In silico modelling of hormone response elements

BACKGROUND: An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of functional regulatory elements in promoters of eukaryotic genes. RESULTS: We present a method for precise prediction of a large group of transcription factor binding sites – steroid hormone response elements. We use a large training set of experimentally confirmed steroid hormone response elements, and adapt a sequence-based statistic method of position weight matrix, for identification of the binding sites in the query sequences. To estimate the accuracy level, a table of correspondence of sensitivity vs. specificity values is constructed from a number of independent tests. Furthermore, feed-forward neural network is used for cross-verification of the predicted response elements on genomic sequences. CONCLUSION: The proposed method demonstrates high accuracy level, and therefore can be used for prediction of hormone response elements de novo. Experimental results support our analysis by showing significant improvement of the proposed method over previous HRE recognition methods

Scalloped channels enhance tear mixing under hydrogel contact lenses.

PurposeTear exchange under a soft contact lens is directly related to the amount of lateral and transverse lens motion. Hydrodynamic modeling suggests that channels placed on the back surface of a soft lens will reduce fluid resistance and increase transverse lens movement. This study measured the effect of posterior lens surface scalloped channels on tear exchange.MethodsTear exchange in the postlens tear film (PoLTF) was estimated using a fluorometer to measure the exponential depletion of high-MW fluorescein under the lens expressed as the time to deplete 95% of dye (T95). A total of 32 subjects wore two pairs of identical lenses except that the experimental lens had 12 scalloped channels placed radially in the midperiphery of the posterior lens surface, whereas lenses without channels served as controls.ResultsThe mean +/- standard error T95 values for the channel lenses was 28 +/- 2 minutes compared with 32 +/- 2 minutes for the control lenses (p = 0.107). There was a marginally significant difference in T95 between two lens groups in Asian eyes (p = 0.054).ConclusionPlacing scallop-shaped channels on high-H2O content soft lenses improved the postlens tear pumping in Asian eyes

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead.

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Common genetic variation in cellular transport genes and epithelial ovarian cancer (EOC) risk

Background Defective cellular transport processes can lead to aberrant accumulation of trace elements, iron, small molecules and hormones in the cell, which in turn may promote the formation of reactive oxygen species, promoting DNA damage and aberrant expression of key regulatory cancer genes. As DNA damage and uncontrolled proliferation are hallmarks of cancer, including epithelial ovarian cancer (EOC), we hypothesized that inherited variation in the cellular transport genes contributes to EOC risk. Methods In total, DNA samples were obtained from 14,525 case subjects with invasive EOC and from 23,447 controls from 43 sites in the Ovarian Cancer Association Consortium (OCAC). Two hundred seventy nine SNPs, representing 131 genes, were genotyped using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). SNP analyses were conducted using unconditional logistic regression under a log-additive model, and the FDR q<0.2 was applied to adjust for multiple comparisons. Results The most significant evidence of an association for all invasive cancers combined and for the serous subtype was observed for SNP rs17216603 in the iron transporter gene HEPH (invasive: OR = 0.85, P = 0.00026; serous: OR = 0.81, P = 0.00020); this SNP was also associated with the borderline/low malignant potential (LMP) tumors (P = 0.021). Other genes significantly associated with EOC histological subtypes (p<0.05) included the UGT1A (endometrioid), SLC25A45 (mucinous), SLC39A11 (low malignant potential), and SERPINA7 (clear cell carcinoma). In addition, 1785 SNPs in six genes (HEPH, MGST1, SERPINA, SLC25A45, SLC39A11 and UGT1A) were imputed from the 1000 Genomes Project and examined for association with INV EOC in white-European subjects. The most significant imputed SNP was rs117729793 in SLC39A11 (per allele, OR = 2.55, 95% CI = 1.5-4.35, p = 5.66x10-4). Conclusion These results, generated on a large cohort of women, revealed associations between inherited cellular transport gene variants and risk of EOC histologic subtypes

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A cross-sectional study examining predictors of visit frequency to local green space and the impact this has on physical activity levels

Background Lack of physical activity (PA) is a growing public health concern. There is a growing body of literature that suggests a positive relationship may exist between the amount of local green space near one?s home and PA levels. For instance, park proximity has been shown to predict PA levels amongst certain populations. However, there is little evidence for the role of relatedness towards nature and perceptions of local green space on this relationship. The aim of this study was to examine, in a National UK sample, whether subjective indices associated with local green space were better predictors of visit frequency to local green space and PA levels compared to objectively measured quantity of local green space. Methods A cross-sectional survey was designed. From a random sample, 2079 working age adults responded to an online survey in September 2011. Demographics, self-reported PA, objective measures of the local environment (including local green space, road coverage, and environmental deprivation), were assessed in conjunction with perceptions of local green space and nature relatedness. Quantity of local green space was assessed by cross-referencing respondents? home postcodes with general land use databases. Regression models were conducted to assess which of our independent variables best predicted visit frequency to local green space and/or meeting PA guidelines. In addition, an ordinal regression was run to examine the relationship between visit frequency to local green space and the likelihood of meeting national PA guidelines. Results Nature relatedness was the strongest predictor for both visit frequency to local green space and meeting PA guidelines. Results show that perceived quality is a better predictor of visit frequency to local green space than objective quantity of local green space. The odds of achieving the recommended amount of PA was over four times greater for people who visited local green space once per week compared to never going (OR 4.151; 95 % CI, 2.40 to 7.17). Conclusions These results suggest that perceptions of local green space and nature relatedness play an important role in the relationship between local green space and PA. Considering the known health benefits of PA, our results are potentially important for public health interventions, policy making and environmental planning

O ensino das ciências experimentais no liceu, em Portugal, na I República (1910-1926)

O ensino das ciências experimentais (ECE) em Portugal ficou, como pretendemos demonstrar, fortemente marcado pela instauração da República, que comemorou no ano transacto o seu centenário. A República de 1910 pretendeu reformar toda a mentalidade portuguesa, através do pilar base – a educação – pela qual seria capaz de sacudir a nossa maneira de ser, lançando desta forma o país para um progresso de nível europeu. O estudo a que nos propomos, uma investigação documental no domínio da História da Ciência1, visa aprofundar os conhecimentos existentes sobre esta época e perceber o impacto da reforma do ECE, principalmente nos Liceus, caracterizando as principais figuras, políticas e docentes responsáveis pela sua conceptualização e aplicação. Através desta investigação procuraremos lançar as primeiras bases para descobrir as origens deste pensamento, querendo ainda comparar os fundamentos psicopedagógicos, epistemológicos e sociológicos da época com as principais ideias actualmente presentes no ensino da Ciência. Com este trabalho pretendemos, num primeiro momento, apresentar e divulgar o desenho da investigação e os seus objectivos, na procura de estabelecer parcerias e receber contributos da comunidade académica interessada por esta problemática