bluuebunny/crossref_metadata_2025_split huggingface dataset:
Obesity and Pancreatic Cancer
Authors: Xu Mu , Jung Xiaoman , Hines O. Joe , Eibl Guido , Chen Yijun 
Published: January 2018

Abstract
Currently, there are no effective preventive strategies for pancreatic cancer. Obesity has been increasingly recognized as a strong but modifiable risk factor of pancreatic cancer. In this article, we aim to review the literature regarding weight loss on prevention of pancreatic cancer. Epidemiological and laboratory studies have shown that obesity is associated with increased incidence of pancreatic cancer and potentially worse cancer outcome. Whereas the underlying pathomechanisms remain unclear, chronic inflammation, insulin resistance, and altered intestinal microbiota are all implicated in the carcinogenic effect of obesity. Weight loss, especially the durable and significant weight loss after bariatric surgery, has been shown to reduce the risks of multiple cancers and may become a good intervention for pancreatic cancer prevention.
A Qualitative Study of Multidisciplinary Providers' Experiences With the Transfer Process for Injured Children and Ideas for Improvement
Authors: Gawel Marcie , Emerson Beth , Giuliano John S. , Rosenberg Alana , Minges Karl E. , Feder Shelli , Violano Pina , Morrell Patricia , Petersen Judy , Christison-Lagay Emily , Auerbach Marc 
Published: January 2018

Objective
Most injured children initially present to a community hospital, and many will require transfer to a regional pediatric trauma center. The purpose of this study was 1) to explore multidisciplinary providers' experiences with the process of transferring injured children and 2) to describe proposed ideas for process improvement.

Methods
This qualitative study involved 26 semistructured interviews. Subjects were recruited from 6 community hospital emergency departments and the trauma and transport teams of a level I pediatric trauma center in New Haven, Conn. Participants (n = 34) included interprofessional providers from sending facilities, transport teams, and receiving facilities. Using the constant comparative method, a multidisciplinary team coded transcripts and collectively refined codes to generate recurrent themes across interviews until theoretical saturation was achieved.

Results
Participants reported that the transfer process for injured children is complex, stressful, and necessitates collaboration. The transfer process was perceived to involve numerous interrelated components, including professions, disciplines, and institutions. The 5 themes identified as areas to improve this transfer process included 1) Creation of a unified standard operating procedure that crosses institutions/teams, 2) Enhancing "shared sense making" of all providers, 3) Improving provider confidence, expertise, and skills in caring for pediatric trauma transfer cases, 4) Addressing organization and environmental factors that may impede/delay transfer, and 5) Fostering institutional and personal relationships.

Conclusions
Efforts to improve the transfer process for injured children should be guided by the experiences of and input from multidisciplinary frontline emergency providers.
Premorbid Activity Limitation Stages Are Associated With Posthospitalization Discharge Disposition
Authors: Na Ling , Hennessy Sean , Xie Dawei , Saliba Debra , Pan Qiang , Kwong Pui L. , Kurichi Jibby E. , Bogner Hillary R. , Streim Joel E. 
Published: January 2018

Objective
Activity of daily living stages and instrumental activity of daily living stage have demonstrated associations with mortality and health service use among older adults. This cohort study aims to assess the associations of premorbid activity limitation stages with acute hospital discharge disposition among community-dwelling older adults.

Design
Study participants were Medicare beneficiaries aged 65 yrs or older who enrolled in the Medicare Current Beneficiary Survey between 2001 and 2009. Associations of premorbid stages with discharge dispositions were estimated with multinomial logistic regression models adjusted for covariates.

Results
The proportions of elderly Medicare patients discharged to home with self-care, home with services, postacute care facilities, and other dispositions were 59%, 15%, 19%, and 7%, respectively. The following adjusted relative risk ratios and 95% confidence intervals of postacute care facilities versus home with self-care discharge increased with higher premorbid activity limitation stages (except nonfitting stage III): 1.7 (1.5–2.0), 2.4 (2.0–2.9), 2.4 (1.9–3.0), and 2.5 (1.6–4.1) for activity of daily living stages I–IV; a similar pattern was found for instrumental activity of daily living stages. The adjusted relative risk ratios of discharge to home with services also increased with higher premorbid activity limitation stages compared with no limitation.

Conclusions
Routinely assessed activity limitation stages predict posthospitalization discharge disposition among older adults and may be used to anticipate postacute care and services use by elderly Medicare beneficiaries.
HOTAIR ancient sequence suggests regulatory roles both in cis and trans
Authors: Nepal Chirag , Hadzheiv Yavor , Pundhir Sachin , Mydel Piotr , Lenhard Boris , Müeller Ferenc , Andersen Jesper B 
Published: January 2018

ABSTRACTHOTAIRis a long noncoding RNA transcribed betweenHOXC11andHOXC12in mammals. The proposed function(s) ofHOTAIRlacks consensus as to whether it regulates HoxD cluster genes intransor HoxC cluster genes incis. We have identified a 32-nucleotide long conserved noncoding element (CNE) asHOTAIRancient sequence which has a paralogous copy embedded inHOXD11noncoding transcript. All vertebrates except teleosts have two copies of CNE and the paralogous CNEs exhibit sequence complementarity in the transcribed orientation. Moreover, paralogous CNEs underwent compensatory mutations suggesting they co-evolved and might hybridize. In both human and mouse,HOTAIRCNE exhibits characteristic features of a poised enhancer inHOTAIR-unexpressed stem cells and of an active enhancer inHOTAIR-expressed cells. Tight correlation between the transcriptional activity of the CNE andHOTAIRpromoter suggestsHOTAIRtranscription is crucial for enhancer activity. InHOTAIR-expressed cells,HOTAIRexpression is positively correlated withHOXC11incisand negatively correlated withHOXD11intrans, suggesting a dual modality ofHOTAIRancient sequence.
Replication timing shapes the cancer epigenome and the nature of chromosomal rearrangements
Authors: Du Qian , Bert Saul A. , Armstrong Nicola J. , Caldon C. Elizabeth , Song Jenny Z. , Nair Shalima S. , Gould Cathryn M. , Luu Phuc Loi , Khoury Amanda , Qu Wenjia , Zotenko Elena , Stirzaker Clare , Clark Susan J. 
Published: January 2018

HighlightsReplication timing alterations are conserved in cancers of different cell originsLong-range epigenetic deregulation in cancer involves altered replication timingCancer late-replicating loci are hypomethylated and acquire facultative heterochromatinReplication timing status potentiates cis and trans chromosomal rearrangementsSummaryReplication timing is known to facilitate the establishment of epigenome, however, the intimate connection between DNA replication timing and changes to the genome and epigenome in cancer remain uncharted. Here, we perform Repli-Seq and integrated epigenome analysis and show that early-replicating loci are predisposed to hypermethylation and late-replicating loci to hypomethylation, enrichment of H3K27me3 and concomitant loss of H3K9me3. We find that altered replication timing domains correspond to long-range epigenetically deregulated regions in prostate cancer, and a subset of these domains are remarkably conserved across cancers from different tissue origins. Analyses of 214 prostate and 35 breast cancer genomes reveal that late-replicating DNA is prone to cis and early-replicating DNA to trans chromosomal rearrangements. We propose that differences in epigenetic deregulation related to spatial and temporal positioning between early and late replication potentiate the landscape of chromosomal rearrangements in cancer.
Functional repurposing of regulatory element activity during mammalian evolution
Authors: Carelli Francesco N. , Liechti Angélica , Halbert Jean , Warnefors Maria , Kaessmann Henrik 
Published: January 2018

ABSTRACTThe spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It also suggested that inheritable alterations in the epigenetic and sequence context of regulatory elements might underlie evolutionary changes of their principal activity, which could result in changes in the transcriptional profile of genes under their control or even facilitate the birth of new genes. Here, based on integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, we provide support for this hypothesis by detecting 449 regulatory elements with signatures of activity turnover in sister species from the primate and rodent lineages (termed “P/E” elements). Through the comparison with outgroup species, we defined the directionality of turnover events, which revealed that most instances represent transformations of ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5’ exons. Notably, P/E elements have distinct GC sequence compositions and stabilizing 5’ splicing (U1) regulatory motif patterns, which may predispose them to functional repurposing during evolution. Moreover, we trace changes in the U1 and polyadenylation signal densities and distributions that accompanied and likely drove the evolutionary activity switches. Overall, our work suggests rather widespread evolutionary remodelling of regulatory element functions. Functional repurposing thus represents a notable mechanism that likely facilitated regulatory innovation and the origination of new genes and exons during mammalian evolution.
Large differences in small RNA composition between human biofluids
Authors: Godoy Paula M. , Bhakta Nirav R. , Barczak Andrea J. , Cakmak Hakan , Fisher Susan , Mackenzie Tippi C. , Patel Tushar , Price Richard W. , Smith James F. , Woodruff Prescott G. , Erle David J. 
Published: January 2018

SUMMARYExtracellular miRNAs and other small RNAs are implicated in cellular communication and may be useful as disease biomarkers. We systematically compared small RNAs in 12 human biofluid types using RNA-seq. miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads in all biofluids, but the ratio of miRNA to tDR reads varied from 72 in plasma to 0.004 in bile. miRNA levels were highly correlated across all biofluids but levels of some miRNAs differed markedly between biofluids. tDR populations differed extensively between biofluids. Y RNA fragments were seen in all biofluids and accounted for >10% of reads in blood plasma, serum, and CSF. Reads mapping exclusively to piRNAs were very rare except in seminal plasma. These results demonstrate extensive differences in small RNAs between human biofluids and provide a useful resource for investigating extracellular RNA biology and developing biomarkers.
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
Authors: Fu Yu , Wu Pei-Hsuan , Beane Timothy , Zamore Phillip D. , Weng Zhiping 
Published: January 2018

AbstractRNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules. We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species in both RNA-seq and small RNA-seq libraries generated from mouse testis. Our approach yields high-quality data while allowing unique tagging of all molecules in high-depth libraries. Using simulated and real datasets, we demonstrate that our methods increase the reproducibility of RNA-seq and small RNA-seq data. Notably, we find that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine PCR duplicate frequency. Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis.
Molecular control of gene expression byBrucellaBaaR, an IclR-family repressor
Authors: Herrou Julien , Czyż Daniel M. , Fiebig Aretha , Willett Jonathan W. , Kim Youngchang , Wu Ruiying , Babnigg Gyorgy , Crosson Sean 
Published: January 2018

AbstractTheBrucella abortusgeneral stress response sigma factor, σE1, directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection. Characterizing the functions of σE1regulated genes therefore contributes to understanding ofB. abortusphysiology and infection biology. Transcription of the IclR family regulator, Bab2_0215, is indirectly activated by σE1but its function remains undefined. We present a structural and functional characterization of Bab2_0215, which we have namedBrucellaadipic acid activated regulator (BaaR). BaaR adopts a classic IclR-family fold and directly regulates the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase (acaD2), and represses transcription. We identified three carboxylic acids (adipic acid tetradecanedioic acid, ε-aminocaproic acid) and a lactone (ε-caprolactone) that enhance transcription from thebaaRandacaD2promoters. However, neither the activating acids nor caprolactone enhance transcription by binding directly to BaaR. Induction ofbaaRtranscription by adipic acid requires the genebab2_0213, which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a set of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program regulated downstream of σE1.
To the letter vs the spirit
Authors: Heggen Campbell , Sridharan VG , Subramaniam Nava 
Published: January 2018

PurposeThe purpose of this paper is to examine why firms governed by the same environmental management standards within an industry exhibit contrasting responses, with some adhering to the letter and others achieving the spirit behind the standards.Design/methodology/approachUsing Arenaet al.(2010) as an analytical schema to examine the institutional dynamics behind such contrasting responses, the paper analyses archival and interview data relating to firm strategy, control technology and human expertise in two contrasting Australian forestry firms.FindingsThe embedding and decoupling of environmental standards with a firm’s environmental management practices is influenced, first, by the extent to which founder directors and senior management integrate environmental responsibility with the underlying business motives and, second, by the use of organisational beliefs and values systems to institutionalise the integrated strategic rationality throughout the firm. Finally, informed by the institutionalised strategic rationality, the participation and expertise of actors across the organisational hierarchy determine the level to which the design and execution of the eco-control technologies move beyond merely monitoring compliance, and act to facilitate continuous improvement, knowledge integration and organisational learning at the operational level.Originality/valueThis paper responds to institutional theorists’ call for a holistic explanation that considers the interactions among several intra-organisational factors to explain the dynamics behind why some firms decouple while others do not, even though the firms exist in the same social and regulatory context.
Blame game or dialogue? Financial, professional and democratic accountabilities in a complex health care setting
Authors: Pellinen Jukka , Mättö Toni , Sippola Kari , Rautiainen Antti 
Published: January 2018

PurposeThe purpose of this paper is to investigate how the complexity of the network governance setting affects accountability practices. The authors pay particular attention to the organizational characteristics that may enable a common understanding of multiple accountability relationships, or lead to problems in reconciling competing forms of accountability, thereby appearing as blame game-type behavior.Design/methodology/approachThe authors conducted a case study with 31 semi-structured interviews in a Finnish health care organization (FHC) that offers basic public health care services. The organization represents a co-operative arrangement with the main city and three smaller municipalities. The FHC has faced difficulties in balancing budget constraints with the provision of statutory care to citizens. This case is analyzed with the help of theories relating to accountability, the blame game, and dialogue.FindingsThe authors found that in the FHC operating under austerity constraints, attempts to reconcile financial, professional, and democratic accountability were made but, instead of dialogue and consensus, the different stakeholder groups resorted to defensive tactics in order to protect their resources, position, or sense of professional obligation. The authors suggest that in a context of network governance, accompanied by an increasing emphasis on financial accountability, organizational practices are susceptible to conflicting accountabilities and behavior characterized in this paper as a blame game.Originality/valueThe study contributes to the empirical studies on accountability in the new public governance context by analyzing the complex accountability relations between stakeholder groups with different agendas. The authors suggest organizational characteristics that may exacerbate conflicts between different stakeholder groups and prevent constructive dialogue. Furthermore, the study analyzes the composition of democratic accountability within the studied organization.
E-service usage and satisfaction in Botswana
Authors: Jaiyeoba Olumide Olasimbo , Chimbise Totwana Tito , Roberts-Lombard Mornay 
Published: January 2018

PurposeThe purpose of this paper is to establish the level of usage of e-services (websites and e-mail) by Botswana Public Officers Medical Aid Scheme (BPOMAS) and PULA Medical Aid (PULA) customers; the level of satisfaction; perceived value; and benefits derived from the website and e-mail services.Design/methodology/approachIn total, 200 BPOMAS members and 100 PULA members were sampled. Systematic sampling technique was used to select the participants. A questionnaire mainly guided by the E-S-QUAL and E-RecS-QUAL scales was designed to gain an in-depth understanding of customers’ perceptions and experiences of e-service quality.FindingsIt was established that there is a positive and significant relationship between the usage of e-services and benefits derived from e-services and between the usage of e-services and satisfaction. In addition, a nexus of relationship was observed between perceived value of the e-services and satisfaction.Research limitations/implicationsThe management of healthcare services in Botswana needs to understand customers’ value perceptions of e-services and e-service quality in order to establish where to make the most of their efforts.Practical implicationsThe managers of healthcare insurance providers should consider stepping up e-service usage and satisfaction levels, supported by client-centred training programmes, to assist clinicians deliver care to the expectation of patients.Originality/valueThere is an acute lack of research in the Botswana context, particularly into the link between e-service usage and satisfaction in the health insurance industry. This paper contributes to the extant literature by elucidating the nexus of relationship between e-service usage and satisfaction in Botswana.
Integrated FAHP-FPROMETHEE for thermal insulation of masonry buildings
Authors: Seddiki Mohammed , Anouche Karima , Bennadji Amar 
Published: January 2018

Purpose
The need for the thermal insulation of masonry buildings in Algeria is no longer debated. This paper aims to propose an integrated fuzzy multi-criteria decision aid method for the thermal insulation of masonry buildings to rank the thermal insulation solutions.

Design/methodology/approach
The proposed method combines the fuzzy analytical hierarchy process with the fuzzy preference ranking organization method for enrichment evaluation.

Findings
A case study using the proposed method is detailed in this paper. The building users’ preferences obtained by the fuzzy analytical hierarchy process had a higher level of consistency and accuracy. The case study demonstrates how in a highly uncertain field such as thermal insulation of masonry buildings, the fuzzy preference ranking organization method for enrichment evaluation can prevent the loss of valuable evaluation data and overcome difficulty in integrating linguistic assessments of the thermal insulation alternatives.

Originality/value
The proposed method extends current knowledge by using the fuzzy analytical hierarchy process to consider uncertainties regarding the building users’ preferences, and the fuzzy preference ranking organization method for enrichment evaluation to get a complete ranking of the thermal insulation solutions taking into account the uncertainties related to the alternatives’ evaluations.
An efficient iterative algorithm for the natural convection equations based on finite element method
Authors: Wang Lei , Li Jian , Huang Pengzhan 
Published: January 2018

Purpose
This paper aims to propose a new highly efficient iterative method based on classical Oseen iteration for the natural convection equations.

Design/methodology/approach
First, the authors solve the problem by the Oseen iterative scheme based on finite element method, then use the error correction strategy to control the error arising.

Findings
The new iterative method not only retains the advantage of the Oseen scheme but also saves computational time and iterative step for solving the considered problem.

Originality/value
In this work, the authors introduce a new iterative method to solve the natural convection equations. The new algorithm consists of the Oseen scheme and the error correction which can control the errors from the iterative step arising for solving the nonlinear problem. Comparing with the classical iterative method, the new scheme requires less iterations and is also capable of solving the natural convection problem at higher Rayleigh number.