bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
Authors: McLaren William , Pritchard Bethan , Rios Daniel , Chen Yuan , Flicek Paul , Cunningham Fiona 
Published: June 2010

Abstract
Summary: A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species.
Availability: The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html for installation instructions) is open source software.
Contact: wm2@ebi.ac.uk; fiona@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Transthoracic bioimpedance and brain natriuretic peptide levels accurately indicate additional diastolic dysfunction in patients with chronic advanced systolic heart failure
Authors: Malfatto Gabriella , Branzi Giovanna , Giglio Alessia , Villani Alessandra , Facchini Camilla , Ciambellotti Francesca , Facchini Mario , Parati Gianfranco 
Published: June 2010

AimsDiastolic dysfunction in patients with heart failure has prognostic relevance, possibly because of its relationship with worsening haemodynamic status. In the quest for simpler indexes of haemodynamic status in patients, brain natriuretic peptide (BNP) levels have been proposed as a surrogate of diastolic function. To date, the value of combining BNP levels with non‐invasive haemodynamic monitoring by transthoracic electric bioimpedance (TEB) for the prediction of diastolic function has not been evaluated.Methods and resultsWe compared left ventricular diastolic function measured by tissue Doppler imaging (TDI) with TEB results and BNP levels in 120 patients with chronic advanced systolic heart failure on optimal treatment (70 ± 9 years, NYHA 2.4 ± 0.8, ejection fraction 31 ± 5%). Of the TEB variables measured, we only considered thoracic fluid content (TFC). To describe diastolic function, we used the TDI of the velocity of displacement of the mitral annulus (E′) and the ratio E/E′. In all patients, E/E′ was significantly related to TFC and to BNP levels (P < 0.001). Moreover, the combination of BNP ≥ 350 pg/mL and TFC ≥ 35/kΩ identified patients with diastolic dysfunction (defined as E/E′ ≥ 15) with high sensitivity and specificity (95 and 94%, respectively).ConclusionThe combination of transthoracic bioimpedance monitoring and BNP measurement accurately indicated the presence of diastolic dysfunction in most patients. These user‐friendly and operator‐independent tools may be useful as a screening assessment for diastolic dysfunction, and consequently abnormal central haemodynamic status, either in ambulatory patients or when an adequate echocardiographic evaluation is not readily available.
MoMAR-D: a technological challenge to monitor the dynamics of the Lucky Strike vent ecosystem
Authors: Colaço A. , Blandin J. , Cannat M. , Carval T. , Chavagnac V. , Connelly D. , Fabian M. , Ghiron S. , Goslin J. , Miranda J. M. , Reverdin G. , Sarrazin J. , Waldmann C. , Sarradin P. M. 
Published: June 2010

Abstract
Colaço, A., Blandin, J., Cannat, M., Carval, T., Chavagnac, V., Connelly, D., Fabian, M., Ghiron, S., Goslin, J., Miranda, J. M., Reverdin, G., Sarrazin, J., Waldmann, C., and Sarradin, M. 2011. MoMAR-D: a technological challenge to monitor the dynamics of the Lucky Strike vent ecosystem. – ICES Journal of Marine Science, 68: 416–424. The MoMAR (monitoring the Mid-Atlantic Ridge) project was initiated in 1998 by the InterRidge programme to promote and coordinate long-term multidisciplinary monitoring of hydrothermal vents at the Mid-Atlantic Ridge (MAR). The major objective of the project is to study vent ecosystem dynamics using a multidisciplinary approach from geophysics to microbiology over a period of a few decades. MoMAR-D is a demonstration project of MoMAR, partially funded by the European network of excellence ESONET (http://www.esonet-noe.org/). MoMAR-D aims to deploy and manage a multidisciplinary observing system at the Lucky Strike vent field for 1 year. This large hydrothermal field is located at the centre of one of the most volcanically active segments of the MAR. The project has been set up to monitor this region to capture evidence of volcanic events, observe interactions between faulting, magmatism, and hydrothermal circulations, and to evaluate the potential impacts of these environmental factors on the unusual communities colonizing hydrothermal vents. The MoMAR-D infrastructure consists of two sea monitoring nodes (SEAMON) acoustically linked to a surface buoy with satellite communication to a land-based station. The first node will be mainly dedicated to geophysical studies, whereas the second will focus on ecological studies and chemical fluxes. The infrastructure should have been deployed in September 2010 during the MoMARSAT cruise.
Distribution of paralarvae and small juvenile cephalopods in relation to primary production in an upwelling area off southern Brazil
Authors: Vidal Erica A. G. , Haimovici Manuel , Hackbart Vivian C. S. 
Published: June 2010

Abstract
Vidal, E. A. G., Haimovici, M., and Hackbart, V. C. S. 2010. Distribution of paralarvae and small juvenile cephalopods in relation to primary production in an upwelling area off southern Brazil. – ICES Journal of Marine Science, 67: 1346–1352. The distribution of paralarvae and small juvenile cephalopods sampled by a rectangular midwater trawl (opening area 8 m2) over the continental shelf off Cape Santa Marta Grande, southern Brazil (28°09′S–29°56′S) during spring 1989 is discussed. An intrusion of Brazil Current Tropical Water (22°C; 36.5) separates warm, less-saline water (22°C; 35.2) from cooler, more-saline water (15°C; 36.4). Prevailing northeasterly winds led to upwelling of South Atlantic Central Water over the shelf, promoting high Chl a concentrations. Three species constituted 99% of the 628 cephalopods collected: Illex argentinus (n = 540; 4–40 mm mantle length, ML), Argonauta nodosa (n = 46; 2–19 mm ML), and Loligo sanpaulensis (n = 42, 2–21 mm ML). Segregation of I. argentinus juveniles of similar size suggests school formation as small as 10 mm ML. The presence of mature males along with fertilized female A. nodosa indicates mating early in life. There was a consistent and direct link between high plankton production and high densities of juvenile cephalopods through a short and ecologically efficient food chain. The relationship between production, pycnocline intensity, and the density of paralarvae and juveniles revealed suitable conditions for survival and growth during the upwelling season.
A review of potential factors relevant to coping in patients with advanced cancer
Authors: Thomsen Thora Grothe , Rydahl‐Hansen Susan , Wagner Lis 
Published: June 2010

Aims.  The aim was to identify characteristics that are considered to describe coping in patients with advanced cancer, as seen from a patient perspective. Based on the identified characteristics, the second aim was to identify potential factors that are relevant to coping in patients with advanced cancer.Background.  Patients with advanced or incurable cancer often express a need for professional help to cope with their complex situation. Furthermore, the support of health care professionals may often be dominated by a focus on symptom treatment and its effectiveness and less on the kind of needs that the patients consider most important.Design.  Systematic review.Methods.  Based on guidelines from the Centre for Review and Dissemination, York University, a systematic literature search identified 30 articles. Using Lazarus and Folkman’s theory of coping as the theoretical framework, relevant data were extracted, analysed and synthesised.Results.  Based on the identification of 160 characteristics, seven potential factors emerged: ‘Creating meaning’, ‘Support systems’, ‘Minimising the impact of cancer’, ‘Bodily and mental functioning’, ‘Control’ and ‘Uncertainty’ and ‘Emotions’.Conclusions.  The results indicate that emotion‐focused coping may be used more often by patients with advanced cancer than problem‐focused coping. However, it cannot be ruled out that this finding relates to a nomenclature of coping function that is too limited. Furthermore, the results indicate that the seven potential factors may be related to both the appraisal process and the coping process.Relevance to clinical practice.  By choosing, as the theoretical framework, Lazarus and Folkman’s theory about the connection between the stress, appraisal and coping processes, it has been possible to highlight how the identified factors may be used as the underlying basis of clinical questions focusing on the patients’ appraisal of and coping with the concrete situation.
Statin use prior to ischemic stroke onset is associated with decreased in‐hospital mortality
Authors: Hassan Yahaya , Al‐Jabi Samah W. , Aziz Noorizan Abd , Looi Irene , Zyoud Sa’ed H. 
Published: June 2010

AbstractStatins can reduce the risk of stroke in at‐risk populations and improve survival after acute ischemic stroke (AIS) among patients with previous statin use. This study aimed to investigate the impact of statin use before AIS onset on in‐hospital mortality and identify the factors related to in‐hospital mortality among patients with and without previous statin use. A retrospective cohort study of all patients with AIS attending hospital from June 1, 2008 to December 31, 2008. Data were collected from medical records including demographic information, diagnostic information, risk factors, previous statin use, and vital discharge status. Chi‐square, Fisher’s exact tests, student’s t‐test, and Mann–Whitney U test, whatever appropriate, were used to test the significance between the variables, and multiple logistic regression was used to identify factors associated with in‐hospital mortality. Altogether, 386 patients with AIS were studied, of which 113 (29.3%) had a documented previous statin use. A total of 62 (16.1%) patients with AIS died in hospital. In‐hospital mortality was significantly lower among previous statin users (P = 0.013). The presence of atrial fibrillation (AF) increased in‐hospital mortality among patients with or without previous statin use. The independent predictors for in‐hospital mortality among AIS patients without previous statin use were the presence of diabetes mellitus (P = 0.047), AF (P = 0.045), and renal impairment (P < 0.001). The prophylactic administration of statins significantly reduces post‐AIS in‐hospital mortality. Furthermore, the identification of predictors of in‐hospital mortality might reduce death rates and enhance the application of specific therapeutic and management strategies to patients at a high risk of dying.
Effects of nitric oxide synthase inhibitors 1‐(2‐trifluoromethylphenyl) – imidazole (TRIM) and 7‐nitroindazole (7‐NI) on learning and memory in mice
Authors: Mutlu Oguz , Ulak Güner , Belzung Catherine 
Published: June 2010

AbstractNitric oxide (NO) plays an important role in hippocampal long‐term potentiation (LTP), which is involved in memory processes. This led to the hypothesis that nitric oxide synthase (NOS) inhibitors will have disturbing effects on learning and memory. The aim of our study was to investigate the effects of the new selective neuronal and inducible NOS inhibitor 1‐ (2‐trifluoromethylphenyl) imidazole (TRIM) (10–50 mg/kg) on learning and memory and compare it to the nonselective NOS inhibitor 7‐NI (15–45 mg/kg) using different behavioral tests in Swiss mice, thus clarifying the role of neuronal NOS (nNOS) and endothelial NOS (eNOS) in cognitive processes. TRIM had no specific effect on either learning or memory parameters, while 7‐NI (30 mg/kg) disturbed spatial memory in the probe trial of the Morris water maze test, which was performed on the last day of the test. No differences between TRIM and the control groups were observed, while 7‐NI (30 and 45 mg/kg) significantly disturbed memory in the novel object recognition test. In the social transmission of food preference test, both TRIM (50 mg/kg) and 7‐NI (45 mg/kg) impaired hippocampal olfactory memory, but the total food consumption was also significantly decreased at these doses. In the passive avoidance test, TRIM did not disturb the performance, while memory impairment was observed, even with lower doses of 7‐NI. All of these results suggest that TRIM has no clear effect on cognitive impairment compared to 7‐NI and that inhibition of both nNOS and eNOS are necessary for the deterioration of memory processes.
The
Pseudomonas aeruginosa
Exopolysaccharide Psl Facilitates Surface Adherence and NF-κB Activation in A549 Cells
Authors: Byrd Matthew S. , Pang Bing , Mishra Meenu , Swords W. Edward , Wozniak Daniel J. 
Published: June 2010

ABSTRACT

In order for the opportunistic Gram-negative pathogen
Pseudomonas aeruginosa
to cause an airway infection, the pathogen interacts with epithelial cells and the overlying mucous layer. We examined the contribution of the biofilm polysaccharide Psl to epithelial cell adherence and the impact of Psl on proinflammatory signaling by flagellin. Psl has been implicated in the initial attachment of
P
.
aeruginosa
to biotic and abiotic surfaces, but its direct role in pathogenesis has not been evaluated (L. Ma, K. D. Jackson, R. M. Landry, M. R. Parsek, and D. J. Wozniak, J. Bacteriol. 188:8213–8221, 2006). Using an NF-κB luciferase reporter system in the human epithelial cell line A549, we show that both Psl and flagellin are necessary for full activation of NF-κB and production of the interleukin 8 (IL-8) chemokine. We demonstrate that Psl does not directly stimulate NF-κB activity, but indirectly as a result of increasing contact between bacterial cells and epithelial cells, it facilitates flagellin-mediated proinflammatory signaling. We confirm differential adherence of Psl and/or flagellin mutants by scanning electron microscopy and identify Psl-dependent membrane structures that may participate in adherence. Although we hypothesized that Psl would protect
P
.
aeruginosa
from recognition by the epithelial cell line A549, we instead observed a positive role for Psl in flagellin-mediated NF-κB activation, likely as a result of increasing contact between bacterial cells and epithelial cells.

IMPORTANCE
Pseudomonas aeruginosa
is the predominant airway pathogen causing morbidity and mortality in individuals affected by the genetic disease cystic fibrosis.
P
.
aeruginosa
can also cause severe pneumonia, burn wound infections, and sepsis, making its overall impact on human health significant. The attachment of
P
.
aeruginosa
to host tissues, often leading to recalcitrant biofilm infections, and inflammation induced by flagellin are both important mechanisms of virulence. We explored the role of the biofilm polysaccharide Psl in the pathogenesis of
P
.
aeruginosa
and found that Psl is required for surface adherence to A549 epithelial cells, and as an adhesin, it facilitates flagellin-mediated NF-κB activation. This work was done to better understand the initial events of infection and revealed that a biofilm polysaccharide contributes to inflammation in a novel manner.
Early gastric cancer in Europe
Authors: EVERETT S M , AXON A T R 
Published: June 2010

Despite mass population screening and an incidence of EGC in Japan that is at least double that of the West, there seem to be no genuine differences in the clinicopathological features of the disease between the two regions. The macroscopic appearance, size, depth of invasion, frequency of lymph node invasion, and histology of EGC are all remarkably similar in Japan, Europe and America, as are sex and age distributions.Patients with EGC are a number of years younger than those with advanced cancer. This is not surprising: Tsukuma et alfollowed 56 cases of EGC that were not surgically treated and estimated that the median “duration of EGC” before becoming advanced was 37 months.87 This suggests that EGC undergoes a period of slow growth before becoming advanced. Further differences between early and advanced cancers include a higher frequency of synchronous cancers and a longer symptom duration in EGC.Unfavourable prognostic factors in EGC include lymph node invasion, and invasion through the muscularis mucosae, though it is not clear whether these are independent. Repeated attempts have been made to identify other prognostic factors, but no clear pattern has emerged, with the possible exceptions of patient age, tumour size, and the presence of ulceration.The postsurgical outcome of EGC in the West is marginally less favourable than in Japan. In view of the similar clinical and pathological features in the two regions it seems likely, therefore, that this is because of the more aggressive surgical techniques traditionally used in Japan. Conversely, however, EMR has recently emerged as an important technique in Japan. Despite the advantages of low operative mortality and normal function of the postoperative stomach, there are also a number of potential disadvantages. It would seem sensible, therefore, to await the results of long term follow up studies before widespread adoption of EMR in Europe. Nevertheless, this technique should be considered for frail patients unfit for more radical surgery.
T cells of the human intestinal lamina propria are high producers of interleukin-10
Authors: Braunstein J , Qiao L , Autschbach F , Schürmann G , Meuer S 
Published: June 2010

Background and aim—Some of the recently observed functional features characteristic of immunocompetent cells residing in the human intestinal lamina propria could be mediated by interleukin- 10 (IL-10). To investigate the role of IL-10 in the human intestinal mucosa, the regulation of IL-10 production by lamina propria T lymphocytes (LPL-T) was determined and compared with that of peripheral blood T lymphocytes (PBL-T).Methods—Following activation by using different stimuli, IL-10 release by LPL-T and PBL-T into the supernatant was measured by enzyme linked immunosorbent assay (ELISA). In parallel, cell growth was determined by [3H]-thymidine incorporation.Results—Neither LPL-T nor PBL-T release IL-10 constitutively. Triggering through CD2 or the T cell receptor (TCR)/CD3 complex in the presence of autologous monocytes induces significantly greater IL-10 secretion by LPL-T than by PBL-T. Engagement of the CD45 receptor enhances IL-10 release and proliferation of CD2 triggered CD45RO+ PBL-T. In contrast, it reduces CD2 induced IL-10 production by LPL-T without altering cell growth significantly .Conclusions—Activated LPL-T release relatively high amounts of IL-10. Enhanced IL-10 production by activated LPL-T, in comparison with activated PBL-T, is not only related to the presence of a higher proportion of CD45RO+ T cells in the intestinal lamina propria, but is also caused by increased sensitivity of LPL-T to CD2 co-stimulation. The differential responsiveness of LPL-T, compared with PBL-T, to CD45 engagement demonstrates that CD45 could be involved in the altered CD2 reactivity of LPL-T.
Enhanced mucosal permeability and nitric oxide synthase activity in jejunum of mast cell deficient mice
Authors: Komatsu S , Grisham M B , Russell J M , Granger D N 
Published: June 2010

Background—Recent reports have described a modulating influence of nitric oxide (NO) on intestinal mucosal permeability and have implicated a role for mast cells in this NO mediated process.Aims—To assess further the contribution of mast cells to the mucosal permeability changes elicited by the NO synthase (NOS) inhibitor NG-nitro-l-arginine methylester (l-NAME), using mast cell deficient (W/WV) and mast cell replete mice (+/+).Methods—Chromium-51 EDTA clearance (from blood to jejunal lumen), jejunal NOS and myeloperoxidase (MPO) activities, and plasma nitrate/nitrite levels were monitored.Results—The increased EDTA clearance elicited by intraluminal l-NAME in W/WV mice (4.4-fold) was significantly greater than the response observed in control (+/+) mice (1.8-fold). The exacerbated response in W/Wv mice was greatly attenuated by pretreatment with either dexamethasone (1.3-fold) or the selective inducible NOS inhibitor, aminoguanidine (1.4-fold), and partially attenuated by the mast cell stabiliser, lodoxamide (2.9-fold). Jejunal inducible NOS activity was significantly higher in W/WV than in +/+ mice, while jejunal MPO was lower in W/WV mice than in +/+ mice, suggesting that the higher inducible NOS in W/WV does not result from the recruitment of inflammatory cells into the gut. The higher inducible NOS activity in the jejunum of W/WV was significantly reduced by dexamethasone treatment.Conclusions—Our results suggest that mast cells normally serve to inhibit inducible NOS activity tonically in the gut and that inhibitors of NOS elicit a larger permeability response when this tonic inhibitory influence is released by mast cell depletion.
Experimental pain in the stomach: a model based on electrical stimulation guided by gastroscopy
Authors: Drewes A M , Arendt-Nielsen L , Jensen J H , Hansen J B , Krarup H B , Tage-Jensen U 
Published: June 2010

Background—Abdominal pain is often variable in intensity and difficult to characterise due to its referred pain pattern. Clinical pain is furthermore confounded by various emotional and cognitive factors.Aims—To develop and apply an experimental model to induce localised gastric pain.Subjects—Twelve healthy male volunteers.Methods—Stimulating electrodes were mounted on a biopsy forceps and electric stimuli were delivered during gastroscopy. Single, five repeated, and continuous stimuli were given at four locations in the stomach. Pain detection thresholds and pain intensities were assessed together with localisation of the referred pain area.Results—Pain detection thresholds were higher in the prepyloric region compared with those obtained at the lesser and greater curvature. Increasing stimulus intensity resulted in augmented pain perception and repeated stimuli elicited pain at a lower stimulus intensity than single stimuli. Continuous stimuli evoked constant (33%), increasing (33%), or decreasing (33%) pain. The localisation of referred pain varied considerably in the subjects.Conclusions—The model seems relevant to study basic pain mechanisms elicited by localised stimuli in the stomach. The experimental data support the premise that a gastric focus should always be suspected in patients referred with different kinds of abdominal pain.