Nanodrawing of aligned single carbon nanotubes with a nanopen

Single-walled carbon nanotubes (SWCNTs) are considered pivotal components for molecular electronics. Techniques for SWCNT lithography today lack simplicity, flexibility, and speed of direct, oriented deposition at specific target locations. In this paper SWCNTs are directly drawn and placed with chemical identification and demonstrated orientation using fountain pen nanolithography (FPN) under ambient conditions. Placement across specific electrical contacts with such alignment is demonstrated and characterized. The fundamental basis of the drawing process with alignment has potential applications for other related systems such as inorganic nanotubes, polymers, and biological molecules

The Politics of Welfare Exclusion: Immigration and Disparity in Medicaid Coverage

The rapid growth of the immigrant population in the U.S., along with changes in the demographics and the political landscape, has often raised questions for understanding trends of inequality. Important issues that have received little scholarly attention thus far are excluding immigrants’ social rights through decisive policy choices and the distributive consequences of such exclusive policies. In this paper, we examine how immigration and state policies on immigrants’ access to safety net programs together influence social inequality in the context of health care. We analyze the combined effect of immigration population density and state immigrant Medicaid eligibility rules on the gap of Medicaid coverage rates between native- and foreign-born populations. When tracking inequality in Medicaid coverage and critical policy changes in the post-PRWORA era, we find that exclusive state policies widen the native-foreign Medicaid coverage gap. Moreover, the effect of state policies is conditional upon the size of the immigrant population in that state. Our findings suggest immigrants’ formal integration into the welfare system is crucial for understanding social inequality in the U.S. states

High Prevalence of Sexually Transmitted Infections, and High-Risk Sexual Behaviors Among Indigenous Adolescents of the Comarca Ngäbe-Buglé, Panama.

BACKGROUND: There is scant information on sexually transmitted infection (STI) prevalence and risk factors among Latin American indigenous populations. We investigated STI prevalence and risk factors among adolescents of the Comarca Ngäbe-Buglé indigenous region of Panama. METHODS: A population-based cross-sectional study was conducted among school-going adolescents aged 14 to 19 years. Eligible consenting participants self-completed a questionnaire and provided blood and urine samples. Female participants provided additional self-administered genital swabs. Seroprevalences of human immunodeficiency virus (HIV), syphilis, hepatitis B (HBsAg, anti-HBc), and herpes simplex virus type 2 (HSV-2) were determined in all participants; genital Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) by PCR among participants who reported sexual experience or were seropositive for HIV/syphilis/HSV2/HBsAg; high-risk human papillomavirus (HPV) by qualitative DNA assay and bacterial vaginosis (BV) by Gram-stain among female participants. Risk factors were identified by estimating adjusted odds ratios (AOR) using random-effects logistic regression. RESULTS: We enrolled 700 participants (median age, 17 years [female participants]; 18 years [male participants]) from 20 schools. Sexual experience was reported by 536 participants (76.6%). The HIV/STI prevalences among females and males were: HIV 0.4% and 1.0%, high-titer active syphilis 1.3% and 6.6%, HSV-2 16.1% and 16.1%, HBsAg 1.3% and 1.4%, anti-HBc 3.2% and 1.4%, NG 1.8% and 1.7%, CT 17.5% and 10.7%; among females: BV 42.9% and HPV 33.2%. CT was independently associated with being female (AOR, 2.02; 95% confidence interval [CI], 1.20-3.41); high-titer active syphilis with being male (AOR, 4.51; 95% CI, 1.17-17.40). Bacterial vaginosis was associated with sexual behavior (≥3 lifetime sex partners: AOR, 3.81; 95% CI, 1.29-11.26), HPV with sexual experience (AOR, 4.05; 95% CI, 1.62-10.09). CONCLUSIONS: School-going indigenous adolescents in rural Panama have substantial STI burden. Targeted STI screening is required

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations

JBrowse: a dynamic web platform for genome visualization and analysis

BACKGROUND: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. RESULTS: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. CONCLUSIONS: JBrowse is a mature web application suitable for genome visualization and analysis

Haplotype analysis of TP53 polymorphisms, Arg72Pro and Ins16, in BRCA1 and BRCA2 mutation carriers of French Canadian descent

Research articl

The Human Phenotype Ontology project:linking molecular biology and disease through phenotype data

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online