bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processed pseudogenes acquired somatically during cancer development
Authors: Cooke Susanna L. , Shlien Adam , Marshall John , Pipinikas Christodoulos P. , Martincorena Inigo , Tubio Jose M.C. , Li Yilong , Menzies Andrew , Mudie Laura , Ramakrishna Manasa , Yates Lucy , Davies Helen , Bolli Niccolo , Bignell Graham R. , Tarpey Patrick S. , Behjati Sam , Nik-Zainal Serena , Papaemmanuil Elli , Teixeira Vitor H. , Raine Keiran , O’Meara Sarah , Dodoran Maryam S. , Teague Jon W. , Butler Adam P. , Iacobuzio-Donahue Christine , Santarius Thomas , Grundy Richard G. , Malkin David , Greaves Mel , Munshi Nikhil , Flanagan Adrienne M. , Bowtell David , Martin Sancha , Larsimont Denis , Reis-Filho Jorge S. , Boussioutas Alex , Taylor Jack A. , Hayes Neil D. , Janes Sam M. , Futreal P. Andrew , Stratton Michael R. , McDermott Ultan , Campbell Peter J. ,   ICGC Breast Cancer Group, Provenzano Elena , van de Vijver Marc , Richardson Andrea L. , Purdie Colin , Pinder Sarah , Mac Grogan Gaetan , Vincent-Salomon Anne , Larsimont Denis , Grabau Dorthe , Sauer Torill , Garred Øystein , Ehinger Anna , Van den Eynden Gert G. , van Deurzen C.H.M , Salgado Roberto , Brock Jane E. , Lakhani Sunil R. , Giri Dilip D. , Arnould Laurent , Jacquemier Jocelyne , Treilleux Isabelle , Caldas Carlos , Chin Suet-Feung , Fatima Aquila , Thompson Alastair M. , Stenhouse Alasdair , Foekens John , Martens John , Sieuwerts Anieta , Brinkman Arjen , Stunnenberg Henk , Span Paul N. , Sweep Fred , Desmedt Christine , Sotiriou Christos , Thomas Gilles , Broeks Annegein , Langerod Anita , Aparicio Samuel , Simpson Peter T. , van ’t Veer Laura , Erla Eyfjörd Jórunn , Hilmarsdottir Holmfridur , Jonasson Jon G. , Børresen-Dale Anne-Lise , Lee Ming Ta Michael , Wong Bernice Huimin , Tan Benita Kiat Tee , Hooijer Gerrit K.J. 
Published: April 2014

AbstractCancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context.
The nature and extent of contributions by defective ribosome products to the HLA peptidome
Authors: Bourdetsky Dmitry , Schmelzer Christian E. H. , Admon Arie 
Published: April 2014

SignificanceRapid degradation of newly synthesized proteins, followed by presentation of the resulting peptides by the MHC molecules, serves as an early alert for the immune system during pathogen infection. This study defines the relative contribution to the MHC peptidome of defective ribosome products (DRiPs), which are newly synthesized and rapidly degraded proteins, vs. mature proteins, degraded at the end of their functional lifetimes (retirees). The rates of synthesis of the individual MHC peptides and their source proteins were followed using stable isotope labeling and quantitative proteomics and peptidomics analyses. We conclude that DRiPs are a significant source of MHC peptides. Many of these DRiPs are misassembled surplus subunits of protein complexes and therefore are degraded soon after synthesis.
Colloidal aggregation and dynamics in anisotropic fluids
Authors: Mondiot Frédéric , Botet Robert , Snabre Patrick , Mondain-Monval Olivier , Loudet Jean-Christophe 
Published: April 2014

SignificanceThe formulation of colloidal particle/liquid crystal (LC) composites is a well-identified route toward the design of smart responsive materials with tunable optical or mechanical properties. However, the particles aggregate because they distort the intrinsic order of LC phases, which costs elastic energy. For micrometer-sized inclusions, the resulting elastic forces dominate the coarsening of the system. In this paper, we find a previously unidentified regime where elastic interactions no longer prevail when the particles are downsized to the nanometer scale. Instead, the system evolution is governed by an anisotropic Brownian diffusion coupled to attractive depletion interactions. This finding opens up new possibilities to better control the clustering of colloids in such media. We provide both experimental evidence and numerical simulations.
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
Authors: Leung Alvin , Bader Gary D. , Reimand Jüri 
Published: April 2014

Abstract
Summary: Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery. HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks.
Availability and implementation: HyperModules is available in Cytoscape App Store and as a command line tool at www.baderlab.org/Sofware/HyperModules .
Contact: Juri.Reimand@utoronto.ca or Gary.Bader@utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online
A risk-based approach to evaluating northeast US fish community vulnerability to climate change
Authors: Gaichas S. K. , Link J. S. , Hare J. A. 
Published: April 2014

Abstract
Risk assessment methods are used worldwide to evaluate threats posed by fisheries and other impacts on living marine resources, and to prioritize management of these threats. We derive a simplified risk analysis for aggregate fish communities as a preliminary tool to identify priorities for further detailed assessment. Because some of the largest observed rates of sea surface temperature increase are on the northeast US continental shelf, we focused on climate change-driven risks to marine communities in this region. We evaluated climate vulnerability for six communities across two ecosystems: both commercial and non-commercial demersal fish, pelagic fish, and benthic invertebrates in the Gulf of Maine (GOM) and Mid-Atlantic bight (MAB). We first evaluated the probability that anticipated climate changes (e.g. warming water, decreased salinity, increased acidity, altered boundary currents) would occur in these regions, and rated the potential severity of change over the next 10 years. Then, we evaluated the sensitivity of each biological community in each region using 12 attributes (e.g. habitat and prey specificity, temperature and acidity sensitivity, larval dispersal, adult mobility, population productivity, etc.). Exposure to the key climate risks was related to community sensitivity in each region for an overall assessment of climate vulnerability. Climate risks from increased surface water temperature, sea level rise, and earlier spring were rated moderate to high in both regions, with additional moderate to high risks in the GOM from increased bottom temperature, stratification, and river inputs. Benthic invertebrates were rated most sensitive, with demersals intermediate and pelagics lowest. Two MAB communities were rated more sensitive than corresponding GOM communities, but greater short-term climate risks in the GOM indicated increased exposure for GOM communities. Overall, this simple analysis may help prioritize short-term regional climate risk management action, thus addressing key conditions related to fishery fluctuations beyond fishing itself.
Addressing Patient Safety in Rapid Response Activations for Nonhospitalized Persons
Authors: Lakshminarayana Pradeep H. , Darby Joseph M. , Simmons Richard L. 
Published: April 2014

Background
Rapid response teams (RRTs) have been widely accepted as useful adjuncts to the care of inpatients with unanticipated emergencies. One study suggested that leadership of such teams could be assigned to midlevel providers, especially when nonhospitalized person (NHP)–related emergencies occur. However, in our tertiary medical center, a critical care medicine (CCM) physician always leads all RRT events including those related to NHPs.

Objective
In this study, we postulate reasons in favor of a single structured RRT led by an intensivist for both inpatients and NHPs.

Methods
An observational study conducted at an academic medical center. Demographic and clinical characteristics of NHP-related RRT events were evaluated over a 9-month period.

Measurements and Main Results
Rapid response teams were activated 1,952 times, of which, 154 events were NHP related. Only 42 RRT activations occurred for employees and visitors. Most of the NHP activations (112 events) occurred in response to events involving persons who were on the premises because of preexisting illnesses, either visiting physician offices (46 events), undergoing ambulatory diagnostic procedures (30 events), in transit to the emergency department (13 events), or undergoing emergency psychiatry evaluation (11 events). Most patients (83 NHPs) required admission to the hospital including 22 NHPs to intensive care units (ICUs) either directly from the event location or subsequently from the emergency department. The physician team leader admitted 20 NHPs directly from the scene, of which, 13 were admitted directly to ICUs.

Conclusion
Nonhospitalized patients requiring RRT activation often have complex pre-existent illnesses. A standardized team composition for both inpatients and NHPs in crisis is an appropriate administrative structure enhancing patient safety in hospitals where ambulatory and inpatient facilities are combined.
Disclosing Adverse Events to Patients: International Norms and Trends
Authors: Wu Albert W. , McCay Layla , Levinson Wendy , Iedema Rick , Wallace Gordon , Boyle Dennis J. , McDonald Timothy B. , Bismark Marie M. , Kraman Steve S. , Forbes Emma , Conway James B. , Gallagher Thomas H. 
Published: April 2014

Objectives
There is a growing expectation in health systems around the world that patients will be fully informed when adverse events occur. However, current disclosure practices often fall short of this expectation.

Methods
We reviewed trends in policy and practice in 5 countries with extensive experience with adverse event disclosure: the United States, the United Kingdom, Canada, New Zealand, and Australia.

Results
We identified 5 themes that reflect key challenges to disclosure: (1) the challenge of putting policy into large-scale practice, (2) the conflict between patient safety theory and patient expectations, (3) the conflict between legal privilege for quality improvement and open disclosure, (4) the challenge of aligning open disclosure with liability compensation, and (5) the challenge of measurement related to disclosure.

Conclusions
Potential solutions include health worker education coupled with incentives to embed policy into practice, better communication about approaches beyond the punitive, legislation that allows both disclosure to patients and quality improvement protection for institutions, apology protection for providers, comprehensive disclosure programs that include patient compensation, delinking of patient compensation from regulatory scrutiny of disclosing physicians, legal and contractual requirements for disclosure, and better measurement of its occurrence and quality. A longer-term solution involves educating the public and health care workers about patient safety.
Actin-Dependent and -Independent Functions of Cortical Microtubules in the Differentiation ofArabidopsisLeaf Trichomes
Authors: Sambade Adrian , Findlay Kim , Schäffner Anton R. , Lloyd Clive W. , Buschmann Henrik 
Published: April 2014

AbstractArabidopsis thaliana tortifolía2 carries a point mutation in α-tubulin 4 and shows aberrant cortical microtubule dynamics. The microtubule defect of tortifolia2 leads to overbranching and right-handed helical growth in the single-celled leaf trichomes. Here, we use tortifolia2 to further our understanding of microtubules in plant cell differentiation. Trichomes at the branching stage show an apical ring of cortical microtubules, and our analyses support that this ring is involved in marking the prospective branch site. tortifolia2 showed ectopic microtubule bundles at this stage, consistent with a function for microtubules in selecting new branch sites. Overbranching of tortifolia2 required the C-terminal binding protein/brefeldin A-ADP ribosylated substrate protein ANGUSTIFOLIA1, and our results indicate that the angustifolia1 mutant is hypersensitive to alterations in microtubule dynamics. To analyze whether actin and microtubules cooperate in the trichome cell expansion process, we generated double mutants of tortifolia2 with distorted1, a mutant that is defective in the actin-related ARP2/3 complex. The double mutant trichomes showed a complete loss of growth anisotropy, suggesting a genetic interaction of actin and microtubules. Green fluorescent protein labeling of F-actin or microtubules in tortifolia2 distorted1 double mutants indicated that F-actin enhances microtubule dynamics and enables reorientation. Together, our results suggest actin-dependent and -independent functions of cortical microtubules in trichome differentiation.
Trauma through the lens of service coordinators: exploring their awareness of adverse life events among adults with intellectual disabilities
Authors: M. Keesler John 
Published: April 2014

Purpose
– With an expansion of trauma knowledge in the field of intellectual disabilities (ID) there is a responsibility among service providers to be trauma-informed. Among those providers are service coordinators (SCs) who are involved in the lives of individuals through the assessment of needs and linkage with necessary supports. The purpose of this paper is to explore SCs’ understanding of individuals’ experiences of adverse life events, trauma, and related services.

Design/methodology/approach
– Semi-structured interviews were conducted among 15 SCs, encompassing the experiences of 29 individuals with mild ID. Data were analyzed using a grounded theory approach.

Findings
– From SCs’ perspective, individuals’ experiences were comprised of three major categories – experiencing adversity, responding to adversity and adapting to adversity – influenced by precipitating and perpetuating conditions. Despite a lack of familiarity with the term “trauma,” in general, SCs possessed a rich understanding of individuals’ comprehensive experiences including types of events, responses to events, environmental factors, and implications of respective services.

Originality/value
– This is an original approach to understanding the awareness of trauma among an integral group of providers for individuals with ID. This paper shows that, although there is a need to reframe current knowledge, SCs can be an asset to facilitate organizational endeavors to become trauma-informed thus having a potential impact on individuals’ quality of life.
Community dialectical behaviour therapy for emotionally dysregulated adults with intellectual disabilities
Authors: Baillie Aubrey , Slater Sean 
Published: April 2014

Purpose– The purpose of this paper is to reflexively examine the challenges of implementing a community dialectical behaviour therapy (DBT) service for adults with intellectual disabilities (ID) and describes the practical lessons learned about how to maximise the effectiveness of DBT with this client group.Design/methodology/approach– A brief overview of DBT is provided and reference is made to literature which highlights the potential benefits of providing a DBT service to clients with an ID. This is followed by a discussion of the clinical presentation of the clients receiving DBT in the service that is the focus of this case study. Using a reflexive approach, a detailed discussion follows of the challenges faced in implementing a community DBT service for the clients served.Findings– Solutions to a variety of challenges faced in four years of service delivery are described, key lessons learned are highlighted, together with issues meriting further research.Research limitations/implications– This case study and its implications are limited to community DBT services. Another limitation is that, although outcome data have been collected over the past two years, the dataset is not yet large enough to draw statistical conclusions.Practical implications– The paper describes adaptations to treatment structure and strategy which the authors believe are necessary to improve treatment outcomes in community DBT services for adults with ID. In particular, the practical experience suggests that a didactic approach to teaching DBT skills is not effective and should be replaced by the “community of learners” approach that involves the trainer contingently responding to client input. Pre-set lesson plans inhibit the trainers’ ability to respond contingently.Originality/value– The existing literature on providing a DBT service for people with an ID has principally focused on providing a rationale for providing this type of intervention, and on assessing outcomes. Given that this is still a relatively new type of provision for this client group, a detailed examination of process issues is called for.
Getting unstuck along the clinical pathway: an integrated multi-agency approach
Authors: Richards Luci , Uchendu Nwamaka , O’Hara Jean 
Published: April 2014

Purpose
– The purpose of this paper is to highlight how the management of an adult with intellectual disabilities and complex medical conditions by a multi-disciplinary and multi-agency team approach across a clinical pathway (primary, secondary and tertiary care, health, social and third sector agencies) can be used to improve the person's physical and mental health outcome.

Design/methodology/approach
– Literature review and case report in which the paper describes the presentation of the patient with multiple complex physical health conditions, mild intellectual disability and challenging behaviour and description of the management process and the observed outcome.

Findings
– The patient required input from the multi-disciplinary community intellectual disabilities team and multi-agency team including social services and community support team, admission to a specialist intellectual disabilities ward to optimise her management. She improved relatively well and was discharged to the community. On discharge she continued to receive ongoing psychiatric, psychological and community psychiatric nurse input and maintains the sustained improvement in her mental health. She no longer displays risky or challenging behaviour, her mood has improved and there is no self-harm ideation. She remains anxious at times, however, her symptoms are much improved and do not affect her daily functioning.

Originality/value
– This case highlights the profound and enduring psychiatric and behavioural sequelae following brain malignancy and treatment and how essential a multi-disciplinary and multi-agency approach is in the successful management of complex issues. Her symptoms appeared relatively treatment resistant until she had a specialist inpatient admission. This case study also demonstrates the strengths and advantages of having specialist care pathway for such complex presentations, allowing for integrated community, secondary and tertiary care, and for the care system to work together in a coordinated and managed way.
Identifying and ranking the effective factors on customer values
Authors: Ghandehary Mahsa , Harati Hojjat , Khazaei Pool Javad 
Published: April 2014

Purpose
– The purpose of this study is to identify and rank the effective factors on customer values from the perspective of banking customers.

Design/methodology/approach
– This study is a practical and descriptive survey. In order to rank the factors affecting customer values, a fuzzy analytical hierarchical process has been used. The data were gathered through Delphi method and questionnaires.

Findings
– The results of this study indicate that the factors affecting customer values include costs, relational benefits, brand perceptions, and services quality. These factors influence customer values, respectively. The results also indicate that financial costs among costs, operational benefit among relational benefits, trust in employee behavior in customer brand perceptions, and finally confidence in service quality dimensions have the highest priority.

Research limitations/implications
– The proposed model and research findings will greatly help researchers and practitioners understand the factors influencing customer value using a fuzzy analytic hierarchy process (FAHP) in the banking industry.

Originality/value
– In this study, for the first time, factors influencing customer value are studied by using a FAHP in the banking industry. The use of this method in this study has a certain authenticity.
Exploring the factor structure of the CareerEDGE employability development profile
Authors: Dacre Pool Lorraine , Qualter Pamela , J. Sewell Peter 
Published: April 2014

Purpose– There has been little empirical research conducted in relation to graduate employability and diagnostic tools available in this area are very limited. The purpose of this paper is to introduce and explore the factor structure of a new measure of employability development, the CareerEDGE Employability Development Profile (EDP).Design/methodology/approach– The EDP was completed by 807 undergraduate students, providing data for exploratory and confirmatory factor analyses.Findings– The analyses suggest that the EDP is multidimensional and maps clearly onto the CareerEDGE model of graduate employability.Research limitations/implications– These findings are discussed and interpreted as offering support for the use of the EDP with students as a developmental tool and as a measurement tool for use in the design, implementation and evaluation of employability interventions or other research purposes.Originality/value– The provision of a practical employability development tool that is suitable for use with students of any Higher Education institution. The findings also add to the limited literature on graduate employability.