bluuebunny/crossref_metadata_2025_split huggingface dataset:
The degradation of airway tight junction protein under acidic conditions is probably mediated by transient receptor potential vanilloid 1 receptor
Authors: Xu Rui , Li Qi , Zhou Jia , Zhou Xiang-dong , Perelman Juliy M. , Kolosov Victor P. 
Published: September 2013

Acidic airway microenvironment is one of the representative pathophysiological features of chronic inflammatory respiratory diseases. Epithelial barrier function is maintained by TJs (tight junctions), which act as the first physical barrier against the inhaled substances and pathogens of airway. As previous studies described, acid stress caused impaired epithelial barriers and led the hyperpermeability of epithelium. However, the specific mechanism is still unclear. We have showed previously the existence of TRPV (transient receptor potential vanilloid) 1 channel in airway epithelium, as well as its activation by acidic stress in 16HBE cells. In this study, we explored the acidic stress on airway barrier function and TJ proteins in vitro with 16HBE cell lines. Airway epithelial barrier function was determined by measuring by TER (trans-epithelial electrical resistance). TJ-related protein [claudin-1, claudin-3, claudin-4, claudin-5, claudin-7 and ZO-1 (zonula occluden 1)] expression was examined by western blotting of insoluble fractions of cell extraction. The localization of TJ proteins were visualized by immunofluorescent staining. Interestingly, stimulation by pH 6.0 for 8 h slightly increased the epithelial resistance in 16HBE cells insignificantly. However, higher concentration of hydrochloric acid (lower than pH 5.0) did reduce the airway epithelial TER of 16HBE cells. The decline of epithelial barrier function induced by acidic stress exhibited a TRPV1-[Ca2+]i-dependent pathway. Of the TJ proteins, claudin-3 and claudin-4 seemed to be sensitive to acidic stress. The degradation of claudin-3 and claudin-4 induced by acidic stress could be attenuated by the specific TRPV1 blocker or intracellular Ca2+ chelator BAPTA/AM [1,2-bis-(o-aminophenoxy)ethane-N,N,N',N'-tetra-acetic acid tetrakis(acetoxymethyl ester)].
A user-oriented web crawler for selectively acquiring online content in e-health research
Authors: Xu Songhua , Yoon Hong-Jun , Tourassi Georgia 
Published: September 2013

Abstract
Motivation: Life stories of diseased and healthy individuals are abundantly available on the Internet. Collecting and mining such online content can offer many valuable insights into patients’ physical and emotional states throughout the pre-diagnosis, diagnosis, treatment and post-treatment stages of the disease compared with those of healthy subjects. However, such content is widely dispersed across the web. Using traditional query-based search engines to manually collect relevant materials is rather labor intensive and often incomplete due to resource constraints in terms of human query composition and result parsing efforts. The alternative option, blindly crawling the whole web, has proven inefficient and unaffordable for e-health researchers.
Results: We propose a user-oriented web crawler that adaptively acquires user-desired content on the Internet to meet the specific online data source acquisition needs of e-health researchers. Experimental results on two cancer-related case studies show that the new crawler can substantially accelerate the acquisition of highly relevant online content compared with the existing state-of-the-art adaptive web crawling technology. For the breast cancer case study using the full training set, the new method achieves a cumulative precision between 74.7 and 79.4% after 5 h of execution till the end of the 20-h long crawling session as compared with the cumulative precision between 32.8 and 37.0% using the peer method for the same time period. For the lung cancer case study using the full training set, the new method achieves a cumulative precision between 56.7 and 61.2% after 5 h of execution till the end of the 20-h long crawling session as compared with the cumulative precision between 29.3 and 32.4% using the peer method. Using the reduced training set in the breast cancer case study, the cumulative precision of our method is between 44.6 and 54.9%, whereas the cumulative precision of the peer method is between 24.3 and 26.3%; for the lung cancer case study using the reduced training set, the cumulative precisions of our method and the peer method are, respectively, between 35.7 and 46.7% versus between 24.1 and 29.6%. These numbers clearly show a consistently superior accuracy of our method in discovering and acquiring user-desired online content for e-health research.
Availability and implementation: The implementation of our user-oriented web crawler is freely available to non-commercial users via the following Web site: http://bsec.ornl.gov/AdaptiveCrawler.shtml. The Web site provides a step-by-step guide on how to execute the web crawler implementation. In addition, the Web site provides the two study datasets including manually labeled ground truth, initial seeds and the crawling results reported in this article.
Contact: xus1@ornl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Patient safety and estimation of renal function in patients prescribed new oral anticoagulants for stroke prevention in atrial fibrillation: a cross-sectional study
Authors: MacCallum Peter K , Mathur Rohini , Hull Sally A , Saja Khalid , Green Laura , Morris Joan K , Ashman Neil 
Published: September 2013

ObjectiveIn clinical trials of dabigatran and rivaroxaban for stroke prevention in atrial fibrillation (AF), drug eligibility and dosing were determined using the Cockcroft-Gault equation to estimate creatine clearance as a measure of renal function. This cross-sectional study aimed to compare whether using estimated glomerular filtration rate (eGFR) by the widely available and widely used Modified Diet in Renal Disease (MDRD) equation would alter prescribing or dosing of the renally excreted new oral anticoagulants.ParticipantsOf 4712 patients with known AF within a general practitioner-registered population of 930 079 in east London, data were available enabling renal function to be calculated by both Cockcroft-Gault and MDRD methods in 4120 (87.4%).ResultsOf 4120 patients, 2706 were <80 years and 1414 were ≥80 years of age. Among those ≥80 years, 14.9% were ineligible for dabigatran according to Cockcroft-Gault equation but would have been judged eligible applying MDRD method. For those <80 years, 0.8% would have been incorrectly judged eligible for dabigatran and 5.3% would have received too high a dose. For rivaroxaban, 0.3% would have been incorrectly judged eligible for treatment and 13.5% would have received too high a dose.ConclusionsWere the MDRD-derived eGFR to be used instead of Cockcroft-Gault in prescribing these new agents, many elderly patients with AF would either incorrectly become eligible for them or would receive too high a dose. Safety has not been established using the MDRD equation, a concern since the risk of major bleeding would be increased in patients with unsuspected renal impairment. Given the potentially widespread use of these agents, particularly in primary care, regulatory authorities and drug companies should alert UK doctors of the need to use the Cockcroft-Gault formula to calculate eligibility for and dosing of the new oral anticoagulants in elderly patients with AF and not rely on the MDRD-derived eGFR.
Reporting of harms data in RCTs: a systematic review of empirical assessments against the CONSORT harms extension
Authors: Hodkinson Alex , Kirkham Jamie J , Tudur-Smith Catrin , Gamble Carrol 
Published: September 2013

ObjectiveTo determine the standard of reporting of harms-related data, in randomised controlled trials (RCTs) according to the Consolidated Standards of Reporting Trials (CONSORT) statement extension for harms.DesignSystematic review.Data sourcesThe Cochrane library, Ovid MEDLINE, Scopus and ISI Web of Knowledge were searched for relevant literature.Eligibility criteria for selecting studiesWe included publications of studies that used the CONSORT harms extension to assess the reporting of harms in RCTs.ResultsWe identified 7 studies which included between 10 and 205 RCTs. The clinical areas of the 7 studies were: hypertension (1), urology (1), epilepsy (1), complimentary medicine (2) and two not restricted to a clinical topic. Quality of the 7 studies was assessed by a risk of bias tool and was found to be variable. Adherence to the CONSORT harms criteria reported in the 7 studies was inadequate and variable across the items in the checklist. Adverse events are poorly defined, with 6 studies failing to exceed 50% adherence to the items in the checklist.ConclusionsReaders of RCT publications need to be able to balance the trade-offs between benefits and harms of interventions. This systematic review suggests that this is compromised due to poor reporting of harms which is evident across a range of clinical areas. Improvements in quality could be achieved by wider adoption of the CONSORT harms criteria by journals reporting RCTs.
A qualitative study of patients’ perceptions and priorities when living with primary frozen shoulder
Authors: Jones Susan , Hanchard Nigel , Hamilton Sharon , Rangan Amar 
Published: September 2013

ObjectivesTo elucidate the experiences and perceptions of people living with primary frozen shoulder and their priorities for treatment.DesignQualitative study design using semistructured interviews.SettingGeneral practitioner (GP) and musculoskeletal clinics in primary and secondary care in one National Health Service Trust in England.Participants12 patients diagnosed with primary frozen shoulder were purposively recruited from a GP's surgery, community clinics and hospital clinics. Recruitment targeted the phases of frozen shoulder: pain predominant (n=5), stiffness predominant (n=4) and residual stiffness predominant following hospital treatment (n=2). One participant dropped out. Inclusion criteria: adult, male and female patients of any age, attending the clinics, who had been diagnosed with primary frozen shoulder.ResultsThe most important experiential themes identified by participants were: pain which was severe as well as inexplicable; inconvenience/disability arising from increasing restriction of movement (due to pain initially, gradually giving way to stiffness); confusion/anxiety associated with delay in diagnosis and uncertainty about the implications for the future; and treatment-related aspects. Participants not directly referred to a specialist (whether physiotherapist, physician or surgeon) wanted a faster, better-defined care pathway. Specialist consultation brought more definitive diagnosis, relief from anxiety and usually self-rated improvement. The main treatment priority was improved function, though there was recognition that this might be facilitated by relief of pain or stiffness. There was a general lack of information from clinicians about the condition with over-reliance on verbal communication and very little written information.ConclusionsAwareness of frozen shoulder should be increased among non-specialists and the best available information made accessible for patients. Our results also highlight the importance of patient participation in frozen shoulder research.
Massacres and Media Representations
Authors: Dutta Nandana 
Published: September 2013

This article examines the cultural politics of representations of violence in Assam. It shows how the 1983 coverage of the Nellie massacre provides the framework for all media coverage, and the media, along with the region, are both ‘identified’ in terms of violent representations. It looks at the depiction of massacres in the North-East (NE) of India in the media and suggests that both media and region are affected by this process. From the first visuals of Nellie featured in India Today in 1983 to the recent carnage in the Kokrajhar region reported widely in both print and visual media, the consolidation of an interpretative frame of violence for the region as it reels under the effects of insurgent activities seems to be attributable to the media more than to any other agency. This depiction I suggest feeds into the neglect narrative that has characterized the region’s perception of treatment by ‘mainstream India’. Studying the neglect narrative, the deployment of long-term and wider concerns and the production of a ‘representation effect’ that partially aestheticizes violence this article argues that the media is affected in its modes and rhetoric by its visual repetition of the violent incident and it also, in the process, helps to make the viewer immune and indifferent to such violence.
Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Authors: Cingolani Pablo , Cao Xiaoyi , Khetani Radhika S , Chen Chieh-Chun , Coon Melissa , Sammak Alya’a , Bollig-Fischer Aliccia , Land Susan , Huang Yun , Hudson Matthew E , Garfinkel Mark D , Zhong Sheng , Robinson Gene E , Ruden Douglas M 
Published: September 2013

Abstract

Background
Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly used method, bisulfite sequencing, cannot distinguish 5-methylcytosine from 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine that is catalyzed by the TET family of dioxygenases. Furthermore, some analysis software programs under-represent non-CG DNA methylation and hydryoxymethylation for a variety of reasons. Therefore, we used an unbiased analysis of bisulfite sequencing data combined with molecular and bioinformatics approaches to distinguish 5-methylcytosine from 5-hydroxymethylcytosine. By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing.

Results
We confirmed, using unbiased analyses of whole-genome shotgun bisulfite sequencing (BS-seq) data, with both new data and published data, the previous finding that CG DNA methylation is enriched in exons in honey bees. However, we also found evidence that cytosine methylation and hydroxymethylation at non-CG sites is enriched in introns. Using antibodies against 5-hydroxmethylcytosine, we confirmed that DNA hydroxymethylation at non-CG sites is enriched in introns. Additionally, using a new technique, Pvu-seq (which employs the enzyme PvuRts1l to digest DNA at 5-hydroxymethylcytosine sites followed by next-generation DNA sequencing), we further confirmed that hydroxymethylation is enriched in introns at non-CG sites.

Conclusions
Cytosine hydroxymethylation at non-CG sites might have more functional significance than previously appreciated, and in honey bees these modifications might be related to the regulation of alternative mRNA splicing by defining the locations of the introns.
HIV and hepatitis C virus test uptake at methadone clinics in Southern China: opportunities for expanding detection of bloodborne infections
Authors: Xia Ying-Hua , Chen Wen , Tucker Joseph D , Wang Charles , Ling Li 
Published: September 2013

Abstract

Background
HIV and hepatitis C (HCV) co-infection is highly common among Chinese injection drug users but it is difficult to reach IDUs at traditional VCT (Voluntary HIV counseling treatment) clinics. A new national model integrating HIV/HCV testing with methadone maintenance treatment was started in 2006. The purpose of this study was to investigate HIV and HCV test uptake and associated factors at methadone clinics in Guangdong Province, China.

Methods
A cross-sectional design using routine surveillance data and laboratory testing confirmation was applied to determine rates of HIV and HCV test uptake. Multi-level modeling was used to examine individual-level and clinic-level correlates of increased test uptake.

Results
45 out of 49 methadone clinics in Guangdong Province agreed to participate in the study. Among all 13,270 individuals, 10,046 (75.7%) had HIV test uptake and 10,404 (78.4%) had HCV uptake. At the individual level, methadone clients 30 years or older were more likely to have HIV and HCV test uptake (p <0.001 for both). At the clinic level, methadone clinics with greater health care personnel were more likely to have HIV (p =0.01) and HCV (p = 0.044) test uptake. HIV test uptake significantly correlated with HCV test uptake (correlation coefficient=0.64).

Conclusion
Methadone clinics provide an opportunity for routine integrated HIV and HCV screening among drug users in China. Increased test uptake in young drug users and increased health care personnel at clinics may further improve screening.
Teleconsultation in children with abdominal pain: a comparison of physician triage recommendations and an established paediatric telephone triage protocol
Authors: Staub Gabrielle Marmier , von Overbeck Jan , Blozik Eva 
Published: September 2013

AbstractBackgroundQuality assessment and continuous quality feedback to the staff is crucial for safety and efficiency of teleconsultation and triage. This study evaluates whether it is feasible to use an already existing telephone triage protocol to assess the appropriateness of point-of-care and time-to-treat recommendations after teleconsultations.MethodsBased on electronic patient records, we retrospectively compared the point-of-care and time-to-treat recommendations of the paediatric telephone triage protocol with the actual recommendations of trained physicians for children with abdominal pain, following a teleconsultation.ResultsIn 59 of 96 cases (61%) these recommendations were congruent with the paediatric telephone protocol. Discrepancies were either of organizational nature, due to factors such as local referral policies or gatekeeping insurance models, or of medical origin, such as milder than usual symptoms or clear diagnosis of a minor ailment.ConclusionsA paediatric telephone triage protocol may be applicable in healthcare systems other than the one in which it has been developed, if triage rules are adapted to match the organisational aspects of the local healthcare system.
Bone-stromal cells up-regulate tumourigenic markers in a tumour-stromal 3D model of prostate cancer
Authors: Windus Louisa CE , Glover Tristan T , Avery Vicky M 
Published: September 2013

Abstract

Background
The cellular and molecular mechanisms that mediate interactions between tumour cells and the surrounding bone stroma are to date largely undetermined in prostate cancer (PCa) progression. The purpose of this study was to evaluate the role of alpha 6 and beta 1 integrin subunits in mediating tumour-stromal interactions.

Methods
Utilising 3D in vitro assays we evaluated and compared 1. Monocultures of prostate metastatic PC3, bone stromal derived HS5 and prostate epithelial RWPE-1 cells and 2. Tumour-stromal co-cultures (PC3 + HS5) to ascertain changes in cellular phenotype, function and expression of metastatic markers.

Results
In comparison to 3D monocultures of PC3 or HS5 cells, when cultured together, these cells displayed up-regulated invasive and proliferative qualities, along with altered expression of epithelial-to-mesenchymal and chemokine protein constituents implicated in metastatic dissemination. When co-cultured, HS5 cells were found to re-express N-Cadherin and chemokine receptor CXCR7. Alterations in N-Cadherin expression were found to be mediated by soluble factors secreted by PC3 tumour cells, while chemokine receptor re-expression was dependent on direct cell-cell interactions. We have also shown that integrins beta 1 and alpha 6 play an integral role in maintaining cell homeostasis and mediating expression of E-Cadherin, N-Cadherin and vimentin, in addition to chemokine receptor CXCR7.

Conclusions
Collectively our results suggest that both PC3 and HS5 cells provide a “protective” and reciprocal milieu that promotes tumour growth. As such 3D co-cultures may serve as a more complex and valid biological model in the drug discovery pipeline.
A national study on nurses’ retention in healthcare facilities in underserved areas in Lebanon
Authors: El-Jardali Fadi , Alameddine Mohamad , Jamal Diana , Dimassi Hani , Dumit Nuhad Y , McEwen Mary K , Jaafar Maha , Murray Susan F 
Published: September 2013

Abstract

Background
Nursing shortages and maldistribution are priority issues for healthcare systems around the globe. Such imbalances are often aggravated in underserved areas, especially in developing countries. Despite the centrality of this issue, there is a dearth of studies that examine the retention of nurses in underserved areas in the Middle East Region. This study investigates the characteristic and the factors associated with the retention of nurses working in rural areas in Lebanon.

Methods
This study uses a non-experimental cross-sectional design to survey nurses working in underserved areas of Lebanon. Underserved areas in Lebanon were identified using WHO definition. A total of 103 health facilities (hospitals and primary healthcare centers) located in these areas were identified and all nurses working at these facilities received a copy of the survey questionnaire. The questionnaire included five sections: demographic, work-life, career plan, job satisfaction, and assessment of work environment. Analysis included univariate and bivariate (chi-square, Student’s t-test and ANOVA) tests to describe the respondents and examine the significance between nurses’ characteristics and their intent to stay. A logistic regression model was constructed to identify factors associated with nurses’ intent to stay in underserved areas.

Results
A total of 857 nurses from 63 Primary Healthcare (PHC) centers and hospitals responded to the questionnaire (75.5% response rate). Only 35.1% of nurses indicated their intent to stay in their current job over the coming one to three years. Surveyed nurses were most satisfied with relationship with co-workers and least satisfied with extrinsic rewards. Rural nurses working in PHC centers were more satisfied than their hospital counterparts on all aspects of work and had significantly higher intention to stay (62.5% compared to 31.5% in hospitals, P < 0.001). Regression analysis revealed that nurses less likely to report intent to stay were younger, unmarried, with less years of work experience and were not working towards a higher degree. Analysis reveals a directly proportional relationship between nurses’ reported job satisfaction and their intent to stay.

Conclusion
This study reveals poor retention of nurses in rural and underserved areas in Lebanon, especially in the hospital sector. The status quo is disquieting as it reflects an unstable and dissatisfied nursing workforce. Developing targeted retention strategies for younger nurses and those working in hospitals as well as the offering of professional development opportunities and devising an incentive scheme targeting rural nurses is pivotal to enhance nurses’ job satisfaction and retention in rural settings.
A physiologically-based flow network model for hepatic drug elimination I: regular lattice lobule model
Authors: Rezania Vahid , Marsh Rebeccah , Coombe Dennis , Tuszynski Jack 
Published: September 2013

Abstract
We develop a physiologically-based lattice model for the transport and metabolism of drugs in the functional unit of the liver, called the lobule. In contrast to earlier studies, we have emphasized the dominant role of convection in well-vascularized tissue with a given structure. Estimates of convective, diffusive and reaction contributions are given. We have compared drug concentration levels observed exiting the lobule with their predicted detailed distribution inside the lobule, assuming that most often the former is accessible information while the latter is not.