bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stability SCAD: a powerful approach to detect interactions in large-scale genomic study
Authors: Gou Jianwei , Zhao Yang , Wei Yongyue , Wu Chen , Zhang Ruyang , Qiu Yongyong , Zeng Ping , Tan Wen , Yu Dianke , Wu Tangchun , Hu Zhibin , Lin Dongxin , Shen Hongbing , Chen Feng 
Published: March 2014

AbstractBackgroundEvidence suggests that common complex diseases may be partially due to SNP-SNP interactions, but such detection is yet to be fully established in a high-dimensional small-sample (small-n-large-p) study. A number of penalized regression techniques are gaining popularity within the statistical community, and are now being applied to detect interactions. These techniques tend to be over-fitting, and are prone to false positives. The recently developed stability least absolute shrinkage and selection operator (SLASSO) has been used to control family-wise error rate, but often at the expense of power (and thus false negative results).ResultsHere, we propose an alternative stability selection procedure known as stability smoothly clipped absolute deviation (SSCAD). Briefly, this method applies a smoothly clipped absolute deviation (SCAD) algorithm to multiple sub-samples, and then identifies cluster ensemble of interactions across the sub-samples. The proposed method was compared withSLASSO and two kinds of traditional penalized methods by intensive simulation. The simulation revealed higher power and lower false discovery rate (FDR) withSSCAD. An analysis using the new method on the previously published GWAS of lung cancer confirmed all significant interactions identified withSLASSO, and identified two additional interactions not reported withSLASSO analysis.ConclusionsBased on the results obtained in this study,SSCAD presents to be a powerful procedure for the detection of SNP-SNP interactions in large-scale genomic data.
Therapy duration and long-term outcomes in extra-pulmonary tuberculosis
Authors: Pusch Tobias , Pasipanodya Jotam G , Hall Ronald G , Gumbo Tawanda 
Published: March 2014

Abstract

Background
Tuberculosis is classified as either pulmonary or extra-pulmonary (EPTB). While much focus has been paid to pulmonary tuberculosis, EPTB has received scant attention. Moreover, EPTB is viewed as one wastebasket diagnosis, as “the other” which is not pulmonary.

Methods
This is a retrospective cohort study of all patients treated for EPTB in the state of Texas between January 2000 and December 2005, who had no pulmonary disease. Clinical and epidemiological factors were abstracted from electronic records of the Report of Verified Case of Tuberculosis. The long-term outcome, which is death by December 2011, was established using the Social Security Administration Death Master File database. Survival in EPTB patients was compared to those with latent tuberculosis, as well as between different types of EPTB, using Cox proportional hazard models. A hybrid of the machine learning method of classification and regression tree analyses and standard regression models was used to identify high-order interactions and clinical factors predictive of long-term all-cause mortality.

Results
Four hundred and thirty eight patients met study criteria; the median study follow-up period for the cohort was 7.8 (inter-quartile range 6.0-10.1) years. The overall all-cause mortality rate was 0.025 (95% confidence interval [CI]: 0.021-0.030) per 100 person-year of follow-up. The significant predictors of poor long-term outcome were age (hazard ratio [HR] for each year of age-at-diagnosis was 1.05 [CI: 1.04-1.06], treatment duration, type of EPTB and HIV-infection (HR = 2.16; CI: 1.22, 3.83). Mortality in genitourinary tuberculosis was no different from latent tuberculosis, while meningitis had the poorest long-term outcome of 46.2%. Compared to meningitis the HR for death was 0.50 (CI: 0.27-0.91) for lymphatic disease, 0.42 (CI: 0.21-0.81) for bone/joint disease, and 0.59 (CI: 0.27-1.31) for peritonitis. The relationship between mortality and therapy duration for each type of EPTB was a unique “V” shaped curve, with the lowest mortality observed at different therapy durations for each, beyond which mortality increased.

Conclusions
EPTB is comprised of several different diseases with different outcomes and durations of therapy. The “V” shaped relationship between therapy duration and outcome leads to the hypothesis that longer duration of therapy may lead to higher patient mortality.
Ethnic disparities in acquiring 2009 pandemic H1N1 influenza: a case–control study
Authors: Navaranjan Debeka , Rosella Laura C , Kwong Jeffrey C , Campitelli Michael , Crowcroft Natasha 
Published: March 2014

Abstract

Background
Novel risk factors were associated with the 2009 pandemic A/H1N1 virus (pH1N1). Ethnicity was among these risk factors. Ethnic disparities in hospitalization and death due to pH1N1 were noted. The purpose of this study is to determine whether there are ethnic disparities in acquiring the 2009 pandemic H1N1.

Methods
We conducted a test-negative case–control study of the risk of pH1N1 infection using data from Ontario, Canada. Cases were laboratory confirmed to have influenza using reverse-transcriptase polymerase chain reaction (RT-PCR), and controls were obtained from the same population and were RT-PCR negative. Multivariate logistic regression was used to determine the association between ethnicity and pH1N1 infection, while adjusting for demographic, clinical and ecological covariates.

Results
Adult cases were more likely than controls to be self-classified as East/Southeast Asian (OR = 2.59, 95% CI 1.02-6.57), South Asian (OR = 6.22, 95% CI 2.01-19.24) and Black (OR = 9.72, 95% CI 2.29-41.27). Pediatric cases were more likely to be self-identified as Black (OR = 6.43, 95% CI 1.83-22.59). However, pediatric cases without risk factors for severe influenza infection were more likely to be South Asian (OR 2.92, 95% CI 1.11-7.68), Black (OR 16.02, 95% CI 2.85-89.92), and West Asian/Arab, Latin American or Multi-racial groups (OR 3.09 95% CI 1.06-9.00).

Conclusions
pH1N1 cases were more likely to come from certain ethnic groups compared to test-negative controls. Insights into whether these disparities arise due to social or biological factors are needed in order to understand what approaches can be taken to reduce the burden of a future influenza pandemic.
Nutrition and physical activity randomized control trial in child care centers improves knowledge, policies, and children’s body mass index
Authors: Alkon Abbey , Crowley Angela A , Neelon Sara E Benjamin , Hill Sherika , Pan Yi , Nguyen Viet , Rose Roberta , Savage Eric , Forestieri Nina , Shipman Linda , Kotch Jonathan B 
Published: March 2014

Abstract

Background
To address the public health crisis of overweight and obese preschool-age children, the Nutrition And Physical Activity Self Assessment for Child Care (NAP SACC) intervention was delivered by nurse child care health consultants with the objective of improving child care provider and parent nutrition and physical activity knowledge, center-level nutrition and physical activity policies and practices, and children’s body mass index (BMI).

Methods
A seven-month randomized control trial was conducted in 17 licensed child care centers serving predominantly low income families in California, Connecticut, and North Carolina, including 137 child care providers and 552 families with racially and ethnically diverse children three to five years old. The NAP SACC intervention included educational workshops for child care providers and parents on nutrition and physical activity and consultation visits provided by trained nurse child care health consultants. Demographic characteristics and pre - and post-workshop knowledge surveys were completed by providers and parents. Blinded research assistants reviewed each center’s written health and safety policies, observed nutrition and physical activity practices, and measured randomly selected children’s nutritional intake, physical activity, and height and weight pre- and post-intervention.

Results
Hierarchical linear models and multiple regression models assessed individual- and center-level changes in knowledge, policies, practices and age- and sex-specific standardized body mass index (zBMI), controlling for state, parent education, and poverty level. Results showed significant increases in providers’ and parents’ knowledge of nutrition and physical activity, center-level improvements in policies, and child-level changes in children’s zBMI based on 209 children in the intervention and control centers at both pre- and post-intervention time points.

Conclusions
The NAP SACC intervention, as delivered by trained child health professionals such as child care health consultants, increases provider knowledge, improves center policies, and lowers BMI for children in child care centers. More health professionals specifically trained in a nutrition and physical activity intervention in child care are needed to help reverse the obesity epidemic.

Trial registration
National Clinical Trials Number NCT01921842
Inflammatory and cytotoxic effects of acrolein, nicotine, acetylaldehyde and cigarette smoke extract on human nasal epithelial cells
Authors: Comer David M , Elborn Joseph Stuart , Ennis Madeleine 
Published: March 2014

AbstractBackgroundCigarette smoke induces a pro-inflammatory response in airway epithelial cells but it is not clear which of the various chemicals contained within cigarette smoke (CS) should be regarded as predominantly responsible for these effects. We hypothesised that acrolein, nicotine and acetylaldehyde, important chemicals contained within volatile cigarette smoke in terms of inducing inflammation and causing addiction, have immunomodulatory effects in primary nasal epithelial cell cultures (PNECs).MethodsPNECs from 19 healthy subjects were grown in submerged cultures and were incubated with acrolein, nicotine or acetylaldehyde prior to stimulation withPseudomonas aeruginosalipopolysaccharide (PA LPS). Experiments were repeated using cigarette smoke extract (CSE) for comparison. IL-8 was measured by ELISA, activation of NF-κB by ELISA and Western blotting, and caspase-3 activity by Western blotting. Apoptosis was evaluated using Annexin-V staining and the terminal transferase-mediated dUTP nick end-labeling (TUNEL) method.ResultsCSE was pro-inflammatory after a 24 h exposure and 42% of cells were apoptotic or necrotic after this exposure time. Acrolein was pro-inflammatory for the PNEC cultures (30 μM exposure for 4 h inducing a 2.0 fold increase in IL-8 release) and also increased IL-8 release after stimulation with PA LPS. In contrast, nicotine had anti-inflammatory properties (0.6 fold IL-8 release after 50 μM exposure to nicotine for 24 h), and acetylaldehyde was without effect. Acrolein and nicotine had cellular stimulatory and anti-inflammatory effects respectively, as determined by NF-κB activation. Both chemicals increased levels of cleaved caspase 3 and induced cell death.ConclusionsAcrolein is pro-inflammatory and nicotine anti-inflammatory in PNEC cultures. CSE induces cell death predominantly by apoptotic mechanisms.
Cardiac responses to elevated seawater temperature in Atlantic salmon
Authors: Jørgensen Sven Martin , Castro Vicente , Krasnov Aleksei , Torgersen Jacob , Timmerhaus Gerrit , Hevrøy Ernst Morten , Hansen Tom Johnny , Susort Sissel , Breck Olav , Takle Harald 
Published: March 2014

Abstract

Background
Atlantic salmon aquaculture operations in the Northern hemisphere experience large seasonal fluctuations in seawater temperature. With summer temperatures often peaking around 18-20°C there is growing concern about the effects on fish health and performance. Since the heart has a major role in the physiological plasticity and acclimation to different thermal conditions in fish, we wanted to investigate how three and eight weeks exposure of adult Atlantic salmon to 19°C, previously shown to significantly reduce growth performance, affected expression of relevant genes and proteins in cardiac tissues under experimental conditions.

Results
Transcriptional responses in cardiac tissues after three and eight weeks exposure to 19°C (compared to thermal preference, 14°C) were analyzed with cDNA microarrays and validated by expression analysis of selected genes and proteins using real-time qPCR and immunofluorescence microscopy. Up-regulation of heat shock proteins and cell signaling genes may indicate involvement of the unfolded protein response in long-term acclimation to elevated temperature. Increased immunofluorescence staining of inducible nitric oxide synthase in spongy and compact myocardium as well as increased staining of vascular endothelial growth factor in epicardium could reflect induced vascularization and vasodilation, possibly related to increased oxygen demand. Increased staining of collagen I in the compact myocardium of 19°C fish may be indicative of a remodeling of connective tissue with long-term warm acclimation. Finally, higher abundance of transcripts for genes involved in innate cellular immunity and lower abundance of transcripts for humoral immune components implied altered immune competence in response to elevated temperature.

Conclusions
Long-term exposure of Atlantic salmon to 19°C resulted in cardiac gene and protein expression changes indicating that the unfolded protein response, vascularization, remodeling of connective tissue and altered innate immune responses were part of the cardiac acclimation or response to elevated temperature.
Research across the disciplines: a road map for quality criteria in empirical ethics research
Authors: Mertz Marcel , Inthorn Julia , Renz Günter , Rothenberger Lillian Geza , Salloch Sabine , Schildmann Jan , Wöhlke Sabine , Schicktanz Silke 
Published: March 2014

AbstractBackgroundResearch in the field ofEmpirical Ethics(EE) uses a broad variety of empirical methodologies, such as surveys, interviews and observation, developed in disciplines such as sociology, anthropology, and psychology. Whereas these empirical disciplines see themselves as purely descriptive, EE also aims at normative reflection. Currently there is literature about the quality of empirical research in ethics, but little or no reflection onspecificmethodological aspects that must be considered when conductinginterdisciplinaryempirical ethics. Furthermore, poor methodology in an EE study results in misleading ethical analyses, evaluations or recommendations. This not only deprives the study of scientific and social value, but also risks ethical misjudgement.DiscussionWhile empirical and normative-ethical research projects have quality criteria in their own right, we focus on the specific quality criteria for EE research. We develop a tentative list of quality criteria – a “road map” – tailored to interdisciplinary research in EE, to guide assessments of research quality. These quality criteria fall into the categories ofprimary research question, theoretical framework and methods,relevance,interdisciplinary research practiceandresearch ethics and scientific ethos.SummaryEE research is an important and innovative development in bioethics. However, a lack of standards has led to concerns about and even rejection of EE by various scholars. Our suggested orientation list of criteria, presented in the form of reflective questions, cannot be considered definitive, but serves as a tool to provoke systematic reflection during the planning and composition of an EE research study. These criteria need to be tested in different EE research settings and further refined.
Measuring satisfaction with health care in young persons with inflammatory bowel disease -an instrument development and validation study
Authors: Sadlo Andrea , Altevers Julia , Peplies Jenny , Kaltz Birgit , Claßen Martin , Bauer Alexandra , Koletzko Sibylle , Timmer Antje 
Published: March 2014

AbstractBackgroundPatient satisfaction is a relevant prognostic factor in young persons with chronic disease and may be both age and disease specific. To assess health care quality from the patient’s view in young persons with inflammatory bowel disease, an easy to use, valid, reliable and informative specific instrument was needed.MethodsAll parts of the study were directed at persons with inflammatory bowel disease aged 15 to 24 (“youth”). A qualitative internet patient survey was used to generate items, complemented by a physician survey and literature search. A 2nd internet survey served to reduce items based on perceived importance and representativeness. Following pilot testing to assess ease of use and face validity, 150 respondents to a postal survey in patients from a paediatric clinical registry were included for validation analyses. Construct validity was assessed by relating summary scores to results from global questions on satisfaction with care using ANOVA. To assess test-retest reliability using intraclass correlation coefficients (ICC), a subset of patients were assessed twice within 3 months.Results302 persons with IBD and 55 physicians participated in the item generating internet survey, resulting in 3,954 statements. After discarding redundancies 256 statements were presented in the 2nd internet survey. Of these, 32 items were retained. The resulting instrument assesses both the perceived relevance (importance) of an item as well as the performance of the care giver for each item for calculation of a summary satisfaction score (range 0 to 1). Sensibility testing showed good acceptance for most items. Construct validity was good, with mean scores of 0.63 (0.50 to 0.76), 0.71 (0.69 to 0.74) and 0.81 (0.79 to 0.83) for no, some and good global satisfaction (ANOVA, p < 0.001). Test-retest reliability was satisfactory (ICC 0.6 to 0.7).ConclusionsWe developed an easy to use, patient oriented, valid instrument to assess satisfaction with care in young persons with IBD for use in survey research.
Par6 is an essential mediator of apoptotic response to transforming growth factor beta in NMuMG immortalized mammary cells
Authors: Avery-Cooper Geordon , Doerr Meghan , Gilbert Richard WD , Youssef Mahmoud , Richard Amy , Huether Patricia , Viloria-Petit Alicia M 
Published: March 2014

Abstract

Background
We previously observed that the TGFbeta-Par6 pathway mediates loss of polarity and apoptosis in NMuMG cells. Here we investigate the contribution of Par6 versus TGFbeta receptor I activation to TGFbeta-induced apoptosis in association with changes in apico-basal polarity. We focus on the effect of Par6 activation on alpha6beta4 integrin expression and localization, and Nuclear Factor-kappaB (p65/RelA) activation, previously shown to mediate polarity-dependent cell survival.

Methods
Using immunoblotting and/or immunofluorescence we investigated the effect of TGFbeta1 on apoptosis, alpha6, beta4 and beta1 integrin expression/localization, and p65/RelA phosphorylation/localization in monolayer and three-dimensional (3D) cultures of NMuMG cells with an overactive or inactive Par6 pathway. Results were quantified by band densitometry or as percent of 3D structures displaying a phenotype. Differences among means were compared by two-way ANOVA.

Results
Blocking Par6 activation inhibits TGFbeta-induced apoptosis. Par6 overactivation enhances TGFbeta-induced apoptosis, notably after 6-day exposure to TGFbeta (p < 0.001), a time when parental NMuMG cells no longer respond to TGFbeta apoptotic stimuli. 48-hour TGFbeta treatment reduced beta4 integrin levels in NMuMG monolayers and significantly reduced the basal localization of alpha6 (p < 0.001) and beta4 (p < 0.001) integrin in NMuMG 3D structures, which was dependent on both Par6 and TGFbeta receptor I activation and paralleled apoptotic response. After 6-day exposure to TGFbeta, Par6-dependent changes to beta4 integrin were no longer apparent, but there was reduced phosphorylation of p65/RelA (p < 0.001) only in Par6 overexpressing cells. Differences in p65/RelA localization were not observed among the different cell lines after 48-hour TGFbeta exposure.

Conclusions
Par6 and TGFbeta receptor I activation are both necessary for TGFbeta-induced apoptosis in NMuMG cells. Importantly, Par6 overexpression enhances the sensitivity of NMuMG to TGFbeta-induced apoptosis, notably upon prolonged exposure to this growth factor, when NMuMG parental cells are usually apoptosis-resistant. Thus, endogenous Par6 level might be important in determining whether TGFbeta will function as either a pro-apoptotic or pro-survival factor in breast cancer, and potentially aid in predicting patient’s prognosis and therapy response.
What predicts negative effects of rheumatoid arthritis? A follow-up two years after diagnosis
Authors: Gåfvels Catharina , Hägerström Margareta , Nordmark Birgitta , Wändell Per 
Published: March 2014

AbstractWe aimed at analyzing important predictive factors for experienced negative emotional and social effects of rheumatoid arthritis (RA) two years after diagnosis in patients aged 18–65 years. The first group included 41 participants, who had psychosocial problems (PSP) already at diagnosis, and who received an intervention by a medical social worker to improve coping capacity and social situation. The second group included 54 patients (NPSP) without such problems at diagnosis. All completed a questionnaire mapping their social situation, the Hospital Anxiety and Depression Scale (HADS), the Sense of Coherence Scale (SOC) and the General Coping Questionnaire (GCQ) at diagnosis and after 24 months. The most pronounced predictive factor for a strong impact of the disease was high scores on HADS depression scale. After 24 months, PSP participants had a more strained life situation, with higher scores on anxiety and depression and lower on SOC, in comparison with NPSP. NPSP participants improved their coping strategies regarding self-trust, cognitive revaluation, protest and intrusion, but deteriorated regarding problem focusing and social trust. PSP patients kept their initial coping strategies, except for intrusion decreasing over time, and seemed to have a more rigid coping pattern. However, the experienced negative impact of the disease increased over time in both groups despite improvement in sickness related data. Mostly influenced areas were economy, leisure time activities and social life. We conclude that psychosocial consequences of RA are more connected to emotional and social vulnerability than are RA-related clinical factors.
Necrosis and apoptotic index as prognostic factors in non-small cell lung carcinoma: a review
Authors: Gkogkou Charalampos , Frangia Konstantina , Saif Muhammad W , Trigidou Rodoula , Syrigos Konstantinos 
Published: March 2014

Abstract
Necrosis and apoptosis represent two pathogenetically distinct types of cell death. Necrosis is associated with pathologic conditions while apoptosis is a physiological process of programmed cell death, which is associated with normal tissue growth and is frequently impaired in various forms of cancer. Tumor necrosis and apoptotic index (AI) have been previously evaluated as prognostic biomarkers in lung cancer, but their exact clinical value remains unclear. The aim of this study was to perform a systematic review of the MEDLINE literature on the prognostic significance of these histopathological markers in patients with non-small cell lung carcinoma (NSCLC). Although a substantial body of evidence suggests that tumor necrosis may be a strong predictor of aggressive tumor behavior and reduced survival in patients with NSCLC, the independent prognostic value of this biomarker remains to be firmly established. Furthermore, previous data on the prognostic significance of apoptotic index in NSCLC are relatively limited and largely controversial. More prospective studies are necessary in order to further validate tumor necrosis and AI as prognostic markers in NSCLC.