HPV-related oropharyngeal cancer: a review on burden of the disease and opportunities for prevention and early detection

The incidence of oropharyngeal cancer (OPC) related to infection with human papillomavirus (HPV) is rising, making it now the most common HPV-related malignancy in the United States. These tumors present differently than traditional mucosal head and neck cancers, and those affected often lack classic risk factors such as tobacco and alcohol use. Currently, there are no approved approaches for prevention and early detection of disease, thus leading many patients to present with advanced cancers requiring intense surgical or nonsurgical therapies resulting in significant side effects and cost to the health-care system. In this review, we outline the evolving epidemiology of HPV-related OPC. We also summarize the available evidence corresponding to HPV-related OPC prevention, including efficacy and safety of the HPV vaccine in preventing oral HPV infections. Finally, we describe emerging techniques for identifying and screening those who may be at high risk for developing these tumors

Human Papillomavirus Risk Perceptions Among Young Adult Sexual Minority Cisgender Women and Nonbinary Individuals Assigned Female at Birth

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148405/1/psrh12087_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148405/2/psrh12087.pd

In vivo differentiation of common basal cell carcinoma subtypes by microvascular and structural imaging using dynamic optical coherence tomography

The subtype of basal cell carcinoma (BCC) influences the choice of treatment. Optical coherence tomography (OCT) is a non-invasive imaging tool, and a recent development of an angiographic version of OCT has extended the application of OCT to image the cutaneous microvasculature (so-called dynamic OCT, D-OCT). This study explores D-OCT's ability to differentiate the common BCC subtypes by microvascular and structural imaging. Eighty-one patients with 98 BCC lesions, consisting of three subtypes: 27 superficial BCC (sBCC), 55 nodular BCC (nBCC) and 16 infiltrative BCC (iBCC) were D-OCT scanned at three European dermatology centres. Blinded evaluations of microvascular and structural features were performed, followed by extensive statistical analysis of risk ratio (RR) and multiple correspondence analysis. nBCC lesions displayed most characteristic structural and vascular features. Serpiginous vessels, branching vessels, vessels creating a circumscribed figure and sharply demarcated hyporeflective ovoid structures in the dermis were all associated with a higher risk of the subtype being nBCC. The presence of highly present lines and dark peripheral borders at the margin of ovoid structures was negatively associated with iBCC. Lastly, the finding of hyporeflective ovoid structures protruding from epidermis correlated with sBCC. We identified various microvascular and structural D-OCT features that may aid non-invasive identification of BCC subtypes. This would allow clinicians to individualize and optimize BCC treatment as well as aid follow-up of non-surgical treatment

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. It automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat

The Arthrobacter Species FB24 Arth_1007 (DnaB) Intein Is a Pseudogene

An Arthrobacter species FB24 gene (locus tag Arth_1007) was previously annotated as a putative intein-containing DnaB helicase of phage origin (Arsp-FB24 DnaB intein). However, it is not a helicase gene because the sequence similarity is limited to inteins. In fact, the flanking exteins total only 66 amino acids. Therefore, the intein should be referred to as the Arsp-FB24 Arth_1007 intein. The Arsp-FB24 Arth_1007 intein failed to splice in its native precursor and in a model precursor. We previously noted that the Arsp-FB24 Arth_1007 intein is the only putative Class 3 intein that is missing the catalytically essential Cys at position 4 of intein Motif F, which is one of the three defining signature residues of this class. Additionally, a catalytically essential His in position 10 of intein Motif B is also absent; this His is the most conserved residue amongst all inteins. Splicing activity was not rescued when these two catalytically important positions were ‘reverted’ back to their consensus residues. This study restores the unity of the Class 3 intein signature sequence in active inteins by demonstrating that the Arsp-FB24 Arth_1007 intein is an inactive pseudogene

JLab Measurements of the 3He Form Factors at Large Momentum Transfers

The charge and magnetic form factors, FC and FM, of 3He have been extracted in the kinematic range 25 fm-2 < Q2 < 61 fm-2 from elastic electron scattering by detecting 3He recoil nuclei and electrons in coincidence with the High Resolution Spectrometers of the Hall A Facility at Jefferson Lab. The measurements are indicative of a second diffraction minimum for the magnetic form factor, which was predicted in the Q2 range of this experiment, and of a continuing diffractive structure for the charge form factor. The data are in qualitative agreement with theoretical calculations based on realistic interactions and accurate methods to solve the three-body nuclear problem

The Dependence of the Superconducting Transition Temperature of Organic Molecular Crystals on Intrinsically Non-Magnetic Disorder: a Signature of either Unconventional Superconductivity or Novel Local Magnetic Moment Formation

We give a theoretical analysis of published experimental studies of the effects of impurities and disorder on the superconducting transition temperature, T_c, of the organic molecular crystals kappa-ET_2X and beta-ET_2X (where ET is bis(ethylenedithio)tetrathiafulvalene and X is an anion eg I_3). The Abrikosov-Gorkov (AG) formula describes the suppression of T_c both by magnetic impurities in singlet superconductors, including s-wave superconductors and by non-magnetic impurities in a non-s-wave superconductor. We show that various sources of disorder lead to the suppression of T_c as described by the AG formula. This is confirmed by the excellent fit to the data, the fact that these materials are in the clean limit and the excellent agreement between the value of the interlayer hopping integral, t_perp, calculated from this fit and the value of t_perp found from angular-dependant magnetoresistance and quantum oscillation experiments. If the disorder is, as seems most likely, non-magnetic then the pairing state cannot be s-wave. We show that the cooling rate dependence of the magnetisation is inconsistent with paramagnetic impurities. Triplet pairing is ruled out by several experiments. If the disorder is non-magnetic then this implies that l>=2, in which case Occam's razor suggests that d-wave pairing is realised. Given the proximity of these materials to an antiferromagnetic Mott transition, it is possible that the disorder leads to the formation of local magnetic moments via some novel mechanism. Thus we conclude that either kappa-ET_2X and beta-ET_2X are d-wave superconductors or else they display a novel mechanism for the formation of localised moments. We suggest systematic experiments to differentiate between these scenarios.Comment: 18 pages, 5 figure

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources

The current issue of Nucleic Acids Research includes descriptions of 58 new and 73 updated data resources. The accompanying online Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, now lists 1230 carefully selected databases covering various aspects of molecular and cell biology. While most data resource descriptions remain very brief, the issue includes several longer papers that highlight recent significant developments in such databases as Pfam, MetaCyc, UniProt, ELM and PDBe. The databases described in the Database Issue and Database Collection, however, are far more than a distinct set of resources; they form a network of connected data, concepts and shared technology. The full content of the Database Issue is available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/)