Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of paeonol on expression of COX-2 and p27 in HT-29 cells.

AIM To investigate the effect of paeonol on controlling the proliferation of colorectal cancer cell line HT-29 and to discuss its possible mechanism. METHODS The inhibitory effect of paeonol on proliferation of HT-29 cells was detected by MTT assay. The results of apoptosis were measured by flow cytometry. Immunocytochemical staining was performed to detect the expression of cyclooxygenase-2 (COX-2) and protein p27 in HT-29 cells treated with paeonol at different concentrations. Reverse transcription-polymerase chain reaction (RT-PCR) was used for mRNA analysis. RESULTS From the data of both MTT and flow cytometry, we observed that cell proliferation was inhibited by different concentrations of paeonol. By immunocytochemical staining, we found that HT-29 cells treated with paeonol (0.024-1.504 mmol/L) reflected reduced expression of COX-2 and increased expression of p27 in a dose-dependent manner. RT-PCR showed that paeonol down-regulated COX-2 and up-regulated p27 in a dose- and time-dependent manner in HT-29 cells. CONCLUSION One of the apoptotic mechanisms of paeonol is down-regulation of COX-2. p27 is up-regulated simultaneously and plays an important part in controlling cell proliferation and is a crucial factor in the Fas/FasL apoptosis pathway.
Exhaled Nitric Oxide in Evaluation of Young Adults with Chronic Cough

Background. Bronchial asthma (A) is frequently diagnosed in patients with chronic cough. The study was conducted to determine whether an evaluation of fractional exhaled nitric oxide (FeNO) concentration can be used as a screening test for asthma in young adults with chronic cough (CCP). Methods. The study was performed on 540 (mean age 26.5; range 18–45 years), nonsmoking young CCP. All patients had resting spirometry within normal limits and no abnormalities on chest radiographs. Skin prick tests with common aeroallergens, bronchial provocation challenge with histamine, and evaluation of FeNO concentration were performed in all patients. One hundred healthy, nonsmoking, nonatopic subjects were used as control subjects (HC). Results. Asthma (A) was diagnosed in 178 CCP (32.96%). Other frequent diagnoses included rhinitis/sinusitis (R) and gastroesophageal reflux (GERD). The median FeNO concentration in A (86 ppb; 95% CI 72 to 94,5 ppb) was significantly greater than in R (37 ppb; 95% CI 35,6 to 42,9 ppb; p < 0.0001), GERD (14,8 ppb; 95%CI 13.3 to 16.2 ppb; p < 0.0001), or in HC (13 ppb; 95%CI 11 to 15 ppb; p < 0.0001). Significant correlation was found between logFeNO and bronchial reactivity expressed as logPC20 (r = −0.529; 95%CI −0.616 to −0.429; p < 0.0001), but even stronger correlation was demonstrated between logFeNO and peripheral blood eosinophilia (r = 0.757; 95%CI 0.717 to 0.792). Receiver Operator Characteristic (ROC) curve analysis revealed that CCP can be screened for A by measuring FeNO concentration. Using 40 ppb as a cut-off value for the FeNO concentration, the specificity 82.6% and sensitivity 88.3% can be achieved. Conclusion. In clinical practice, assessment of FeNO concentration can be used as a screening test for asthma in young adults who have chronic cough.
A Novel Method for the Assessment of Cellular Composition and Beta‐Cell Viability in Human Islet Preparations

Current methodologies to evaluate islet cell viability are largely based on tests that assess the exclusion of DNA‐binding dyes. While these tests identify cells that have lost selective membrane permeability, they do not allow us to recognize apoptotic cells, which do not yet stain with DNA‐binding dyes. Furthermore, current methods of analysis do not discriminate between cell subsets in the preparation and, in particular, they do not allow for selectively defining β‐cell viability.
AutoGP: Exploring the Capabilities and Limitations of Gaussian Process Models

We investigate the capabilities and limitations of Gaussian process models by jointly exploring three complementary directions: (i) scalable and statistically efficient inference; (ii) flexible kernels; and (iii) objective functions for hyperparameter learning alternative to the marginal likelihood. Our approach outperforms all previously reported GP methods on the standard MNIST dataset; performs comparatively to previous kernel-based methods using the RECTANGLES-IMAGE dataset; and breaks the 1% error-rate barrier in GP models using the MNIST8M dataset, showing along the way the scalability of our method at unprecedented scale for GP models (8 million observations) in classification problems. Overall, our approach represents a significant breakthrough in kernel methods and GP models, bridging the gap between deep learning approaches and kernel machines.
Fuji apple (Malus domestica Borkh. cv. Red Fuji) pomace extracts as a source of antimicrobial and antioxidant polyphenols

This study aimed to assess the antibacterial and antioxidant properties of both crude polyphenol extract (CPE) and purified polyphenol extract (PPE) obtained from Fuji apple pomace. The antibacterial capacity of both extracts against Staphylococcus aureus was investigated by evaluating the inhibition zones, minimum bactericidal concentrations (MBC), growth curves and bacterial morphology of S. aureus treated with CPE or PPE, as well as the performance in simulated food systems. The antioxidant activity of CPE or PPE was assessed using the ABTS radical scavenging and ferric reducing antioxidant power (FRAP) assays. The results showed that PPE exhibited potent antibacterial activity against S. aureus, which was further confirmed by the bacterial morphology. It was revealed that PPE only exerted strong antibacterial effect in starch-based food system while CEP did not show such effect in all systems. The results of the ABTS and FRAP assays indicated that both PPE and CPE possess strong antioxidant activity, from which PPE showed much higher capacity than that of CPE. Therefore, PPE from Fuji apple pomace can be used as a novel antibacterial agent for food preservation and natural antioxidant for functional food and nutraceutical products.
Children’s International Polyposis (CHIP) study: a randomized, double-blind, placebo-controlled study of celecoxib in children with familial adenomatous polyposis

Objective To evaluate the efficacy and safety of celecoxib versus placebo in the prevention and treatment of colorectal polyposis in children with familial adenomatous polyposis (FAP). Methods In this Phase III, double-blind, randomized, placebo-controlled, multicenter trial patients aged 10–17 years with FAP were randomized to celecoxib (16 mg/kg/day) or placebo for up to 5 years. Patients underwent annual assessments, including colonoscopies, to detect the time from randomization to the earliest occurrence of ≥20 polyps (>2 mm in size) or colorectal malignancy. The study was terminated early due to low rate of observed endpoints combined with a lower than expected enrollment rate. Descriptive results are provided. Results Of 106 randomized patients, 55 were treated with celecoxib (mean age 12.6 years; 52.7% female) and 51 were given placebo (mean age 12.2 years; 54.9% female). Disease progression (≥20 polyps, >2 mm in size) was observed in seven (12.7%) and 13 (25.5%) patients, respectively. The median time to disease progression was 2.1 years in the celecoxib group and 1.1 years for placebo. No patient developed colorectal cancer. The rate of adverse events (AEs) was similar in both groups (75.5% and 72.9%, respectively). Three patients in the celecoxib group (none in the placebo group) experienced serious AEs. Conclusion In children with FAP, celecoxib was a well-tolerated treatment that was associated with a lower rate of colorectal polyposis and a longer time to disease progression compared with placebo. Due to the low rate of observed endpoints, the long-term impact of these results could not be ascertained.
Risk of stroke in long-term dialysis patients compared with the general population.

BACKGROUND Patients undergoing maintenance dialysis are at increased risk of stroke. STUDY DESIGN We performed a nationwide retrospective cohort study to determine the risks for ischemic stroke and hemorrhagic stroke among incident hemodialysis (HD) and peritoneal dialysis (PD) patients in comparison to a reference group in Taiwan. SETTING & PARTICIPANTS Data for 74,192 HD patients, 5,974 PD patients, and 669,773 nondialysis individuals who were older than 18 years and had no history of stroke or cancer were retrieved from the National Health Insurance Research Database for 1998-2009. PREDICTORS Patient demographics, comorbid conditions. OUTCOME First hospitalization for stroke, defined as a diagnosis at discharge (either primary or 1 of 4 secondary diagnoses) of ischemic or hemorrhagic stroke using International Classification of Diseases, Ninth Revision, Clinical Modification codes. RESULTS HD and PD patients had higher incidences of hospitalized ischemic stroke (102.6 and 100.1/10,000 person-years) and hemorrhagic stroke (74.7 and 59.4/10,000 person-years) in comparison to the age- and sex-matched reference cohort (42.4 and 13.0/10,000 person-years, respectively). In addition to HD and PD therapy, older age, male sex, diabetes, and hypertension were found to be independent risk factors for both ischemic and hemorrhagic strokes. Using the HD group as the comparison group, we found that PD patients had a lower risk of hemorrhagic stroke (HR, 0.75; 95% CI, 0.58-0.96), and there was no significant difference in risks of ischemic stroke between PD and HD patients after adjusting for all potential confounders and competing risk of death, and matched by propensity scores. LIMITATIONS This was a retrospective study, and some important variables were not available. CONCLUSIONS Patients undergoing dialysis are at elevated risk of stroke. Patients undergoing PD appear to be less likely to develop hemorrhagic stroke than those undergoing HD. Comprehensive control of hypertension and diabetes is necessary when delivering dialysis treatment.
Serogrouping and seroepidemiology of North European hantaviruses using a novel broadly targeted synthetic nucleoprotein antigen array

ABSTRACT Introduction: Hantaviruses are globally distributed zoonotic pathogens. Great diversity and high antigenic cross-reactivity makes diagnosis by traditional methods cumbersome. Materials and methods: ‘Megapeptides’, 119–120-mers from the amino terminus of the nucleoprotein of 16 hantaviruses, representing the four major branches of the hantavirus phylogenetic tree, were utilized in a novel IgG-based hantavirus suspension multiplex immunoassay (HSMIA) for detection of past hantavirus infections in 155 North European human samples. We compared HSMIA with established EIAs and focus reduction neutralization test (FRNT). Results and discussion: The Puumala hantavirus (PUUV) component in the HSMIA gave concordant results with a PUUV IgG EIA in 142 sera from Northern Sweden (of which 31 were EIA positive, 7 borderline and 104 EIA negative, sensitivity 30/31 = 97%, specificity 104/ 104 = 100%, 134/135 = 99% concordance), with another immunoassay in 40 PUUV IgG positive sera from Finland (36/40 = 90% sensitivity), and was concordant in 8 of 11 cases with PUUV and DOBV neutralization titers, respectively. Two major IgG reactivity patterns were found: (i) a PUUV-specific pattern covering phylogroup IV and its serogroups B and C; and (ii) a Dobrava virus (DOBV)-specific pattern, covering the serogroup A portion of phylogroup III. In addition, we found several minor patterns with reactivity to only one or two megapeptides indicating additional hantaviruses infecting humans in the Swedish and Finnish populations. Conclusion: The broadly reactive and rational HSMIA yielded results highly correlated with the established PUUV EIAs and the NT results. It is a sensitive and specific assay, which will be suited for efficient serosurveillance of hantaviruses in humans. Its use in animals should be further investigated.
Effects of the nematode-trapping fungus, Monacrosporium ellipsosporium on Meloidogyne incognita populations in field soi1

SUMMARY Monacrosporium ellipsosporiwn was frequently observed associated with Meloidogyne egg masses in some field soils and in potted cultures of the nematode. Six geographic isolates varied in their relative predacity toward larvae emerging from egg masses. An aggressive isolate, chosen for rapidity and abundance of trap formation in vitro, was tested in greenhouse and field tests for protection of tomato from M. incognita. A test of tomato in potted field soi1 inoculated at 1, 5 and 10 g fungal inoculum/l5 cm pot, 15 days before nematode inoculation, showed significant reduction,in plant damage at the 5 and 10 g levels, but none at the 1 g rate. Galling was reduced 42 Oo and 49 “0, respectively, in the 5 and 10 g fungal treatments. Larvae in the soi1 and females/plant were also similarly reduced, but were the same as controls at the 1 g rate. In a tield test using two levels of fungus on wheat grain substrate mixed into transplant holes for tomato seedlings, the improved plant growth and M. incognira reduction obtained at harvest were also in direct relationship to amounts of the fungus used, but the treatments did not differ statistically from the control.
Sources and Levels of Ambient Ocean Sound near the Antarctic Peninsula

Arrays of hydrophones were deployed within the Bransfield Strait and Scotia Sea (Antarctic Peninsula region) from 2005 to 2009 to record ambient ocean sound at frequencies of up to 125 and 500 Hz. Icequakes, which are broadband, short duration signals derived from fracturing of large free-floating icebergs, are a prominent feature of the ocean soundscape. Icequake activity peaks during austral summer and is minimum during winter, likely following freeze-thaw cycles. Iceberg grounding and rapid disintegration also releases significant acoustic energy, equivalent to large-scale geophysical events. Overall ambient sound levels can be as much as ~10–20 dB higher in the open, deep ocean of the Scotia Sea compared to the relatively shallow Bransfield Strait. Noise levels become lowest during the austral winter, as sea-ice cover suppresses wind and wave noise. Ambient noise levels are highest during austral spring and summer, as surface noise, ice cracking and biological activity intensifies. Vocalizations of blue (Balaenoptera musculus) and fin (B. physalus) whales also dominate the long-term spectra records in the 15–28 and 89 Hz bands. Blue whale call energy is a maximum during austral summer-fall in the Drake Passage and Bransfield Strait when ambient noise levels are a maximum and sea-ice cover is a minimum. Fin whale vocalizations were also most common during austral summer-early fall months in both the Bransfield Strait and Scotia Sea. The hydrophone data overall do not show sustained anthropogenic sources (ships and airguns), likely due to low coastal traffic and the typically rough weather and sea conditions of the Southern Ocean.
Toward the role of interaction in Visual Analytics

This paper firstly provides a general introduction in the most important aspects and ideas of Visual Analytics. This multidisciplinary field focuses on the analytical reasoning of typically large and complex (often heterogeneous) data sets and combines techniques from interactive visualizations with computational analysis methods. Hereby, intuitive and efficient user interactions are a fundamental component which has to be efficiently supported by any Visual Analytics system. This integration of interaction techniques into both visual representations and automatic analysis methods supports the human-information discourse and can be realized in various ways which is discussed in the second part of the paper. We give examples of possible applications of Visual Analytics from the domain of biological simulations and highlight the importance and role of the human in the analysis loop.
Fuel for the work required: a practical approach to amalgamating train‐low paradigms for endurance athletes

Using an amalgamation of previously studied “train‐low” paradigms, we tested the effects of reduced carbohydrate (CHO) but high leucine availability on cell‐signaling responses associated with exercise‐induced regulation of mitochondrial biogenesis and muscle protein synthesis (MPS). In a repeated‐measures crossover design, 11 males completed an exhaustive cycling protocol with high CHO availability before, during, and after exercise (HIGH) or alternatively, low CHO but high protein (leucine enriched) availability (LOW + LEU). Muscle glycogen was different (P < 0.05) pre‐exercise (HIGH: 583 ± 158, LOW + LEU: 271 ± 85 mmol kg−1 dw) but decreased (P < 0.05) to comparable levels at exhaustion (≈100 mmol kg−1 dw). Despite differences (P < 0.05) in exercise capacity (HIGH: 158 ± 29, LOW + LEU: 100 ± 17 min), exercise induced (P < 0.05) comparable AMPKα2 (3–4‐fold) activity, PGC‐1α (13‐fold), p53 (2‐fold), Tfam (1.5‐fold), SIRT1 (1.5‐fold), Atrogin 1 (2‐fold), and MuRF1 (5‐fold) gene expression at 3 h post‐exercise. Exhaustive exercise suppressed p70S6K activity to comparable levels immediately post‐exercise (≈20 fmol min−1 mg−1). Despite elevated leucine availability post‐exercise, p70S6K activity remained suppressed (P < 0.05) 3 h post‐exercise in LOW + LEU (28 ± 14 fmol min−1 mg−1), whereas muscle glycogen resynthesis (40 mmol kg−1 dw h−1) was associated with elevated (P < 0.05) p70S6K activity in HIGH (53 ± 30 fmol min−1 mg−1). We conclude: (1) CHO restriction before and during exercise induces “work‐efficient” mitochondrial‐related cell signaling but; (2) post‐exercise CHO and energy restriction maintains p70S6K activity at basal levels despite feeding leucine‐enriched protein. Our data support the practical concept of “fuelling for the work required” as a potential strategy for which to amalgamate train‐low paradigms into periodized training programs.
miR‐34a predicts survival of Ewing's sarcoma patients and directly influences cell chemo‐sensitivity and malignancy

Identification of factors to detect chemotherapy‐resistant tumours at diagnosis is a first priority for risk‐adapted therapy in the oncology of children and young adults, where more individualized, effective, and less toxic treatments are highly desirable. In this study, we analysed the miRNAs discriminating Ewing's sarcoma (EWS) patients with different clinical outcomes in order to identify new indicators of prognosis. miRNA expression was investigated in 49 primary EWSs by using the Agilent human miRNA microarray v.2 and/or qRT‐PCR. Statistical power of the samples studied for miRNA expression was verified, indicating adequate sample size. Microarray analysis defined a signature of five miRNAs (miR‐34a, miR‐23a, miR‐92a, miR‐490‐3p, and miR‐130b) as an independent predictor of risk for disease progression and survival. Validation analysis in the extended sample set indicated that both miR‐34a and miR‐490‐3p achieved sufficient statistical power to predict prognosis. Results were particularly robust for miR‐34a, which appeared associated with either event‐free or overall survival and emerged as a significant predictor also after multivariate analysis. Patients with the highest expression of miR‐34a did not experience adverse events in 5 years; in contrast, patients with the lowest expression recurred within 2 years. High expression of miR34a can be detected also in paraffin‐embedded tissues by in situ hybridization, thus contributing to an easy routine evaluation of this miRNA. Functional analysis of miR‐34a in EWS cell lines indicated that when miR‐34a expression was enforced, cells were less proliferative, less malignant, and sensitized to doxorubicin and vincristine. Expression of miR‐34a could be increased in p53wt cells by treatment with nutlin‐3a. Accordingly, nutlin‐3a synergizes with doxorubicin. Overall, our data indicate that miR‐34a expression is a strong predictor of outcome in EWS. Restoration of miR‐34a activity may be useful to decrease malignancy and increase tumour sensitivity to current drugs, so sparing excessive long‐term toxicity to EWS patients. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
BIORETENTION GARDENS FOR THE REMOVAL OF NITROGEN AND PHOSPHOROUS FROM URBAN RUNOFF

BIORETENTION GARDENS FOR THE REMOVAL OF NITROGEN AND PHOSPHOROUS FROM URBAN RUNOFF Mark Randall Advisor: University of Guelph, 2011 Dr. Andrea Bradford Bioretention gardens are stormwater management practices that offer numerous water quantity and quality benefits. However, previous studies have reported inconsistent removal of nitrogen and phosphorous in these systems. The first phase of this research involved the construction and monitoring of ten vegetated, mesoscale, bioretention cells in a field setting to provide a comparison of the performance of five alternative designs intended to provide nutrient removal. Results indicated that concentrations of total nitrogen and total phosphorous may be reduced by up to 53 and 79%, respectively, in specially designed bioretention gardens. In the second phase of the research, a GIS-based site selection tool was used to identify areas suitable for bioretention implementation based on physical site requirements. Applying this tool to selected urban catchments demonstrated that bioretention gardens may be integrated into existing urban landscapes on a scale large enough to accommodate runoff and associated nutrient loads from small (<15mm) storms.
Causes of death in Korean patients with systemic lupus erythematosus: a single center retrospective study.

OBJECTIVE To determine the causes of death in Korean patients with systemic lupus erythematosus (SLE). METHODS We evaluated retrospectively Korean SLE patients who were monitored in the Center for Rheumatic Disease in Kang-Nam St. Mary's Hospital from 1993 to 1997 and who died. RESULTS Forty-three (7.9%) of 544 patients died. Comparison of demographics and disease activity indices between the deceased and the survivors showed that the age was older and C3 at presentation was lower in the deceased (n = 40) than the survivors (n = 453) (age: 33.8 +/- 13.6 versus 28.3 +/- 10.6 years, p = 0.02, C3: 36.8 +/- 21.4 versus 49.7 +/- 20.8 mg/dl, p = 0.03). Among 40 patients who died, the frequency and causes of death were as follows: 13 from infection (32.5%), 10 SLE-related factors (25.0%), 6 pulmonary hypertension (15.0%), 4 cerebrovascular accidents (10.0%), and 3 thrombotic thrombocytopenic purpura (7.5%). The majority of the SLE-related deaths were non-renal in origin, including 3 cerebral nervous system disease, 2 TTP, 2 acute pulmonary hemorrhage syndrome, 1 acute myocarditis, and 1 multi-system illness. SLE-related renal causes were responsible for only death. The major organisms of infection were gram negative bacilli (69.2%), primarily manifesting as sepsis or bacteremia (76.9%). The patients (n = 13) who died from infection had lower levels of complement and higher levels of anti-ds DNA antibody at presentation than those (n = 27) who died from the other causes (C3: 24.7 +/- 17.8 versus 41.7 +/- 21.5 mg/dl, p = 0.02, anti-dsDNA antibody: 68.0 +/- 73.5 versus 27.0 +/- 35.3 IU, p = 0.04). The mean steroid dose being administered one month before death was also higher in the patients who died of infection (30.5 +/- 15.2 versus 15.2 +/- 7.7 mg/day, p = 0.03). Patients who died of pulmonary hypertension, the third most common cause of mortality, showed extremely high pulmonary pressures at the initial diagnosis, with a short interval to death, and had less major organ involvement at death. There were no deaths due to coronary heart disease or neoplasm in this cohort. CONCLUSION The most common cause of death in 544 Korean lupus patients was infection, mainly manifesting as gram negative bacterial sepsis. SLE-related factors (mostly non-renal) were the next most frequent cause. Death from infection was associated with higher disease activity at presentation and a higher dose of steroid used previously. Death due to pulmonary hypertension was common, whereas death due to coronary heart disease was absent.