Miracle-dz/UniFAR-FTUs huggingface dataset:
Lung Beractant Increases Free Cytosolic Levels of Ca2+ in Human Lung Fibroblasts

Beractant, a natural surfactant, induces an antifibrogenic phenotype and apoptosis in normal human lung fibroblasts (NHLF). As intracellular Ca2+ signalling has been related to programmed cell death, we aimed to assess the effect of beractant on intracellular Ca2+ concentration ([Ca2+]i) in NHLF in vitro. Cultured NHLF were loaded with Fura-2 AM (3 μM) and Ca2+ signals were recorded by microfluorimetric techniques. Beractant causes a concentration-dependent increase in [Ca2+]i with a EC50 of 0.82 μg/ml. The application of beractant, at a concentration of 500 μg/ml, which has been shown to exert an apoptotic effect in human fibroblasts, elicited different patterns of Ca2+ signals in NHLF: a) a single Ca2+ spike which could be followed by b) Ca2+ oscillations, c) a sustained Ca2+ plateau or d) a sustained plateau overlapped by Ca2+ oscillations. The amplitude and pattern of Ca2+ transients evoked by beractant were dependent on the resting [Ca2+]i. Pharmacological manipulation revealed that beractant activates a Ca2+ signal through Ca2+ release from intracellular stores mediated by phospholipase Cβ (PLCβ), Ca2+ release from inositol 1,4,5-trisphosphate receptors (IP3Rs) and Ca2+ influx via a store-operated pathway. Moreover, beractant-induced Ca2+ release was abolished by preventing membrane depolarization upon removal of extracellular Na+ and Ca2+. Finally, the inhibition of store-operated channels prevented beractant-induced NHLF apoptosis and downregulation of α1(I) procollagen expression. Therefore, beractant utilizes SOCE to exert its pro-apoptotic and antifibrinogenic effect on NHLF.
An Experimental Model for Studying Atherosclerosis

The aim of the present study was to clarify if old N -MRI rat, a strain which is easily available in Iran and cheap to maintain, is a suitable alternative to those previously reported. In this model, we compared three quantifiable parameters between old and young rats: biochemically, involving measurement of differences in the lipid profile. Histologically, the differences of the thickness of the wall of the aorta, the apparent degree of splitting within the aortic media, and the formation of foamy lipid layers on the outermost layer of the aorta. Pharmacologically, in vitro contractile responses/mg wet tissue weight to submaximal concentration of phenylephrine (1 µM) and the rate of relaxation min –1 mg –1 tissue weight following administration of 0.1 mM of acetycholine. The proposed model was validated using lovastatin as test drug known for its lipid lowering and anti -atherosclerosis actions. The results showed that this model to be reliable, quantifiable and capable of detecting the effect of orally administered lovastatin. We recommend this model as an easy and accessible experimental model for various atheroscleorosis investigations. Iran. Biomed. J. 7 (2) 65-71, 2003
miR-17 overexpression in cystic fibrosis airway epithelial cells decreases interleukin-8 production

Interleukin (IL)-8 levels are higher than normal in cystic fibrosis (CF) airways, causing neutrophil infiltration and non-resolving inflammation. Overexpression of microRNAs that target IL-8 expression in airway epithelial cells may represent a therapeutic strategy for cystic fibrosis. IL-8 protein and mRNA were measured in cystic fibrosis and non-cystic fibrosis bronchoalveolar lavage fluid and bronchial brushings (n=20 per group). miRNAs decreased in the cystic fibrosis lung and predicted to target IL-8 mRNA were quantified in βENaC-transgenic, cystic fibrosis transmembrane conductance regulator (Cftr)-/- and wild-type mice, primary cystic fibrosis and non-cystic fibrosis bronchial epithelial cells and a range of cystic fibrosis versus non-cystic fibrosis airway epithelial cell lines or cells stimulated with lipopolysaccharide, Pseudomonas-conditioned medium or cystic fibrosis bronchoalveolar lavage fluid. The effect of miRNA overexpression on IL-8 protein production was measured. miR-17 regulates IL-8 and its expression was decreased in adult cystic fibrosis bronchial brushings, βENaC-transgenic mice and bronchial epithelial cells chronically stimulated with Pseudomonas-conditioned medium. Overexpression of miR-17 inhibited basal and agonist-induced IL-8 protein production in F508del-CFTR homozygous CFTE29o− tracheal, CFBE41o− and/or IB3 bronchial epithelial cells. These results implicate defective CFTR, inflammation, neutrophilia and mucus overproduction in regulation of miR-17. Modulating miR-17 expression in cystic fibrosis bronchial epithelial cells may be a novel anti-inflammatory strategy for cystic fibrosis and other chronic inflammatory airway diseases. Overexpression of miR-17 in cystic fibrosis airway epithelial cells decreases interleukin-8 protein production http://ow.ly/MZbXB
Top–Down Enhancement and Suppression of Activity in Category-selective Extrastriate Cortex from an Act of Reflective Attention

Recent research has demonstrated top–down attentional modulation of activity in extrastriate category-selective visual areas while stimuli are in view (perceptual attention) and after they are removed from view (reflective attention). Perceptual attention is capable of both enhancing and suppressing activity in category-selective areas relative to a passive viewing baseline. In this study, we demonstrate that a brief, simple act of reflective attention (“refreshing”) is also capable of both enhancing and suppressing activity in some scene-selective areas (the parahippocampal place area [PPA]) but not others (refreshing resulted in enhancement but not in suppression in the middle occipital gyrus [MOG]). This suggests that different category-selective extrastriate areas preferring the same class of stimuli may contribute differentially to reflective processing of one's internal representations of such stimuli.
The Prostate TheHomozygous P 582 SMutation inthe Oxygen-DependentDegradationDomainofHIF-1 a is AssociatedWith IncreasedRisk for ProstateCancer

BACKGROUND. The heterodimeric transcription factor HIF-1 (hypoxia-inducible factor 1), consisting of a critically regulated HIF-1a subunit and a constitutively expressed HIF-1b subunit, is a master regulator of genes involved in adaptation and survival under low-oxygen conditions. Increased levels of HIF-1 activity are associated with increased tumor aggressiveness, therapeutic resistance, and mortality. METHODS. We studied 402 prostate cancer patients for the presence of the 1772C>T (P582S) and 1790G>A (A588T) mutations within the oxygen-dependent domain of HIF-1a. RESULTS. Homozygosity for the P582Smutation was fourfold greater among prostate cancer patients compared to controls (OR1⁄4 4.10 [C.I. 95% 1.11<OR< 17.87], P1⁄4 0.018). The existence of this mutation in prostate cancer patients was not associated with any of the clinical or pathological characteristics of the disease. No significant differences were found between the frequencies of A588T mutation in prostate cancer patients and controls. CONCLUSIONS. Our data suggest that homozygous HIF1A P582S mutation confers significant susceptibility to prostate cancer. Prostate # 2006 Wiley-Liss, Inc.
Skyline with presorting

The skyline, or Pareto, operator selects those tuples that are not dominated by any others. Extending relational systems with the skyline operator would offer a basis for handling preference queries. Good algorithms are needed for skyline, however, to make this efficient in a relational setting. We propose a skyline algorithm, SFS, based on presorting that is general, for use with any skyline query, efficient, and well behaved in a relational setting.
Language Comprehension in Language-Learning Impaired Children Improved with Acoustically Modified Speech

A speech processing algorithm was developed to create more salient versions of the rapidly changing elements in the acoustic waveform of speech that have been shown to be deficiently processed by language-learning impaired (LLI) children. LLI children received extensive daily training, over a 4-week period, with listening exercises in which all speech was translated into this synthetic form. They also received daily training with computer “games” designed to adaptively drive improvements in temporal processing thresholds. Significant improvements in speech discrimination and language comprehension abilities were demonstrated in two independent groups of LLI children.
Antifungal prophylaxis in lung transplantation.

Fungal infections are among the most serious complications of lung transplantation. The 1-year cumulative incidence of invasive fungal infections in lung transplant recipients is 6 to 10%, which is higher than most other solid organ transplant recipients. Aspergillus spp. are the most common etiologic agents, but Candida spp. , non-Aspergillus mycelial fungi, Cryptococcus, Pneumocystis, and endemic mycoses can cause active infections in this population. Clinical manifestations of fungal infection in lung transplant recipients are protean, and include invasive pulmonary disease, airway and anastomotic infections, posttransplant empyemas, and disseminated infections. Most centers employ either universal or targeted antifungal prophylaxis in some form, but the agents, doses, durations, and monitoring strategies vary widely from one center to another. This review discusses the salient fungal organisms responsible for infection in lung transplant recipients and management strategies for prevention.
Modelling behavioural contagion

The last decade has seen much work on quantitative understanding of human behaviour, with online social interaction offering the possibility of more precise measurement of behavioural phenomena than was previously possible. A parsimonious model is proposed that incorporates several observed features of behavioural contagion not seen in existing epidemic model schemes, leading to metastable behavioural dynamics.
Fast Triangle Counting through Wedge Sampling

Graphs are used to model interactions in a variety of contexts, and there is a growing need to quickly assess the structure of a graph. Some of the most useful graph metrics, especially those measuring social cohesion, are based on triangles. Despite the importance of these triadic measures, associated algorithms can be extremely expensive. We propose a new method based on wedge sampling. This versatile technique allows for the fast and accurate approximation of all current variants of clustering coefficients and enables rapid uniform sampling of the triangles of a graph. Our methods come with provable and practical time-approximation tradeoffs for all computations. We provide extensive results that show our methods are orders of magnitude faster than the state-of-the-art, while providing nearly the accuracy of full enumeration. Our results will enable more wide-scale adoption of triadic measures for analysis of extremely large graphs, as demonstrated on several real-world examples.
Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections

Chronic bacterial airway infections in people with cystic fibrosis (CF) are often caused by Pseudomonas aeruginosa, typically showing high phenotypic diversity amongst co-isolates from the same sputum sample. Whilst adaptive evolution during chronic infections has been reported, the genetic mechanisms underlying the observed rapid within-population diversification are not well understood. Two recent conflicting reports described very high and low rates of homologous recombination in two closely related P. aeruginosa populations from the lungs of different chronically infected CF patients. To investigate the underlying cause of these contrasting observations, we combined the short read datasets from both studies and applied a new comparative analysis. We inferred low rates of recombination in both populations. The discrepancy in the findings of the two previous studies can be explained by differences in the application of variant calling techniques. Two novel algorithms were developed that filter false-positive variants. The first algorithm filters variants on the basis of ambiguity within duplications in the reference genome. The second omits probable false-positive variants at regions of non-homology between reference and sample caused by structural rearrangements. As gains and losses of prophage or genomic islands are frequent causes of chromosomal rearrangements within microbial populations, this filter has broad appeal for mitigating false-positive variant calls. Both algorithms are available in a Python package.
Adipose tissue-secreted miR-27a promotes liver cancer by targeting FOXO1 in obese individuals

The current notion that obesity is a major risk factor for the development of and the mortality associated with a subset of liver cancer is well appreciated. However, detailed mechanistic insights underlying this relationship are lacking. Better understanding of the adipose tissue-secreted miRNAs that play a potential role in defining primary liver cancer development and mediating the obesity-cancer communication offers the potential for new insights into tumor growth and interventions to modulate tumor formation and progression. In this study, we clearly demonstrated that miR-27a is more highly upregulated in cancer, plasma, and adipose samples from obese liver cancer cases, and therefore reasoned that miR-27a excreted from adipose tissue leads to liver cancer development. To address this idea, we prepared miR-27a-overexpressing 3T3-L1 adipocytes and cocultured them with HepG2 liver cancer cells. Our results demonstrated that secretory miR-27a promoted liver cancer cell proliferation through the downregulation of the transcription factor FOXO1 and promoted the G1/S cell cycle transition by decreasing the cell cycle inhibitors p21 and p27 and increasing the cell cycle regulator cyclin D1. These findings improve our understanding of the involvement of miR-27a in obesity-liver cancer communication and might provide a novel putative target for obesity-driven primary liver cancer diagnosis and therapy.
Feature Extraction Based on Decision Boundaries

A novel approach to feature extraction for classification based directly on the decision boundaries is proposed. It is shown how discriminantly redundant features and discriminantly informative features are related to decision boundaries. A procedure to extract discriminantly informative features based on a decision boundary is proposed. The proposed feature extraction algorithm has several desirable properties: (1) it predicts the minimum number of features necessary to achieve the same classification accuracy as in the original space for a given pattern recognition problem; and (2) it finds the necessary feature vectors. The proposed algorithm does not deteriorate under the circumstances of equal class means or equal class covariances as some previous algorithms do. Experiments show that the performance of the proposed algorithm compares favorably with those of previous algorithms. >
Discovering frequent geometric subgraphs

As data mining techniques are being increasingly applied to non-traditional domains, existing approaches for finding frequent itemsets cannot be used as they cannot model the requirement of these domains. An alternate way of modeling the objects in these data sets, is to use a graph to model the database objects. Within that model, the problem of finding frequent patterns becomes that of discovering subgraphs that occur frequently over the entire set of graphs. We present a computationally efficient algorithm for finding frequent geometric subgraphs in a large collection of geometric graphs. Our algorithm is able to discover geometric subgraphs that can be rotation, scaling and translation invariant, and it can accommodate inherent errors on the coordinates of the vertices. Our experimental results show that our algorithms require relatively little time, can accommodate low support values, and scale linearly on the number of transactions.
Natural product derivative Bis(4-fluorobenzyl)trisulfide inhibits tumor growth by modification of β-tubulin at Cys 12 and suppression of microtubule dynamics

Bis(4-fluorobenzyl)trisulfide (BFBTS) is a synthetic molecule derived from a bioactive natural product, dibenzyltrisulfide, found in a subtropical shrub, Petiveria allieacea. BFBTS has potent anticancer activities to a broad spectrum of tumor cell lines with IC50 values from high nanomolar to low micromolar and showed equal anticancer potency between tumor cell lines overexpressing multidrug-resistant gene, MDR1 (MCF7/adr line and KBv200 line), and their parental MCF7 line and KB lines. BFBTS inhibited microtubule polymerization dynamics in MCF7 cells, at a low nanomolar concentration of 54 nmol/L, while disrupting microtubule filaments in cells at low micromolar concentration of 1 μmol/L. Tumor cells treated with BFBTS were arrested at G2-M phase, conceivably resulting from BFBTS-mediated antimicrotubule activities. Mass spectrometry studies revealed that BFBTS bound and modified β-tubulin at residue Cys12, forming β-tubulin-SS-fluorobenzyl. The binding site differs from known antimicrotubule agents, suggesting that BFBTS functions as a novel antimicrotubule agent. BFBTS at a dose of 25 mg/kg inhibited tumor growth with relative tumor growth rates of 19.91%, 18.5%, and 23.42% in A549 lung cancer, Bcap-37 breast cancer, and SKOV3 ovarian cancer xenografts, respectively. Notably, BFBTS was more potent against MDR1-overexpressing MCF7/adr breast cancer xenografts with a relative tumor growth rate of 12.3% than paclitaxel with a rate of 43.0%. BFBTS displays a novel antimicrotubule agent with potentials for cancer therapeutics. [Mol Cancer Ther 2009;8(12):3318–30]
Neonatal hyperbilirubinemia and mutation of the bilirubin uridine diphosphate‐glucuronosyltransferase gene: a common missense mutation among Japanese, Koreans and Chinese

We analyzed the bilirubin uridine diphosphate‐glucuronosyltransferase (B‐UGT) gene in 42 Japanese newborns with hyperbilirubinemia and determined that 21 infants were heterozygous while 3 was homozygous for Gly71Arg. Allele frequency of Gly71Arg was 0.32 in newborns with hyperbilirubinemia, which was significantly higher than 0.13 in healthy Japanese controls. This mutant allele is also prevalent among Korean and Chinese healthy controls with a frequency of 0.23 in both populations. However, this mutation was not detected in 50 healthy German controls. These data suggest that the high frequency of the Gly71Arg mutation of the B‐UGT gene is associated with high incidence of neonatal hyperbilirubinemia in Japanese, Korean and Chinese populations.
A comparative evaluation: Oral leukoplakia surgical management using diode laser, CO2 laser, and cryosurgery

Background The comparatively evaluate the three surgical treatment modalities namely cryosurgery, diode and CO2 laser surgery in terms of healing outcomes on the day of surgery, first and second week post operatively and recurrence at the end of 18 months was assessed. Material and Methods Thirty selected patients were divided randomly into three groups. Each group comprising of ten patients were subjected to one of the three modalities of treatment namely cryosurgery, diode laser or CO2 laser surgery for ablation of OL. Obtained data was analyzed using mainly using Chi-square and Anova tests. Results Study showed statistical significant differences (p > 0.05) for evaluation parameters like pain, edema and scar. The parameters like infection, recurrence, bleeding showed no statistical significance. Pain was significantly higher in CO2 laser surgery group as compared with diode laser group. There was no recurrence observed at the end of the 6 months follow up period in all the three study groups. Conclusions Observations from the study highlights that all three surgical modalities used in this study were effective for treatment of OL, and the overall summation of the results of the study showed that laser therapy (CO2 and Diode) seems to offer better clinically significant results than cryotherapy. Key words:Oral premalignant lesion, leukoplakia, cryosurgery, CO2 laser surgery, diode laser surgery.
The influence of practice and pitch-distance between tones on the absolute identification of pitch.

Abstract : The term absolute pitch customarily implies an ability to name isolated musical tones--an ability possessed by few persons. The usual experimental test of this facility requires O to identify by name (C, G sharp, F, etc.) a series of tones presented singly, each being separated from the one preceding by a designated time-interval. If O's average error of judgment satisfies a certain criterion (musical semitone or less), he is said to have absolute pitch; if his error exceeds the maximum allowed, he is not credited with absolute pitch. In the interest of extending our knowledge about the role of pitch in absolute judgments, this paper poses the following questions: How widely must a given number of pure tones be separated in pitch before the average O can make correct absolute judgments? What happens to the accuracy of absolute judgments of pitch when O is presented smaller and smaller pitch separations? How is the amount of information which O receives about the series related to the pitch-distance between tones? Are the effects of pitch-separation on absolute judgments significantly influenced by practice? How does disuse affect the ability?
Theoretical study of the dielectric constant in porous sandstone saturated with hydrocarbon and water

Porous sandstone reservoirs generally consist of three components: sand grains, hydrocarbons, and water. This paper proposes a hybrid method to predict the effective dielectric constant of such reservoir rocks using a combination of existing formulas and a simplified Fourier expansion method. Taking into consideration fluid distribution in pore space as well as pore structure, we have obtained the relations between the effective dielectric constant of sandstone and water saturation. The calculation results indicate that the effective dielectric constant of sandstone varies as a function of the water saturation when porosity is above 10%, but it cannot predict well the hydrocarbon content in sandstone with low porosity (/spl les/10%). In this study, two different cases are discussed. In the first, water is continuous and oil is in dispersed form in pore space, and in the second, oil is continuous and water is as a dispersed phase in pore space. Very different results are obtained from the two distributions. In Case 1, the effective dielectric constant approximately linearly increases with water saturation, but in Case 2, it is seen that a typical nonlinear relationship exists between the effective dielectric constant and water saturation. Furthermore, three models with microgeometry are considered, and the calculating result shows that the influence of geometry on the effective dielectric constant is large.