Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of dupA in virulence of Helicobacter pylori

Helicobacter pylori (H. pylori) is a gastric human pathogen associated with acute and chronic gastritis, 70% of all gastric ulcers, 85% of all duodenal ulcers, and both forms of stomach cancer, mucosal-associated lymphoid tissue (MALT) lymphoma and adenocarcinoma. Recently, attention has focused on possible relationship between presence of certain virulence factor and H. pylori-associated diseases. Some contradictory data between this bacterium and related disorders has been observed since not all the colonized individuals develop to severe disease. The reported diseases plausibility related to H. pylori specific virulence factors became an interesting story about this organism. Although a number of putative virulence factors have been identified including cytotoxin-associated gene a (cagA) and vacA, there are conflicting data about their actual participation as specific risk factor for H. pylori-related diseases. Duodenal ulcer promoting gene a (dupA) is a virulence factor of H. pylori that is highly associated with duodenal ulcer development and reduced risk of gastric cancer. The prevalence of dupA in H. pylori strains isolated from western countries is relatively higher than in H. pylori strains from Asian countries. Current confusing epidemiological reports will continue unless future sophisticated and molecular studies provide data on functional and complete dupA cluster in H. pylori infected individuals. This paper elucidates available knowledge concerning role of dupA in virulence of H. pylori after a decade of its discovery.
Coach-athlete relationships : a qualitative study of professional sport teams in Australia

This paper examines perceptions of eSective coaching and coach-athlete relationships within professional team sports in Australia. The ˆndings are based on interviews with six male professional coaches and 25 players from cricket, rugby league, and rugby union. Qualitative data analysis reveals that relationships within professional sport settings are based on mutual respect, trust and honesty. The results also indicate that professional coaches and players describe two diSerent types of coach-athlete relationships-the close, `family' oriented relationship or the `professional', arms-length relationship-both of which are considered equally eSective as long as the coaches and athletes share the same attitude towards the relationship. These ˆndings have implications for eSective coaching and how coaches interact to develop relationships with their athletes. They demonstrate that if coaches are to be perceived as eSective, it is crucial to consider individual athlete preferences with respect to the type of relationship formed. This highlights the need for specialised coach training in people management as the professional coaching role increasingly requires attention to personal development in conjunction with the technical, tactical and physical training of their athletes.
Estimating the ground truth from multiple individual segmentations with application to skin lesion segmentation

Having ground truth is critical for evaluating segmentation algorithms and finding the ground truth remains a hard problem. In this paper, three methods to estimate the ground truth for skin lesion segmentation using multiple manual results collected from different experts are proposed and compared. We also analyze the manual segmentations and discuss how to use them more effectively. We conclude that a voting policy produces a slightly better ground truth than the other two optimization based approaches. We propose that a better ground truth should take into account different styles of segmentations.
A CpG island methylator phenotype of colorectal cancer that is contiguous with conventional adenomas, but not serrated polyps

A subset of colorectal cancers (CRCs) harbor the CpG island methylator phenotype (CIMP), with concurrent multiple promoter hypermethylation of tumor-related genes. A serrated pathway in which CIMP is developed from serrated polyps is proposed. The present study characterized CIMP and morphologically examined precursor lesions of CIMP. In total, 104 CRCs treated between January 1996 and December 2004 were examined. Aberrant promoter methylation of 15 cancer-related genes was analyzed. CIMP status was classified according to the number of methylated genes and was correlated with the clinicopathological features, including the concomitant polyps in and around the tumors. The frequency of aberrant methylation in each CRC showed a bimodal pattern, and the CRCs were classified as CIMP-high (CIMP-H), CIMP-low (CIMP-L) and CIMP-negative (CIMP-N). CIMP-H was associated with aberrant methylation of MLH1 (P=0.005) and with an improved recurrence-free survival (RFS) rate following curative resection compared with CIMP-L/N (five-year RFS rate, 93.8 vs. 67.1%; P=0.044), while CIMP-N tumors were associated with frequent distant metastases at diagnosis (P=0.023). No concomitant serrated lesions were present in the tumors, whereas conventional adenoma was contiguous with 11 (10.6%) of 104 CRCs, including four CIMP-H CRCs. CIMP-H was classified in CRCs by a novel CIMP marker panel and the presence of concomitant tumors revealed that certain CIMP-H CRCs may have arisen from conventional adenomas.
2 The Bidirectional Lamb Model

Under periodic boundary conditions, a one-dimensional dispersive medium driven by a Lamb oscillator exhibits a smooth response when the dispersion relation is asymptotically linear or superlinear at large wave numbers, but unusual fractal solution profiles emerge when the dispersion relation is asymptotically sublinear. Strikingly, this is exactly the opposite of the superlinear asymptotic regime required for fractalization and dispersive quantization, also known as the Talbot effect, of the unforced medium induced by discontinuous initial conditions.
Religious Heterogamy, Marital Quality, and Paternal Engagement

Using data from a nationally representative sample of married fathers of school-aged children, we examined the association between religious heterogamy of parents and fathers’ involvement in children’s lives. We further examined whether that association is mediated by marital quality and father–child religious discord. Results showed that greater religious heterogamy is associated with less interaction and more relational distance between fathers and children. Results also suggested that fathers’ reports of marital happiness play an important role in mediating the association between religious heterogamy and paternal engagement. We concluded that religious fathers are more involved in their children’s lives insofar as their wives are equally religious and they are in happy marriages.
binding nitric oxide synthase expression by inhibiting p 52 acetylation and Melatonin suppresses macrophage cyclooxygenase-2 and inducible

http://bloodjournal.hematologylibrary. org/content/108/2/518.full. html Updated information and services can be found at: (1930 articles) Signal Transduction  (973 articles) Phagocytes  (4939 articles) Immunobiology  (2497 articles) Hemostasis, Thrombosis, and Vascular Biology  (1086 articles) Gene Expression  Articles on similar topics can be found in the following Blood collections http://bloodjournal.hematologylibrary. org/site/misc/rights.xhtml#repub_requests Information about reproducing this article in parts or in its entirety may be found online at: http://bloodjournal.hematologylibrary. org/site/misc/rights.xhtml#reprints Information about ordering reprints may be found online at: http://bloodjournal.hematologylibrary. org/site/subscriptions/index.xhtml Information about subscriptions and ASH membership may be found online at:
A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
Management for non-variceal upper gastrointestinal bleeding in elderly patients: the experience of a tertiary university hospital.

BACKGROUND Peptic ulcer bleeding (PUB) is the main cause of non-variceal upper gastrointestinal bleeding (UGIB). Endoscopic treatment and acid suppression with proton-pump inhibitors (PPIs) are most important in the management of PUB and these treatments have reduced mortality. However, elderly patients sometimes have a poor prognostic outcome due to severe comorbidities. METHODS A retrospective study was performed on 504 cases with acute non-variceal UGIB who were examined in our hospital, in order to reveal the risk factor of a poor outcome in elderly patients. RESULTS Two hundred and thirty-four cases needed hemostasis; 11 cases had unsuccessful endoscopic treatments; 31 cases had re-bleeding after endoscopic hemostasis. Forty-three cases died within 30 days after the initial urgent endoscopy, but only seven cases died from bleeding. Elderly patients aged over 65 years had more severe comorbidities, and were prescribed non-steroidal anti-inflammatory drugs (NSAIDs), antiplatelet agents and/or anticoagulation agents, more frequently, compared with non-elderly patients. The significant risk factor of needing hemostatic therapy was the taking of two or more NSAIDs, antiplatelet agents and/or anticoagulation agents. The most important risk of a poor outcome in elderly patients was various kinds of severe comorbidities. And so, it is important to predict such an outcome in these cases. AIMS65 is a simple and relatively useful scoring system that predicts the risk of a poor outcome in UGIB. High-score patients via AIMS65 were associated with a high mortality rate because of death from comorbidities. CONCLUSIONS The elderly patients in whom were prescribed two or more NSAIDs, antiplatelet agents and/or anticoagulation agents, should have UGIB prevented using a PPI. The most significant risk of a poor outcome in elderly patients was severe comorbidities. We recommend that elderly patients with UGIB should be estimated as having a poor outcome as soon as possible via the risk scoring system AIMS65.
Language control is not a one-size-fits-all languages process: evidence from simultaneous interpretation students and the n-2 repetition cost

Simultaneous interpretation is an impressive cognitive feat which necessitates the simultaneous use of two languages and therefore begs the question: how is language management accomplished during interpretation? One possibility is that both languages are maintained active and inhibitory control is reduced. To examine whether inhibitory control is reduced after experience with interpretation, students with varying experience were assessed on a three language switching paradigm. This paradigm provides an empirical measure of the inhibition applied to abandoned languages, the n-2 repetition cost. The groups showed different patterns of n-2 repetition costs across the three languages. These differences, however, were not connected to experience with interpretation. Instead, they may be due to other language characteristics. Specifically, the L2 n-2 repetition cost negatively correlated with self-rated oral L2 proficiency, suggesting that language proficiency may affect the use of inhibitory control. The differences seen in the L1 n-2 repetition cost, alternatively, may be due to the differing predominant interactional contexts of the groups. These results suggest that language control may be more complex than previously thought, with different mechanisms used for different languages. Further, these data represent the first use of the n-2 repetition cost as a measure to compare language control between groups.
Cortical regions involved in eye movements, shifts of attention, and gaze perception

Human vision is an active process that involves shifting attention across the visual scene, with or without moving the eyes. Such shifts of attention can be generated at will (endogenously) or be triggered automatically, i.e., generated in response to exogenous stimuli including socially relevant cues such as someone else's gaze. What are the common and distinct brain mechanisms involved in these processes? To address this question, we carried out a quantitative effect‐location meta‐analysis of 59 brain‐imaging experiments whose results were published using standardized coordinates. For each condition of interest, namely voluntary and visually triggered eye movements, voluntary and visually triggered (covert) shifts of attention, and perception of someone else's gaze, we computed activation likelihood estimation (ALE) maps. Those maps represent at each voxel of the brain the probability of reporting a signal change related to the condition of interest. For eye movements, this analysis confirmed the spatial location of the frontal eye fields, supplementary eye fields, and parietal saccade‐related regions. The map of covert shifts of attention demonstrated highest similarity with the map of saccadic eye movements. Gaze perception showed common activation likelihood with the other conditions in the right intraparietal sulcus and in the lateral precentral gyrus. It demonstrated more similarity with the reflexive than with the voluntary saccades and shifts of attention. We propose that a core network of frontoparietal and temporal brain regions is recruited when we shift the focus of our attention with or without eye movements in response to the appearance of a visual target, as well as when we see someone else shift his or her gaze. Hum Brain Mapp 25:140–154, 2005. © 2005 Wiley‐Liss, Inc.
Concerns Regarding the Use of Dabigatran for Stroke Prevention in Atrial Fibrillation

Dabigatran is an oral thrombin inhibitor which has been approved in several countries as an alternative to vitamin-K-antagonists for the prevention of stroke or embolism in atrial fibrillation patients. Dabigatran is introduced into clinical practice, although many issues regarding this drug are still unclear, like laboratory monitoring, use in elderly patients, drug- and food-interactions and use in patients with renal insufficiency. Additionally, there is no antidote for dabigatran. Thus, aim of the present review is to give an overview of concerns and unresolved issues concerning dabigatran.
The effect of a psychosocial group intervention on loneliness and social support for Japanese women with primary breast cancer.

PURPOSE/OBJECTIVES To examine the effects of a psychosocial group intervention on loneliness and social support in Japanese women with breast cancer. DESIGN Secondary analysis of a randomized, controlled trial. SETTING A breast cancer outpatient area of a National Cancer Center hospital in Japan. SAMPLE 50 women who were less than 65 years old, were diagnosed with primary breast cancer, and had undergone surgery within 4-18 months of the start of the study. METHODS Data were collected as part of a trial of an intervention. The investigators conducted a six-week group intervention consisting of health education, coping skills training, stress management, and psychological support. Subjects completed the revised University of California, Los Angeles, Loneliness Scale and a social support questionnaire at baseline, six weeks, and six months. MAIN RESEARCH VARIABLES Loneliness, number of confidants, satisfaction with confidants, and satisfaction with mutual aid. FINDINGS Fifty (33%) of the 151 invited patients participated and were randomized to either experimental (n = 25) or control (n = 25) groups, and 23 (92%) in each group completed the study. The experimental group had significantly lower scores than the control group for loneliness and significantly higher scores for the number of confidants, satisfaction with confidants, and satisfaction with mutual aid over the six-month study period. CONCLUSIONS This intervention is beneficial for Japanese patients with breast cancer experiencing loneliness and inadequate social support. IMPLICATIONS FOR NURSING The program can be used as an effective support for Japanese patients with cancer to manage their psychosocial concerns associated with illness.
Nurse staffi ng and education and hospital mortality in nine European countries : a retrospective observational study

Background Austerity measures and health-system redesign to minimise hospital expenditures risk adversely aff ecting patient outcomes. The RN4CAST study was designed to inform decision making about nursing, one of the largest components of hospital operating expenses. We aimed to assess whether diff erences in patient to nurse ratios and nurses’ educational qualifi cations in nine of the 12 RN4CAST countries with similar patient discharge data were associated with variation in hospital mortality after common surgical procedures.
Spiral imaging: A critical appraisal

In view of recent applications in cardiovascular and functional brain imaging, this work revisits the basic performance characteristics of spiral imaging in direct comparison to echo‐planar imaging (EPI) and conventional rapid gradient‐echo imaging. Using both computer simulations and experiments on phantoms and human subjects at 2.9 T, the study emphasizes single‐shot applications and addresses the design of a suitable trajectory, the choice of a gridding algorithm, and the sensitivity to experimental inadequacies. As a general result, the combination of a spiral trajectory with regridding of the k‐space data poses no principle obstacle for high‐quality imaging. On the other hand, experimental difficulties such as gradient deviations, resonance offset contributions, and concomitant field effects cause more pronounced and even less acceptable image artifacts than usually obtained for EPI. Moreover, when ignoring parallel imaging strategies that are also applicable to EPI, improvements of image quality via reduced acquisition periods are only achievable by interleaved multishot spirals because partial Fourier sampling and rectangular fields of view (FOVs) cannot be exploited for non‐Cartesian trajectories. Taken together, while spiral imaging may find its niche applications, most high‐speed imaging needs are more easily served by EPI. J. Magn. Reson. Imaging 2005;21:657–668. © 2005 Wiley‐Liss, Inc.
Small Molecule Quantification by Liquid Chromatography-Mass Spectrometry for Metabolites of Drugs and Drug Candidates

Identification and quantification of the metabolites of drugs and drug candidates are routinely performed using liquid chromatography-mass spectrometry (LC-MS). The best practice is to generate a standard curve with the metabolite versus the internal standard. However, to avoid the difficulties in metabolite synthesis, standard curves are sometimes prepared using the substrate, assuming that the signal for substrate and the metabolite will be equivalent. We have tested the errors associated with this assumption using a series of very similar compounds that undergo common metabolic reactions using both conventional flow electrospray ionization LC-MS and low-flow captive spray ionization (CSI) LC-MS. The differences in standard curves for four different types of transformations (O-demethylation, N-demethylation, aromatic hydroxylation, and benzylic hydroxylation) are presented. The results demonstrate that the signals of the substrates compared with those of the metabolites are statistically different in 18 of the 20 substrate-metabolite combinations for both methods. The ratio of the slopes of the standard curves varied up to 4-fold but was slightly less for the CSI method.
A wearable multiplexed silicon nonvolatile memory array using nanocrystal charge confinement

An ultrathin, stretchable memory skin patch that can reliably store bio-signals such as heart rate is newly developed. Strategies for efficient charge confinement in nanocrystal floating gates to realize high-performance memory devices have been investigated intensively. However, few studies have reported nanoscale experimental validations of charge confinement in closely packed uniform nanocrystals and related device performance characterization. Furthermore, the system-level integration of the resulting devices with wearable silicon electronics has not yet been realized. We introduce a wearable, fully multiplexed silicon nonvolatile memory array with nanocrystal floating gates. The nanocrystal monolayer is assembled over a large area using the Langmuir-Blodgett method. Efficient particle-level charge confinement is verified with the modified atomic force microscopy technique. Uniform nanocrystal charge traps evidently improve the memory window margin and retention performance. Furthermore, the multiplexing of memory devices in conjunction with the amplification of sensor signals based on ultrathin silicon nanomembrane circuits in stretchable layouts enables wearable healthcare applications such as long-term data storage of monitored heart rates.
Transmission of Influenza B Viruses in the Guinea Pig

ABSTRACT Epidemic influenza is typically caused by infection with viruses of the A and B types and can result in substantial morbidity and mortality during a given season. Here we demonstrate that influenza B viruses can replicate in the upper respiratory tract of the guinea pig and that viruses of the two main lineages can be transmitted with 100% efficiency between inoculated and naïve animals in both contact and noncontact models. Our results also indicate that, like in the case for influenza A virus, transmission of influenza B viruses is enhanced at colder temperatures, providing an explanation for the seasonality of influenza epidemics in temperate climates. We therefore present, for the first time, a small animal model with which to study the underlying mechanisms of influenza B virus transmission.