Natural history of cervicovaginal papillomavirus infection in young women

BACKGROUND

Genital human papillomavirus (HPV) infection is highly prevalent in sexually active young women. However, precise risk factors for HPV infection and its incidence and duration are not well known.

METHODS

We followed 608 college women at six-month intervals for three years. At each visit, we collected information about lifestyle and sexual behavior and obtained cervicovaginal-lavage samples for the detection of HPV DNA by polymerase chain reaction and Southern blot hybridization. Pap smears were obtained annually.

RESULTS

The cumulative 36-month incidence of HPV infection was 43 percent (95 percent confidence interval, 36 to 49 percent). An increased risk of HPV infection was significantly associated with younger age, Hispanic ethnicity, black race, an increased number of vaginal-sex partners, high frequencies of vaginal sex and alcohol consumption, anal sex, and certain characteristics of partners (regular partners having an increased number of lifetime partners and not being in school). The median duration of new infections was 8 months (95 percent confidence interval, 7 to 10 months). The persistence of HPV for > or =6 months was related to older age, types of HPV associated with cervical cancer, and infection with multiple types of HPV but not with smoking. The risk of an abnormal Pap smear increased with persistent HPV infection, particularly with high-risk types (relative risk, 37.2; 95 percent confidence interval, 14.6 to 94.8).

CONCLUSIONS

The incidence of HPV infection in sexually active young college women is high. The short duration of most HPV infections in these women suggests that the associated cervical dysplasia should be managed conservatively.

Sexual behavior and partner characteristics are the predominant risk factors for genital human papillomavirus infection in young women

Risk factors for cervicovaginal human papillomavirus (HPV) infection were investigated in 604 college women. HPV was detected in 168 (27.8%) of the subjects by L1 consensus primer polymerase chain reaction, Southern blot hybridization, or both. Significant independent risk factors for HPV (P < .05) included age (odds ratios [ORs]: 2.6 for 21-23 years old and 1.6 for > 23, vs. < or = 20), ethnicity (ORs: 3.2 for black, 2.2 for Hispanic, vs. white/other), number of lifetime male vaginal sex partners (ORs: 4.5 for 2, 5.8 for 3 or 4, 10.3 for > or = 5, vs. 1), living with smokers (OR: 1.9), male partner's number of lifetime sex partners (ORs: 2.1 for 2 or 3, 3.1 for 4-10, 2.7 for > or = 11, vs. 1), duration of sexual relationship for > 12 months (OR: 0.6), and male partner currently in college (OR: 0.6). These data demonstrate that the predominant risk factors for genital HPV infection in young women are related not only to their own sexual behaviors but also to those of their male partners.

Antifungal properties of electrically generated metallic ions

A qualitative and quantitative investigation was undertaken to study the susceptibility of unicellular eucaryotic organisms (yeasts) to metallic cations generated by low levels of direct current. Results were characteristic of effects obtained previously using clinical and standard bacteria test organisms. The present study demonstrated that anodic silver (Ag(+)) at low direct currents had inhibitory and fungicidal properties. Broth dilution susceptibility tests were made on several species of Candida and one species of Torulopsis. Growth in all isolates was inhibited by concentrations of electrically generated silver ions between 0.5 and 4.7 mug/ml, and silver exhibited fungicidal properties at concentrations as low as 1.9 mug/ml. The inhibitory and fungicidal concentrations of electrically generated silver ions are lower than those reported for other silver compounds.

Statistical algorithms improve accuracy of gene fusion detection

Gene fusions are known to play critical roles in tumor pathogenesis. Yet, sensitive and specific algorithms to detect gene fusions in cancer do not currently exist. In this paper, we present a new statistical algorithm, MACHETE (Mismatched Alignment CHimEra Tracking Engine), which achieves highly sensitive and specific detection of gene fusions from RNA-Seq data, including the highest Positive Predictive Value (PPV) compared to the current state-of-the-art, as assessed in simulated data. We show that the best performing published algorithms either find large numbers of fusions in negative control data or suffer from low sensitivity detecting known driving fusions in gold standard settings, such as EWSR1-FLI1. As proof of principle that MACHETE discovers novel gene fusions with high accuracy in vivo, we mined public data to discover and subsequently PCR validate novel gene fusions missed by other algorithms in the ovarian cancer cell line OVCAR3. These results highlight the gains in accuracy achieved by introducing statistical models into fusion detection, and pave the way for unbiased discovery of potentially driving and druggable gene fusions in primary tumors.

Characterization of plantar verrucae among individuals with human immunodeficiency virus

Plantar verrucae, caused by human papillomavirus (HPV), are commonly found in patients who have tested positive for the antibodies to human immunodeficiency virus (HIV). A better understanding of the characteristics of plantar verrucae in HIV+ patients in needed. A pilot study was conducted concentrating on three characteristics--the size, the number, and the clinical type--of verrucae present in this population. These parameters were studied in HIV+ and HIV- populations, and they were evaluated in relation to the CD4 levels of HIV+ individuals. The HIV+ individuals presented with plantar verrucae that were larger and more numerous than those found in HIV- individuals. The HIV+ population presented with all three clinical types of plantar verrucae and had significantly more mosaic-type warts than did HIV- individuals. The three characteristics did not correlate with CD4 cell counts, suggesting that the severity and extent of HPV infection do not depend on the level of immunosuppression of the HIV+ patient.

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.

Development of a multi-item scale to quantitatively assess sexual behaviors and the transmission of high- and low-risk human papillomaviruses

BACKGROUND

Epidemiologic research is frequently hindered by the inherent difficulty in quantifying the risk of sexually transmitted disease (STD) acquisition associated with individual patterns of sexual behavior.

GOAL OF THE STUDY

To develop a quantitative sexual behavior risk scale and demonstrate its predictive validity in an assessment of risk factors for incident infection with human papillomaviruses (HPVs).

STUDY DESIGN

Data from a prospective study of HPV infection in female university students was used to generate quantitative multi-item sexual behavior scales which were used in Cox regression analyses.

RESULTS

Although risk was incurred both in casual sexual encounters and in noncasual relationships, risk in these contexts were only weakly correlated. The construction of separate measurement scales was performed.

CONCLUSIONS

Improved precision of measurement of STD risk demonstrated that significant risk was associated with different patterns of sexual behavior and was incurred in both casual and/or noncasual relationships. Scores on the sexual behavior risk scales were highly predictive of incident infection with HPV types of both high and low oncogenic potential.

Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung

Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.

Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation

Targeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Furthermore, these studies link localization to RNA isoform expression, especially 3' Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enables the potential to test if subcellular localization is regulated in situ pervasively. In order to do this, robust statistical measures of subcellular localization and alternative poly-adenylation (APA) at single-cell resolution are needed. Developing a new statistical framework called SPRAWL, we detect extensive cell-type specific subcellular RNA localization regulation in the mouse brain and to a lesser extent mouse liver. We integrated SPRAWL with a new approach to measure cell-type specific regulation of alternative 3' UTR processing and detected examples of significant correlations between 3' UTR length and subcellular localization. Included examples, Timp3, Slc32a1, Cxcl14, and Nxph1 have subcellular localization in the mouse brain highly correlated with regulated 3' UTR processing that includes the use of unannotated, but highly conserved, 3' ends. Together, SPRAWL provides a statistical framework to integrate multi-omic single-cell resolved measurements of gene-isoform pairs to prioritize an otherwise impossibly large list of candidate functional 3' UTRs for functional prediction and study. In these studies of data from mice, SPRAWL predicts that 3' UTR regulation of subcellular localization may be more pervasive than currently known.

Radiographic and neuro-SPECT imaging in an immature third ventricle teratoma: case report

We report a case of an immature teratoma of the third ventricle, which was preoperatively thought to be a choroid plexus papilloma. The diagnosis was made by biopsy since the radiographic (CT, MRI), angiographic and scintigraphic findings ([99mTc]pertechnetate, 99mTc-DTPA, 99mTc-HMPAO brain SPECT) were nonspecific. Disruption of the blood-brain barrier is the mechanism for radionuclidic and contrast tumoral uptake and is demonstrated by marked contrast enhancement on CT and focal concentration on [99mTc]pertechnetate and 99mTc-DTPA images. No suppression of [99mTc]pertechnetate tumor uptake was observed following the administration of potassium perchlorate. Increased concentration of tumor protein is suggested by the increased signal on the T1-weighted magnetic resonance images and high [99mTc]pertechnetate uptake. The tumor's detection on the 99mTc-HMPAO brain SPECT was due to its intraventricular location. A number of potential mechanisms for brain tumor localization of 99mTc-HMPAO are discussed.

Landscape of human protein-coding somatic mutations across tissues and individuals

Although somatic mutations are fundamentally important to human biology, disease, and aging, many outstanding questions remain about their rates, spectrum, and determinants in apparently healthy tissues. Here, we performed high-coverage exome sequencing on 265 samples from 14 GTEx donors sampled for a median of 17.5 tissues per donor (spanning 46 total tissues). Using a novel probabilistic method tailored to the unique structure of our data, we identified 8,470 somatic variants. We leverage our compendium of somatic mutations to quantify the burden of deleterious somatic variants among tissues and individuals, identify molecular features such as chromatin accessibility that exhibit significantly elevated somatic mutation rates, provide novel biological insights into mutational mechanisms, and infer developmental trajectories based on patterns of multi-tissue somatic mosaicism. Our data provides a high-resolution portrait of somatic mutations across genes, tissues, and individuals.