bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linocin and OmpW Are Involved in Attachment of the Cystic Fibrosis-Associated Pathogen Burkholderia cepacia Complex to Lung Epithelial Cells and Protect Mice against Infection
Authors: McClean Siobhán , Healy Marc E. , Collins Cassandra , Carberry Stephen , O'Shaughnessy Luke , Dennehy Ruth , Adams Áine , Kennelly Helen , Corbett Jennifer M. , Carty Fiona , Cahill Laura A. , Callaghan Máire , English Karen , Mahon Bernard P. , Doyle Sean , Shinoy Minu 
Published: February 2016

ABSTRACT

Members of the
Burkholderia cepacia
complex (Bcc) cause chronic opportunistic lung infections in people with cystic fibrosis (CF), resulting in a gradual lung function decline and, ultimately, patient death. The Bcc is a complex of 20 species and is rarely eradicated once a patient is colonized; therefore, vaccination may represent a better therapeutic option. We developed a new proteomics approach to identify bacterial proteins that are involved in the attachment of Bcc bacteria to lung epithelial cells. Fourteen proteins were reproducibly identified by two-dimensional gel electrophoresis from four Bcc strains representative of two Bcc species:
Burkholderia cenocepacia
, the most virulent, and
B. multivorans
, the most frequently acquired. Seven proteins were identified in both species, but only two were common to all four strains, linocin and OmpW. Both proteins were selected based on previously reported data on these proteins in other species.
Escherichia coli
strains expressing recombinant linocin and OmpW showed enhanced attachment (4.2- and 3.9-fold) to lung cells compared to the control, confirming that both proteins are involved in host cell attachment. Immunoproteomic analysis using serum from Bcc-colonized CF patients confirmed that both proteins elicit potent humoral responses
in vivo
. Mice immunized with either recombinant linocin or OmpW were protected from
B. cenocepacia
and
B. multivorans
challenge. Both antigens induced potent antigen-specific antibody responses and stimulated strong cytokine responses. In conclusion, our approach identified adhesins that induced excellent protection against two Bcc species and are promising vaccine candidates for a multisubunit vaccine. Furthermore, this study highlights the potential of our proteomics approach to identify potent antigens against other difficult pathogens.
Profoundly Reduced CD1c
+
Myeloid Dendritic Cell HLA-DR and CD86 Expression and Increased Tumor Necrosis Factor Production in Experimental Human Blood-Stage Malaria Infection
Authors: Loughland Jessica R. , Minigo Gabriela , Burel Julie , Tipping Peta E. , Piera Kim A. , Amante Fiona H. , Engwerda Christian R. , Good Michael F. , Doolan Denise L. , Anstey Nicholas M. , McCarthy James S. , Woodberry Tonia 
Published: February 2016

ABSTRACT

Dendritic cells (DCs) are sentinels of the immune system that uniquely prime naive cells and initiate adaptive immune responses. CD1c (BDCA-1) myeloid DCs (CD1c
+
mDCs) highly express HLA-DR, have a broad Toll-like receptor (TLR) repertoire, and secrete immune modulatory cytokines. To better understand immune responses to malaria, CD1c
+
mDC maturation and cytokine production were examined in healthy volunteers before and after experimental intravenous
Plasmodium falciparum
infection with 150- or 1,800-parasite-infected red blood cells (pRBCs). After either dose, CD1c
+
mDCs significantly reduced HLA-DR expression in prepatent infections. Circulating CD1c
+
mDCs did not upregulate HLA-DR after pRBC or TLR ligand stimulation and exhibited reduced CD86 expression. At peak parasitemia, CD1c
+
mDCs produced significantly more tumor necrosis factor (TNF), whereas interleukin-12 (IL-12) production was unchanged. Interestingly, only the 1,800-pRBC dose caused a reduction in the circulating CD1c
+
mDC count with evidence of apoptosis. The 1,800-pRBC dose produced no change in T cell IFN-γ or IL-2 production at peak parasitemia or at 3 weeks posttreatment. Overall, CD1c
+
mDCs are compromised by
P. falciparum
exposure, with impaired HLA-DR and CD86 expression, and have an increased capacity for TNF but not IL-12 production. A first prepatent
P. falciparum
infection is sufficient to modulate CD1c
+
mDC responsiveness, likely contributing to hampered effector T cell cytokine responses and assisting parasite immune evasion.
Impact on smoking of England's 2012 partial tobacco point of sale display ban: a repeated cross-sectional national study
Authors: Kuipers Mirte A G , Beard Emma , Hitchman Sara C , Brown Jamie , Stronks Karien , Kunst Anton E , McNeill Ann , West Robert 
Published: February 2016

BackgroundA partial tobacco point of sale (PoS) display ban was introduced in large shops (>280 m2floor area) in England on 6 April 2012. The aim of this study was to assess the medium-term effects of the partial tobacco PoS display ban on smoking in England.MethodsData were used from 129 957 respondents participating in monthly, cross-sectional household surveys of representative samples of the English adult population aged 18+ years from January 2009 to February 2015. Interrupted-time series regression models assessed step changes in the level of current smoking and cigarette consumption in smokers and changes in the trends postban compared with preban. Models were adjusted for sociodemographic variables and e-cigarette use, seasonality and autocorrelation. Potential confounding by cigarette price was accounted for by time, as price was almost perfectly correlated with time.ResultsFollowing the display ban, there was no immediate step level change in smoking (−3.69% change, 95% CI −7.94 to 0.75, p=0.102) or in cigarette consumption (β −0.183, 95% CI −0.602 to 0.236). There was a significantly steeper decline in smoking post display ban (−0.46% change, 95% CI −0.72 to −0.20, p=0.001). This effect was demonstrated by respondents in manual occupations (−0.62% change, 95% CI −0.72 to −0.20, p=0.001), but not for those in non-manual occupations (−0.42, 95% CI −0.90 to 0.06, p=0.084). Cigarette consumption declined preban period (β −0.486, 95% CI −0.633 to −0.339, p<0.001), but no significant change in cigarette consumption trend was observed (β 0.019, 95% CI −0.006 to 0.042, p=0.131).ConclusionsThe partial tobacco PoS display ban introduced in England in April 2012 did not lead to an immediate decline in smoking, but was followed by a decline in the trend of smoking prevalence that could not be accounted for by seasonal factors, e-cigarette use or price changes.
The geometry of branch lines
Authors: Yielding Graham 
Published: February 2016

Abstract
A branch line is the line of intersection between two hard-linked fault planes, or between two parts of a single fault plane of more complex geometry. Of interest is whether they provide any information about the kinematic development of the fault system to which they belong. Analysis of branch lines from a variety of normal fault networks, interpreted on seismic reflection datasets, shows that the branch lines are generally aligned parallel to the extension direction. This relationship is shown to be a feature of polymodal (orthorhombic) fault systems produced by three-dimensional strain. Branch lines between bimodal faults (conjugate, with opposing dip) tend to be perpendicular to the slip direction.
Natural Killer Cell–Based Immunotherapy in Acute Myeloid Leukemia: Lessons for the Future
Authors: Muntasell Aura , López-Botet Miguel 
Published: February 2016

Abstract
The article by Curti and colleagues highlights the potential of natural killer (NK) cell–based adoptive cellular immunotherapy in oncology, currently boosted by advances in the knowledge on NK cell biology and in their ex vivo GMP manipulation. Several issues deserve attention to fully achieve the translation of these advances to the clinic. Clin Cancer Res; 22(8); 1831–3. ©2016 AACR.
See related article by Curti et al., p. 1914
Sex and Race/Ethnicity–Related Disparities in Care and Outcomes After Hospitalization for Coronary Artery Disease Among Older Adults
Authors: Li Shanshan , Fonarow Gregg C. , Mukamal Kenneth J. , Liang Li , Schulte Phillip J. , Smith Eric E. , DeVore Adam , Hernandez Adrian F. , Peterson Eric D. , Bhatt Deepak L. 
Published: February 2016

Background—
It is unclear to what extent cardiovascular health disparities exist and can be modified among sexes, racial/ethnic groups, and geographic regions in US hospitals.

Methods and Results—

We conducted a cohort study of 49 358 patients aged 65 years and older, admitted to 366 US hospitals from 2003 to 2009 as part of the Get With The Guidelines—Coronary Artery Disease registry linked with Medicare inpatient data. We examined mortality disparities of sex, race/ethnicity, and geographic region with 3-year mortality. The mediator was defined as receiving optimal quality of care. Logistic regression with generalized estimating equations and mediation analysis were used. Compared with men, women were less likely to receive optimal care (odds ratio=0.92; 95% confidence interval: 0.88–0.95;
P
<0.0001) and more likely to have higher mortality if they received suboptimal care (odds ratio=1.25; 95% confidence interval: 1.00–1.55;
P
=0.05,
P
for interaction=0.04). Approximately 69% of the sex disparity may potentially be reduced by providing optimal quality of care to women. Quality of care did not differ across racial/ethnic groups or geographic regions. Blacks were more likely to die than whites (odds ratio=1.33; 95% confidence interval: 1.21–1.46;
P
<0.0001), and this disparity persisted regardless of the quality of care received.

Conclusions—
Women were less likely than men to receive optimal care at discharge. The observed sex disparity in mortality could potentially be reduced by providing equitable and optimal care. In contrast, the higher mortality observed in black patients could not be accounted for by differences in the quality of care measured in this study.
The Use of Sonographically Guided Botulinum Toxin Type A (Dysport) Injections Into the Tensor Fasciae Latae for the Treatment of Lateral Patellofemoral Overload Syndrome
Authors: Stephen Joanna M. , Urquhart David W.J. , van Arkel Richard J. , Ball Simon , Jaggard Matthew K.J. , Lee Justin C. , Church J.S. 
Published: February 2016

Background: Pain in the anterior and lateral parts of the knee during exercise is a common clinical problem for which current management strategies are often unsuccessful. Purpose: To investigate the effect of an ultrasound-guided botulinum toxin (BT) injection into the tensor fasciae latae (TFL), followed by physical therapy, in patients classified with lateral patellofemoral overload syndrome (LPOS) who failed to respond to conventional treatment. Study Design: Case series; Level of evidence, 4. Methods: A total of 45 patients (mean ± SD age, 32.4 ± 8.6 years) who met the inclusion criteria of (1) activity-related anterolateral knee symptoms, (2) symptoms lasting longer than 3 months, (3) a pathological abnormality confirmed by magnetic resonance imaging, and (4) previous failed physical therapy received an ultrasound-guided injection of BT into the TFL followed by physical therapy. Patient-reported outcomes were collected at 5 intervals: before the injection; at 1, 4, and 12 weeks after the injection; and at a mean 5 years after the injection. In 42 patients, relative iliotibial band (ITB) length changes were assessed using the modified Ober test at the first 4 time points. A computational model was run to simulate the effect of TFL weakening on gluteus medius (GMed) activity. Statistical analysis was undertaken using 1-way analysis of variance and paired t tests with Bonferroni post hoc correction. Results: There was a significant improvement in Anterior Knee Pain Scale scores from before the injection (61 ± 15) to 1 (67 ± 15), 4 (70 ± 16), and 12 weeks (76 ± 16) after the injection and in 87% of patients (39/45 patients available for follow-up) at approximately 5 years (from 62.9 ± 15.4 to 87.0 ± 12.5) after the injection (all P < .010). A significant effect on the modified Ober test was identified as a result of the intervention, with an increase in leg drop found at 1 (3° ± 5°), 4 (4° ± 5°), and 12 (7° ± 6°) weeks after the injection compared with before the injection (all P < .010). Simulating a progressive reduction in TFL strength resulted in corresponding increases in GMed activity during gait. Conclusion: An injection of BT into the TFL, combined with physical therapy, resulted in a significant improvement of symptoms in patients with LPOS, which was maintained at 5-year follow-up. This may result from reduced lateral TFL/ITB tension or to an increase in GMed activity in response to inhibition of the TFL.
Multidrug Resistance Acinetobacter Bacteremia Secondary to Ventilator-Associated Pneumonia: Risk Factors and Outcome
Authors: Brotfain Evgeni , Borer Abraham , Koyfman Leonid , Saidel-Odes Lisa , Frenkel Amit , Gruenbaum Shaun E. , Rosenzweig Vsevolod , Zlotnik Alexander , Klein Moti 
Published: February 2016

Purpose: Acinetobacter baumannii is a multidrug resistant (MDR), gram-negative bacterium commonly implicated in ventilator-associated pneumonia (VAP) in critically ill patients. Patients in the intensive care unit (ICU) with VAP often subsequently develop A baumannii bacteremia, which may significantly worsen outcomes. Materials and Methods: In this study, we retrospectively reviewed the clinical and laboratory records of 129 ICU patients spanning 6 years with MDR A baumannii VAP; 46 (35%) of these patients had concomitant MDR A baumannii bacteremia. Results: The ICU mortality rate was higher in patients with VAP having A baumannii bacteremia compared to nonbacteremic patients (32.4% vs 9.6% respectively, P < .005). Age >65 years, an Acute Physiology and Chronic Health Evaluation II (APACHE-II) score higher than 20, a Sequential Organ Failure Assessment (SOFA) score higher than 7 on the day of bacteremia, and the presence of comorbid disease (chronic obstructive pulmonary disease [COPD] and chronic renal failure) were found to be independent risk factors for in-hospital mortality in this population. Multidrug resistant A baumannii was not an independent risk factor for mortality. Conclusion: Although the presence of comorbid diseases (COPD and chronic renal failure) and severity of disease (APACHE > 20 and SOFA >7) were found to be independent risk factors for ICU mortality, MDR A baumannii bacteremia was not an independent risk factor for mortality in our critically ill population.
Active Labour Market Programme Participation for Unemployment Insurance Recipients
Authors: Filges Trine , Smedslund Geir , Jørgensen Anne-Marie Klint 
Published: February 2016

Objective: This review evaluates the effectiveness of Active Labour Market Programme (ALMP) participation on employment status for unemployment insurance recipients. Methods and Analysis: We followed Campbell Collaboration guidelines to conduct a systematic review. Results: A total of 73 studies met the inclusion criteria and were critically appraised by the review authors. The available evidence suggests that there is a general effect of participating in ALMP. The findings are mixed, however, depending on the approach used to investigate the effect, with no effect found of being assigned to ALMP participation at a particular moment. Authors’ Conclusions: The available evidence does suggest that there is an effect of participating in ALMP, but the effect is small and we found no effect of being assigned to ALMP participation at a particular moment.
Investigation into the utility of an immunocytochemical assay in body cavity effusions for diagnosis of feline infectious peritonitis
Authors: Felten Sandra , Matiasek Kaspar , Gruendl Stefanie , Sangl Laura , Wess Gerhard , Hartmann Katrin 
Published: February 2016

Objectives Feline coronaviruses (FCoVs) exist as two biotypes, feline enteric coronavirus and feline infectious peritonitis virus. Although feline infectious peritonitis (FIP) is a very common disease, the ante-mortem diagnosis of this disease still remains a challenge. Immunofluorescence staining of FCoV in macrophages in effusion has been considered as the reference standard for the diagnosis, but recently this method has been shown to have lower specificity than previously reported. In addition, this method is not widely available and requires the use of fluorescence microscopes. Therefore, it was the aim of this study to evaluate the diagnostic potential of an immunocytochemical (ICC) assay using body cavity effusion. Methods Effusion samples from 27 cats with immunohistochemically confirmed FIP and 29 cats with suspected FIP but a definitive diagnosis of another disease were examined. ICC specimens were evaluated with respect to positive immunostaining. In addition, effusion samples were stained with haematoxylin and eosin and evaluated cytologically. Results A diagnostic sensitivity of 85.2% was recorded for effusion specimens (95% confidence interval [CI] 66.3–95.8), while the diagnostic specificity was only 72.4% (95% CI 52.8–87.3). Conclusions and relevance Once the clinical disease of FIP develops in a cat, it always leads to death, and most of the cats are euthanased within a few days or weeks. As false-positive results might lead to euthanasia of cats suffering from potentially treatable diseases, the diagnostic specificity of a diagnostic tool is the most important factor in a fatal disease like FIP. Thus, the diagnostic utility of this test proved to be insufficient and positive ICC results should be interpreted with caution. Nevertheless, full-body necropsy could not be performed in 13/29 control cats. It is possible that these cats actually suffered from early-stage FIP and that this fact might have influenced the diagnostic specificity of the ICC. Based on the results of the present study, however, ICC of effusion samples currently cannot be recommended to confirm a suspicion of FIP.
First Presentation of Hereditary Leiomyomatosis and Renal Cell Cancer Syndrome in Pregnancy
Authors: Woolner Kathryn , O’Toole Ashley , LaBerge Lauren 
Published: February 2016

Background: Reed’s syndrome, also known as hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome, is an autosomal dominant condition in which affected individuals may develop cutaneous leiomyomas, uterine fibroids, and renal cell carcinoma. Objective: This report describes a unique case of HLRCC because it presented in pregnancy with development of cutaneous pilar leiomyomas. Methods: Review of the literature for previous cases of Reed’s syndrome during pregnancy including PubMed and Medline search. Results: Genetic testing of this patient demonstrated a mutation in the fumarate hydratase ( FH) gene. Review of the literature showed only 1 previous case series that described the onset of cutaneous lesions during pregnancy. Conclusion: This case serves as a reminder that there may exist a correlation between pregnancy and the first manifestation of cutaneous lesions in patients with HLRCC, and thus an increased clinical suspicion is warranted during this period.
The relationship between new media exposure and fast food consumption among Chinese children and adolescents in school: a rural–urban comparison
Authors: Hansstein Francesca Valeria , Hong Yu , Di Chen 
Published: February 2016

Background: In recent decades, China has experienced an exponential growth in the number of internet users, especially among the youngest population, as well as a rapid proliferation of Western-type fast food restaurants. The health consequences of internet availability and fast food consumption among youth have been largely studied in Western countries, but few studies have focused on China. Objectives: This paper has two goals. The first is to evaluate the differences in new media exposure and preferences for fast foods between rural and urban areas. The second goal is to test the association between new media exposure and fast food consumption. The targets of this analysis are Chinese children and adolescents aged 6–18 attending school at the time of the interview. Methods: Research hypotheses were tested using mean-groups comparisons for differences between rural urban sub-samples, and logistic regressions with odds ratios to estimate the relationship between media exposure and preferences towards fast foods. Cross-sectional data from the 2009 China Health and Nutrition Survey were employed. Results: Watching online videos and playing computer games are behaviors associated with higher probabilities of eating at fast food restaurants in both rural and urban young residents, with higher odds in rural areas. Surfing the internet is associated with higher odds of being overweight in both rural and urban settings. Results also show that children living in rural areas spend significantly more time playing computer games, watching TV and videotapes, but less time doing homework than their urban peers. Conclusions: This paper suggests that monitoring the nutritional effects of new media exposure in China is of key importance in order to develop adequate health promotion policies, in both rural and urban areas.
Krüppeling erythropoiesis: an unexpected broad spectrum of human red blood cell disorders due to KLF1 variants
Authors: Perkins Andrew , Xu Xiangmin , Higgs Douglas R. , Patrinos George P. , Arnaud Lionel , Bieker James J. , Philipsen Sjaak ,   the KLF1 Consensus Workgroup
Published: February 2016

AbstractUntil recently our approach to analyzing human genetic diseases has been to accurately phenotype patients and sequence the genes known to be associated with those phenotypes; for example, in thalassemia, the globin loci are analyzed. Sequencing has become increasingly accessible, and thus a larger panel of genes can be analyzed and whole exome and/or whole genome sequencing can be used when no variants are found in the candidate genes. By using such approaches in patients with unexplained anemias, we have discovered that a broad range of hitherto unrelated human red cell disorders are caused by variants in KLF1, a master regulator of erythropoiesis, which were previously considered to be extremely rare causes of human genetic disease.
Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data
Authors: Davidson Robert L , Weber Ralf J M , Liu Haoyu , Sharma-Oates Archana , Viant Mark R 
Published: February 2016

Abstract

Background:
Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly.

Results:
Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub.

Conclusions:
The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility.