Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Classical and Nonclassical Virulence Genes in Enterotoxigenic Escherichia coli Isolates from Chilean Children and tRNA Gene Screening for Putative Insertion Sites for Genomic Islands

ABSTRACT Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea. Three adhesins (Tia, TibA, EtpA), an iron acquisition system (Irp1, Irp2, and FyuA), a GTPase (LeoA), and an autotransporter (EatA) are ETEC virulence-related proteins that, in contrast to the classical virulence factors (enterotoxins and fimbrial colonization factors) have not heretofore been targets in characterizing isolates from epidemiological studies. Here, we determined the occurrence of these nonclassical virulence genes in 103 ETEC isolates from Chilean children with diarrhea and described their association with O serogroups and classical virulence determinants. Because tia, leoA, irp2, and fyuA are harbored by pathogenicity islands inserted into the selC and asnT tRNA genes (tDNAs), we analyzed the regions flanking these loci. Ten additional tDNAs were also screened to identify hot spots for genetic insertions. Associations between the most frequent serogroups and classical colonization factor (CF)-toxin profiles included O6/LT-STh/CS1-CS3-CS21 (i.e., O6 serogroup, heat-labile [LT] and human heat-stable [STh] enterotoxins, and CFs CS1, -3 and -21), O6/LT-STh/CS2-CS3-CS21, and O104-O127/STh/CFAI-CS21. The eatA and etpA genes were detected in more than 70% of the collection, including diverse serogroups and virulence profiles. Sixteen percent of the ETEC strains were negative for classical and nonclassical adhesins, suggesting the presence of unknown determinants of adhesion. The leuX, thrW, and asnT tDNAs were disrupted in more than 65% of strains, suggesting they are hot spots for the insertion of mobile elements. Sequences similar to integrase genes were identified next to the thrW, asnT, pheV, and selC tDNAs. We propose that the eatA and etpA genes should be included in characterizations of ETEC isolates in future epidemiological studies to determine their prevalence in other geographical regions. Sequencing of tDNA-associated genetic insertions might identify new ETEC virulence determinants.
Racial/cultural identity development in foster children placed in transracial foster homes

RACIAL/CULTURAL IDENTITY DEVELOPMENT IN FOSTER CHILDREN PLACED IN TRANSRACIAL FOSTER HOMES by VANESSA BROOKS HERD May 2011 Advisor: Dr. Jazlin Ebenezer Major: Curriculum and Instruction Degree: Doctor of Education This qualitative study was designed to identify how racial and cultural identity is developed and maintained in foster children who are placed in foster homes racially and culturally different than they are. A review of the literature reveals scant studies of transracial foster care but many on transracial adoption. A myopic exploration of transracial foster care has not been undertaken. The importance of this new research is its singular purpose of spotlighting transracial foster care and its relationship to racial identity and cultural identity. This study was developed to contribute to the body of child welfare literature focused on foster care. The goal of this study was to explore how cultural identity is maintained and reinforced by foster families when the foster child has a different racial
Background Review Paper on Total Fat, Fatty Acid Intake and Cancers

This report has benefited from these advances, and aims to present new evidence with a potential impact upon dietary recommendations. In this background review paper, colorectal, prostate, breast, endometrial and ovary cancers will be covered successively, and the effect of total fat will be evaluated for each. The effect of specific FA (saturated, monounsaturated, n–6 and n–3 polyunsaturated, trans FA) will be evaluated on colorectal, prostate and breast cancer. In the latter, the effects of combined inadequate intakes of n–6 and n–3 polyunsaturated FA and of polyunsaturated FA and antioxidants have been shown in some studies, and will also be discussed.
Measurement uncertainties of capacities of multi-antenna system in anechoic chamber and reverberation chamber

It has been shown that multiple-input multiple-output (MIMO) capacity of multi-antenna system can be determined either from direct channel measurements in reverberation chamber or indirectly from antenna far field radiation function measurements in anechoic chamber (combined with numerically generated channel). In this paper, we try to investigate uncertainty of MIMO capacity obtained in these two ways from antenna viewpoint. It is found that the measurement uncertainty of capacity depends on measurement uncertainties of both efficiency and correlation, and that the former tends to dominate, given moderate correlation.
Association Rules with Graph Patterns

We propose graph-pattern association rules (GPARs) for social media marketing. Extending association rules for item-sets, GPARs help us discover regularities between entities in social graphs, and identify potential customers by exploring social influence. We study the problem of discovering top-k diversified GPARs. While this problem is NP-hard, we develop a parallel algorithm with accuracy bound. We also study the problem of identifying potential customers with GPARs. While it is also NP-hard, we provide a parallel scalable algorithm that guarantees a polynomial speedup over sequential algorithms with the increase of processors. Using real-life and synthetic graphs, we experimentally verify the scalability and effectiveness of the algorithms.
Level of Stress and Coping Strategies Adopted by Adolescents with Visual Impairment

Blind and visual disability is a great problem all over the world. Loss of the visual acuity in children requires special attention. the study was aimed to assess the level of stress and coping strategies adopted by adolescents with visual impairment. MethodologyThe research approach adopted for this study was descriptive survey approach, and Non experimental descriptive, corelational design. The study will be conducted in Sri Raman Maharishi academy for blind, J.P. Nagar, Bangalore. In the present study sample consists of 80 adolescents with visual impairment and sampling technique is non-probability, purposive sampling technique was used to select the sample for this study. FindingsThe overall level of stress experienced by adolescents with visual impairment reveals that 42(52.5%) of respondents had moderate level of stress, 36(45%) of respondents had mild level of stress and 2(2.5%) of the respondents had severe level of stress. The overall coping strategies reveals that 73(91.25%) of respondents had moderately adequate coping strategies, 7(8.75%) of respondents had adequate coping strategies and none of the respondents had inadequate coping strategies. The analysis revealed that there is a statistical significant association between the stress levels of adolescents with visual impairment.
Adrenoceptor Hyporeactivity Is Responsible for Escherichia coli Endotoxin‐Induced Acute Vascular Dysfunction in Humans

&NA; Impaired response to catecholamines contributes to the altered hemodynamics in sepsis, which has been attributed to excessive NO formation. We have studied the systemic hemodynamic and local forearm responses and inducible NO synthase (iNOS) expression during experimental endotoxemia in humans. Escherichia coli endotoxin (lipopolysaccharide [LPS]) was administered at doses of 1 or 2 ng/kg to healthy volunteers. In 10 subjects, the systemic pressor effect of phenylephrine was assessed before and after the administration of LPS. In 9 further subjects, forearm blood flow responses to intra‐arterial noradrenaline, acetylcholine, glyceryl trinitrate, and NG‐monomethyl‐L‐arginine (L‐NMMA) were studied at baseline and after LPS administration. Peripheral blood was collected and analyzed for iNOS mRNA and protein. Four hours after LPS, the response of systolic blood pressure (P<0.0005) and heart rate (P<0.05) to phenylephrine was significantly reduced. In the forearm, noradrenaline‐induced vasoconstriction was also reduced by ≈50% (P<0.01), but L‐NMMA responsiveness was unchanged. iNOS mRNA or protein was not increased. Marked vascular adrenoceptor hyporeactivity is detectable in the absence of increased NO activity or iNOS expression in endotoxemia, arguing against major involvement of vascular iNOS activity in the acute systemic vasodilation to LPS.
Chemical Composition of Saffron (Crocus sativus L.) from Four Countries

Saffron, the dried stigmas of Crocus sativus L. , is widely used mainly as herbal medicine or food coloring, and as a flavoring agent. It is cultivated only in a few countries around the world. Comparative analytical and semi-preparative High Performance Liquid Chromatography (HPLC) studies using photodiode array analyses were performed on a Waters HPLC system for the separation of several ingredients from alcoholic extracts of four different saffron types. Ten saffron peaks were identified by comparison of their retention times with those of known reference compounds and quantified from samples of Azerbaijanian, Spanish, Indian and Iranian saffron as follows: picrocrocin, trimethyl hydroxy carboxaldehyde cyclohexene, kaempherol, cis/trans-crocins and safranal. 2-nitroaniline (Sigma Chemical Co.) was used as the internal standard. It was found that the total content of carotenoids in Azerbaijanian and Iranian saffron samples was higher in comparison to other samples. These HPLC analytical procedures are sensitive, reproducible and allow for higher scaling of the instrumental conditions for obtaining sufficient amounts (mg) of the different saffron components for further cytotoxic assessments. Spanish saffron metabolites were collected and tested for their cytotoxicity against human tumor cells. Our results confirm that glycosidic carotenoid-type metabolites are responsible for the antitumor effects demonstrated by saffron.
The relationship among three models of personality psychopathology: DSM-III-R personality disorder, TCI scores and DSQ defences

Background. Current systems of describing personality pathology have significant shortcomings. A polydiagnostic approach is used to study the relationship between psychological, psychoanalytical and psychopathological models of personality. Methods. The subjects were 256 patients enrolled in treatment studies of major depression and bulimia nervosa. Subjects were assessed using the Temperament and Character Inventory (TCI), the Defense Style Questionnaire (DSQ) and the Structured Clinical Interview for DMS-III-R personality disorders (SCID-II). Results. Subjects had high rates of DSM-III-R personality disorders with 52% having at least one personality disorder. Cluster A personality disorders were correlated with low reward dependence, high harm avoidance and low self-directedness and cooperativeness. Cluster B personality disorders were related to high novelty seeking and low self-directedness and cooperativeness. Cluster C personality disorders were correlated with high harm avoidance and low novelty seeking and low self-directedness. Immature defences were related to DSM-III-R personality symptoms, but individual defences were not related to personality clusters in a predictable way. Immature defences were strongly related to low self-directedness and cooperativeness. Both TCI self-directedness scores and immature defence scores were moderately predictive of the presence and number of personality disorders. Conclusion. A widely accepted clinical nosology (DSM-III-R personality disorders) rated using a clinical interview correlates reasonably predictably with two theoretical models derived from different paradigms and rated using self-reports. This might be seen as providing concurrent validity for all three models. However, serious methodological shortcomings confront studies of this type, including sample selection and measurement of personality dysfunction. One way to begin to resolve these problems is to study which personality measures are best related to treatment response and prognosis.
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer*

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis.
Long peptide-based cancer immunotherapy targeting tumor antigen-specific CD4+ and CD8+ T cells

CD4+ T cells promote cytotoxic T lymphocyte (CTL)-mediated anticancer immune responses. We have recently identified ideal tumor-associated antigen (TAA)-derived long peptides (LPs) that elicit not only TAA-specific TH1 response, but also CTLs, through cross-presentation. The LP-specific TH1 cell responses were augmented in cancer patients vaccinated with CTL epitopes. Our findings support the clinical application of LP-based immunotherapy.
Incidence of Defibrillator Shocks After Elective Generator Exchange Following Uneventful First Battery Life

Background A significant number of implantable cardioverter‐defibrillator (ICD) patients do not experience shocks after ICD implant. Elective generator exchange (GE) has been associated with increased risk of infection and ICD lead failure. There is a paucity of contemporary data reporting on shock incidence with replacement devices. Methods and Results Patients undergoing elective GE (n=24 203) who transmit data remotely via a remote monitoring system were analyzed to determine the incidence of ICD shocks after GE. A total of 16 230 patients (67%) did not experience a shock with the first ICD (group A), and 7973 (33%) received at least 1 shock (group B). Patients in group A were older (71.3 versus 68.8 years, P<0.001) and more often female (71% versus 77% male, P<0.001). Over an average follow‐up of 1.9±1.2 years after GE, the proportion of patients with shocks and risk of ICD shocks was lower for those who did not receive a shock during the first battery life (group A: 9.9% versus 27.7%, hazard ratio 0.36, 95% CI 0.34 to 0.38, P<0.001). The cumulative rate of ICD shocks at 5 years after GE was 25.7% in group A and 51.1% in group B. Conclusions In this large cohort of ICD patients implanted across the United States, two thirds did not receive ICD shock therapy prior to GE. The occurrence of ICD shocks prior to GE is an important predictor of shocks after GE; however, even among those without shocks during first battery life, the incidence of shocks at 5 years following GE is >25%. These data should support informed decision making for patients and physicians at the time of ICD generator end of service.
Compactification of the moduli spaces of vortices and coupled vortices

Vortices and coupled vortices arise from Yang-Mills-Higgs theories and can be viewed as generalizations or analogues to Yang-Mills connections and, in particular, Hermitian-Yang-Mills connections. We proved an analytic compactification of the moduli spaces of vortices and coupled vortices on hermitian vector bundles over compact K\"ahler manifolds. In doing so we introduced the concept of ideal coupled vortices and characterized the singularities of ideal coupled vortices as well as Hermitian-Yang-Mills connections.
The Supernova rate per unit mass

We compute the rate of supernovae (SNe) of different types along the Hubble sequence normalized to the near- infrared luminosity and to the stellar mass of the parent galaxies. This is made possible by the new complete catalog of near- infrared galaxy magnitudes obtained by 2MASS. We find that the rates of all SN types, including Ia, Ib/c and II, show a sharp dependence on both the morphology and the (B − K) colors of the parent galaxies and, therefore, on the star formation activity. In particular we find, with a high statistical significance, that the type Ia rate in late type galaxies is a factor ∼20 higher than in E/S0. Similarly, the type Ia rate in the galaxies bluer than B − K = 2.6 is about a factor of 30 larger than in galaxies with B − K > 4.1. These findings can be explained by assuming that a significant fraction of Ia events in late spirals/irregulars originates in a relatively young stellar component.
Ganglioside Induces Caveolin-1 Redistribution and Interaction with the Epidermal Growth Factor Receptor*

Although caveolin-1 is thought to facilitate the interaction of receptors and signaling components, its role in epidermal growth factor receptor (EGFR) signaling remains poorly understood. Ganglioside GM3 inhibits EGFR autophosphorylation and may thus affect the interaction of caveolin-1 and the EGFR. We report here that endogenous overexpression of GM3 leads to the clustering of GM3 on the cell membrane of the keratinocyte-derived SCC12 cell line and promotes co-immunoprecipitation of caveolin-1 and GM3 with the EGFR. Overexpression of GM3 does not affect EGFR distribution but shifts caveolin-1 to the detergent-soluble, EGFR-containing region; consistently, caveolin-1 is retained in the detergent-insoluble membrane when ganglioside is depleted. GM3 overexpression inhibits EGFR tyrosine phosphorylation and receptor dimerization and concurrently increases both the content and tyrosine phosphorylation of EGFR-associated caveolin-1, providing evidence that tyrosine phosphorylation of caveolin-1 inhibits EGFR signaling. Consistently, depletion of ganglioside both increases EGFR phosphorylation and prevents the EGF-induced tyrosine phosphorylation of caveolin-1. GM3 also induces delayed serine phosphorylation of EGFR-unassociated caveolin-1, suggesting a role for serine phosphorylation of caveolin-1 in regulating EGFR signaling. These studies suggest that GM3 modulates the caveolin-1/EGFR association and is critical for the EGF-induced tyrosine phosphorylation of caveolin-1 that is associated with its inhibition of EGFR activation.
Promoter Methylation Precedes Chromosomal Alterations in Colorectal Cancer Development

Background: Colorectal cancers are characterized by genetic and epigenetic alterations. This study aimed to explore the timing of promoter methylation and relationship with mutations and chromosomal alterations in colorectal carcinogenesis. Methods: In a series of 47 nonprogressed adenomas, 41 progressed adenomas (malignant polyps), 38 colorectal carcinomas and 18 paired normal tissues, we evaluated promoter methylation status of hMLH1, O6MGMT, APC, p14ARF, p16INK4A, RASSF1A, GATA-4, GATA-5, and CHFR using methylation-specific PCR. Mutation status of TP53, APC and KRAS were studied by p53 immunohistochemistry and sequencing of the APC and KRAS mutation cluster regions. Chromosomal alterations were evaluated by comparative genomic hybridization. Results: Our data demonstrate that nonprogressed adenomas, progressed adenomas and carcinomas show similar frequencies of promoter methylation for the majority of the genes. Normal tissues showed significantly lower frequencies of promoter methylation of APC, p16INK4A, GATA-4, and GATA-5 (P-values: 0.02, 0.02, 1.1×10−5 and 0.008 respectively). P53 immunopositivity and chromosomal abnormalities occur predominantly in carcinomas (P values: 1.1×10−5 and 4.1×10−10). Conclusions: Since promoter methylation was already present in nonprogressed adenomas without chromosomal alterations, we conclude that promoter methylation can be regarded as an early event preceding TP53 mutation and chromosomal abnormalities in colorectal cancer development.
Receptor tyrosine phosphatase–dependent cytoskeletal remodeling by the hedgehog-responsive gene MIM/BEG4

During development, dynamic remodeling of the actin cytoskeleton allows the precise placement and morphology of tissues. Morphogens such as Sonic hedgehog (Shh) and local cues such as receptor protein tyrosine phosphatases (RPTPs) mediate this process, but how they regulate the cytoskeleton is poorly understood. We previously identified Basal cell carcinoma–enriched gene 4 (BEG4)/Missing in Metastasis (MIM), a Shh-inducible, Wiskott-Aldrich homology 2 domain–containing protein that potentiates Gli transcription (Callahan, C.A., T. Ofstad, L. Horng, J.K. Wang, H.H. Zhen, P.A. Coulombe, and A.E. Oro. 2004. Genes Dev. 18:2724–2729). Here, we show that endogenous MIM is induced in a patched1-dependent manner and regulates the actin cytoskeleton. MIM functions by bundling F-actin, a process that requires self-association but is independent of G-actin binding. Cytoskeletal remodeling requires an activation domain distinct from sequences required for bundling in vitro. This domain associates with RPTPδ and, in turn, enhances RPTPδ membrane localization. MIM-dependent cytoskeletal changes can be inhibited using a soluble RPTPδ-D2 domain. Our data suggest that the hedgehog-responsive gene MIM cooperates with RPTP to induce cytoskeletal changes.
Biomarkers of oxidative stress and smoking in cancer patients.

CONTEXT Increased oxidative stress is a significant part of pathogenesis of smoking-related cancer. AIM The study aims to investigate changes in antioxidant status induced by chronic cigarette smoking in cancer patients and healthy subjects. SETTING AND DESIGN We examined the venous blood samples of 54 healthy subjects, both smokers (25) and non-smokers and of 50 patients with smoking-related cancer, both smokers (34) and non-smokers. MATERIALS AND METHODS We measured the activities of five antioxidant (AO) enzymes: glutathione peroxidase, glutathione transferase (GST), glutathione reductase, superoxide dismutase and catalase in the blood of 50 cancer patients and 54 healthy persons. Damage to cellular structures (level of malonic dialdehyde, micro viscosity of erythrocyte membranes, number of leukocyte DNA breaks) was determined. Statistical analysis of results obtained was performed using conventional and multi-factorial statistical methods. RESULTS Statistically significant increase in GST activity and DNA breaks, but decrease of membranes micro viscosity in cancer patients, compared with healthy subjects were obtained. In the cancer patients, no influence of smoking on studied parameters was found. Correlations of parameters within cancer patients and healthy subjects group did not coincide with each other. CONCLUSIONS Changes of AO status parameters and oxidative damages in cell structures are related to tumor processes indicating the augmentation of oxidative stress in human blood. This study demonstrated potential applicability of a statistical model based on the evaluated biomarkers of oxidative stress to determine a smoking-induced harm of cancer incidence in healthy subjects.