute effects on functional endpoints. Significant effects of teduglutide on gut function may require a longer adaptation period and/or a more frequent administration of the peptide. In perspective, GLP‐2 or its analogues may be relevant to improve intestinal adaptation in pediatric patients with short bowel syndrome.
High Bone Density in Adolescents With Obesity Is Related to Fat Mass and Serum Leptin Concentrations
Authors: Maggio Albane B.R. , Belli Dominique C. , Puigdefabregas Julie Wacker Bou , Rizzoli René , Farpour‐Lambert Nathalie J. , Beghetti Maurice , McLin Valérie A. 
Published: January 2014

ABSTRACTObjectives:Obesity has been associated with increased bone mass, but the mechanisms involved are still poorly understood. We aimed to explore the relation between bone mineral density and factors known to influence bone formation in obese and lean adolescents.Methods:We recruited 24 obese and 25 lean adolescents in a case‐control study. Total body bone mineral density (TB‐BMD) z scores and body composition were determined using dual‐energy x‐ray absorptiometry. We measured 25‐hydroxyvitamin D (25‐OH‐D), glucose, insulin, and leptin concentrations. Physical activity (PA) level was quantified using accelerometer.Results:TB‐BMD z score was higher, whereas 25‐OH‐D and PA levels were lower in obese compared with lean subjects (TB‐BMD z score 1.06 ± 0.96 vs 0.26 ± 0.91, P = 0.004; 25‐OH‐D 9.9 ± 6.4 vs 18.5 ± 7.4 ng mL−1, P < 0.001; PA level 308.3 ± 22.1 vs 406.8 ± 29.2 count min−1, P = 0.01). TB‐BMD z score was not related to 25‐OH‐D or PA levels, but was positively correlated with leptin concentration and fat mass (P < 0.05). Vitamin D concentration was negatively correlated with fat mass (P < 0.001).Conclusions:Despite lower serum vitamin D and PA levels, BMD was higher in adolescents with obesity and associated with higher serum leptin concentrations. Furthermore, adolescents with obesity have lower vitamin D serum concentrations than lean controls, probably owing to its distribution in adipose tissue.
ETHYLENE RESPONSE FACTOR070 Regulates Root Development and Phosphate Starvation-Mediated Responses
Authors: Ramaiah Madhuvanthi , Jain Ajay , Raghothama Kashchandra G. 
Published: January 2014

Abstract
Inorganic phosphate (Pi) availability is a major factor determining growth and consequently the productivity of crops. However, it is one of the least available macronutrients due to its high fixation in the rhizospheres. To overcome this constraint, plants have developed adaptive responses to better acquire, utilize, and recycle Pi. Molecular determinants of these adaptive mechanisms include transcription factors (TFs) that play a major role in transcriptional control, thereby regulating genome-scale networks. In this study, we have characterized the biological role of Arabidopsis thaliana Ethylene Response Factor070 (AtERF070), a Pi starvation-induced TF belonging to the APETALA2/ETHYLENE RESPONSE FACTOR family of TFs in Arabidopsis (Arabidopsis thaliana). It is localized to the nucleus and induced specifically in Pi-deprived roots and shoots. RNA interference-mediated suppression of AtERF070 led to augmented lateral root development resulting in higher Pi accumulation, whereas there were reductions in both primary root length and lateral root number in 12-d-old transgenic seedlings overexpressing AtERF070. When the overexpressing lines were grown to maturity under greenhouse conditions, they revealed a stunted bushy appearance that could be rescued by gibberellic acid application. Furthermore, a number of Pi starvation-responsive genes were modulated in AtERF070-overexpressing and RNA interference lines, thereby suggesting a potential role for this TF in maintaining Pi homeostasis.
Embracing sustainability practices in UK construction organizations
Authors: Opoku Alex , Ahmed Vian 
Published: January 2014

Purpose
– Adopting sustainable construction practices minimizes the overall environmental impact of the built asset throughout its whole life. Currently, there is demand from key stakeholders in the construction industry for organization to deliver sustainable built environment, however, leaders/champions within construction organizations charged with the adoption of sustainable construction practices face many challenges. The purpose of this paper is to present the results of an investigation into the challenges facing intra-organizational leaders charged with the promotion of sustainable construction practices.

Design/methodology/approach
– Qualitative data were collected through semi-structured interview with 15 leaders, followed by an industry-wide survey of 200 intra-organizational leaders in contractor and consultant organizations in the UK construction industry.

Findings
– The results revealed that increased capital cost is the most significant challenge facing construction organizations in attempt to adopt sustainability practices in the delivery of construction projects.

Originality/value
– This study provides the empirical evidence linking leadership within construction organizations and sustainability; filling the gap in literature and serving as a source of reference material for higher education programmes in the built environment.
A game-theoretic model for roadway performance management
Authors: Osman Hesham , Nikbakht Mazdak 
Published: January 2014

Purpose
– The purpose of this paper is to present a socio-technical approach to modeling the behavior of roadway users, asset managers, and politicians toward roadway performance and asset management. This approach models the complex interactions that occur between these agents in a complex system. Most modeling approaches in the domain of infrastructure asset management take a purely asset-centric approach and fail to address these socio-technical interactions.

Design/methodology/approach
– Interactions among political decision makers, asset management strategy developers, and road users are modeled using a game-theoretic approach. The interactions are modeled as a non-cooperative game in which politicians, asset managers, and road users are the main players. Each player is autonomous and aims to come up with the set of moves to maximize their respective level of satisfaction in response to other players’ moves. Multi-attribute utility theory is used to deal with multitude of players’ goals, and the Nash equilibria of the game are south out to develop appropriate strategies for different players.

Findings
– An illustrative example for a road network of a Canadian city is used to demonstrate the developed methodology. The developed methodology demonstrates how behaviors of various agents involved in the sphere of asset management impacts their collective decision-making behavior.

Originality/value
– The developed framework provides asset managers and political decision makers with a valuable tool to evaluate the impact of public policy decisions related to asset managers on road performance and the overall satisfaction of road users.
Stakeholders’ expectations in utilising financial models for public-private partnership projects
Authors: Kurniawan Fredy , Ogunlana Stephen , Motawa Ibrahim 
Published: January 2014

Purpose– The purpose of this paper is to explore stakeholders’ expectations in utilising PPP financial models in order to ensure that each stakeholder understands the expectations of others before negotiating and reaching contract agreement by all the stakeholders.Design/methodology/approach– Five common sets of 40 expectations have been identified through a systematic research approach, and their relative significances were verified based on pilot studies in India and the UK and expert opinion solicited worldwide through a structured questionnaire survey. The survey responses were evaluated by using statistical analyses.Findings– The most important stakeholders’ expectations in utilising PPP financial models were identified at five different stages in a project. They are bankable (at the pre-proposal stage), assessment of project's ability to carry senior debt (at the contract negotiation stage), sensitivity analysis for key commercial issues (at the finance-raising stage), debt service evaluation towards cost overrun and other adverse events (at the construction stage), and assurance of secure operational cash flow (at the operation stage). Although some of the most important expectations are agreed on by all stakeholders, the disagreement of most important expectations should also be considered by the other stakeholder(s) in order to achieve effective and efficient negotiations.Originality/value– The paper draws attention to stakeholders’ expectations in utilising a financial model that is arguably overlooked in evaluating PPP projects. It does so in order to speed up the negotiation process as a means of minimising cost and time expenditures on PPP contract negotiation.
Potential and implications of sustainability action plans
Authors: Thomson Craig , El-Haram Mohamed 
Published: January 2014

Purpose
– Sustainability action plans are emerging as a management tool to facilitate the delivery of sustainability objectives which are planned, measured and achievable in practice. The purpose of this paper is to explore the potential to support an integrated approach to delivering sustainability across the phases of a construction project. A holistic approach to sustainability is promoted which aims to be understandable, managed and aligned with available sustainability assessment methods.

Design/methodology/approach
– The application of a sustainability action plan is explored in the Greater Middlehaven Regeneration Project (UK). Six key stakeholders were interviewed to consider the rational of its application, structure, role of sustainability assessment and contribution to project development and delivery. Two workshops involving practitioners and experts in sustainable construction explored the implications for the wider context.

Findings
– A framework around which sustainability can be managed through a series of integrated tailored action plans applied across each project phase was highlighted. Clear benefits were presented in facilitating the sharing of knowledge, communicating aspirations and in providing leadership to project members.

Research limitations/implications
– The case study enjoys a supportive environment to embed best practice and thus full appreciation of potential barriers to implementation in other contexts was not possible.

Practical implications
– The research illustrates the need to promote a common sustainability legacy across the project phases and highlights the role of a sustainability action plan in facilitating this consistency.

Originality/value
– A holistic approach founded on an understandable philosophy remains innovative in practice and explored are its value and implications.
An integrated framework to support the process of green management adoption
Authors: Garzella Stefano , Fiorentino Raffaele 
Published: January 2014

Purpose– The purpose of this paper is to develop an integrated framework that aims to support the commitment of managers to green management and environmental strategies.Design/methodology/approach– Relevant literature is reviewed and critically assessed. A framework is provided with the objective of supporting the process of green management adoption and the success of environmental strategies.Findings– Green management issues have the potential to inform a wide range of business processes. The proposed framework clarifies that a multi-criteria approach (including the activity sector, drivers of green management adoption, strategic horizon and level of strategy) is needed to analyze the many critical actions that firms can develop to embrace green management. This model allows firms to be well equipped to address environmental challenges in a strategic manner.Practical implications– This paper offers implications of interest to managers, pointing out that many actions may result in the adoption of socially responsible environmental policies. Specifically, the paper suggests strategies and practices that contribute to green management while simultaneously driving environmental, financial and competitive results.Originality/value– This article responds to the needs of managers who are engaged in environmental social responsibility for a framework to assist in identifying and exploiting the most effective ways of coping with the adoption of green management.
Pareto-principle application in non-IT supported CRM processes
Authors: Elbeltagi Ibrahim , Kempen Thijs , Garcia Elaine 
Published: January 2014

Purpose
– This research covers a rather unexplored area of customer relationship management (CRM) by questioning the mechanism between on the one hand the Pareto-principle and on the other hand traditional non-IT supported operational CRM processes. Thus, the paper aims to explore whether a minority of processes and process-aspects deserves credit for achieving a majority of CRM goals.

Design/methodology/approach
– A qualitative approach is the most appropriate due to the assumption that access to the reality of a situation is only possible through social construction. A qualitative approach seeks to answer questions posed by studying different social settings. As noted by Berg, qualitative techniques make it possible for researchers to participate in understanding and perceiving others, as well as permitting them to discover how people structure their daily lives to make them more meaningful.

Findings
– The questioned mechanism of on the one hand traditional non-IT supported operational CRM process-aspects and on the other hand the Pareto-principle is confirmed by the majority of interviewees who answered affirmatively to small things making big differences in customer contact.

Research limitations/implications
– Regarding the limitations of this study, the results are hard to generalise as the research context depends on a single case study. However, the high levels of detail that allows for greater insight into manufacturing SMEs in HGV-Trailer that want to adopt non-IT support operational CRM where there is lack of financial resources justify the choice of this case study.

Practical implications
– This study is important for management to focus and develop social on top of technical competencies. This was clear from the importance of social intercourse as the glue that links all the non-IT supported operational processes from break down to invoices. It helps in removing the uncertainty from the view point of customers and highlights the importance of the care that companies need to give to the human side of the process more than objectifying things. Moreover, the finding provides an important implication for practitioners involved spare-parts purchasing process and the warranty claiming process should continuously assess whether they operate in support of a breakdown or not and subsequently use this insight to prioritize their tasks.

Originality/value
– This research tried to answer how the Pareto-principle applies to traditional non-IT supported operational CRM process-aspects by concluding that the first social intercourse, as well as problem ownership, belongs – from a customers' viewpoint – to the “vital few” leading to “trivial many” results of rational and emotional nature. This is especially true in the breakdown process, and processes that operate in support of breakdowns.
The process and structure of user participation: a BPM system implementation case study
Authors: M.E. de Waal Benny , Batenburg Ronald 
Published: January 2014

Purpose
– The aim of this study is to debunk the relationship between user participation practices and the development and success of information systems/information technology implementations. While most studies practically rely on how many participation activities are performed, the process through which users engage in user participation is not specified.

Design/methodology/approach
– A mixed method approach was applied to study the research questions. A number of relationships were tested by survey data collected among 143 end-users and 49 interviews of employees of a large Dutch social insurance organization that implemented a new and integrative business process management (BPM) system.

Findings
– The results show that specification of the participation context is of key importance for understanding the success of BPM implementation. Quantitative and qualitative analyses show that rich participation activities hold a stronger positive relationship with the BPM system development and implementation success than other participatory activities that only assist development or implementation. Furthermore, it is demonstrated that the updated theory of user participation by Markus and Mao can be turned into a useful instrument for measuring the different aspects of participation.

Originality/value
– Most studies on user participation “only” measure how many participation activities were performed, and not how or why they were performed. Furthermore, the combination of qualitative and quantitative data and instruments resulted in a greater understanding of how exactly user participation was brought into practice and how the consequences of this practice were interrelated.