Anaphe - OO Libraries and Tools for Data Analysis

The Anaphe project is an ongoing effort to provide an Object Oriented software environment for data analysis in HENP experiments. A range of commercial and public domain libraries is used to cover basic functionalities; on top of these libraries a set of HENP-specific C++ class libraries for histogram management, fitting, plotting and ntuple-like data analysis has been developed. In order to comply with the user requirements for a command-line driven tool, we have chosen to use a scripting language (Python) as the front-end for a data analysis tool. The loose coupling provided by the consequent use of (AIDA compliant) Abstract Interfaces for each component in combination with the use of shared libraries for their implementation provides an easy integration of existing libraries into modern scripting languages thus allowing for rapid application development. This integration is simplified even further using a specialised toolkit (SWIG) to create "shadow classes" for the Python language, which map the definitions of the Abstract Interfaces almost at a one-to-one level. This paper will give an overview of the architecture and design choices and will present the current status and future developments of the project

The QCD phase diagram at nonzero quark density

We determine the phase diagram of QCD on the \mu-T plane for small to moderate chemical potentials. Two transition lines are defined with two quantities, the chiral condensate and the strange quark number susceptibility. The calculations are carried out on N_t =6,8 and 10 lattices generated with a Symanzik improved gauge and stout-link improved 2+1 flavor staggered fermion action using physical quark masses. After carrying out the continuum extrapolation we find that both quantities result in a similar curvature of the transition line. Furthermore, our results indicate that in leading order the width of the transition region remains essentially the same as the chemical potential is increased.Comment: 12 pages, 6 figure

POOL development status and production experience

The pool of persistent objects for LHC (POOL) project, part of the large Hadron collider (LHC) computing grid (LCG), is now entering its third year of active development. POOL provides the baseline persistency framework for three LHC experiments. It is based on a strict component model, insulating experiment software from a variety of storage technologies. This paper gives a brief overview of the POOL architecture, its main design principles and the experience gained with integration into LHC experiment frameworks. It also presents recent developments in the POOL works areas of relational database abstraction and object storage into relational database management systems (RDBMS) systems

Type-Specific Cervico-Vaginal Human Papillomavirus Infection Increases Risk of HIV Acquisition Independent of Other Sexually Transmitted Infections

Sexually transmitted infections (STIs) such as herpes simplex virus (HSV)-2 are associated with an increased risk of HIV infection. Human papillomavirus (HPV) is a common STI, but little is know about its role in HIV transmission. The objective of this study was to determine whether cervico-vaginal HPV infection increases the risk of HIV acquisition in women independent of other common STIs.This prospective cohort study followed 2040 HIV-negative Zimbabwean women (average age 27 years, range 18-49 years) for a median of 21 months. Participants were tested quarterly for 29 HPV types (with L1 PCR primers) and HIV (antibody testing on blood samples with DNA or RNA PCR confirmation). HIV incidence was 2.7 per 100 woman-years. Baseline HPV prevalence was 24.5%, and the most prevalent HPV types were 58 (5.0%), 16 (4.7%), 70 (2.4%), and 18 (2.3%). In separate regression models adjusting for baseline variables (including age, high risk partner, positive test for STIs, positive HSV-2 serology and condom use), HIV acquisition was associated with having baseline prevalent infection with HPV 58 (aHR 2.13; 95% CI 1.09-4.15) or HPV 70 (aHR 2.68; 95% CI 1.08-6.66). In separate regression models adjusting for both baseline variables and time-dependent variables (including HSV-2 status, incident STIs, new sexual partner and condom use), HIV acquisition was associated with concurrent infection with any non-oncogenic HPV type (aHR 1.70; 95% CI 1.02-2.85), any oncogenic HPV type (aHR 1.96; 95% CI 1.16-3.30), HPV 31 (aHR 4.25; 95% CI 1.81-9.97) or HPV 70 (aHR 3.30; 95% CI 1.50-7.20). Detection of any oncogenic HPV type within the previous 6 months was an independent predictor of HIV acquisition, regardless of whether HPV status at the HIV acquisition visit was included (aHR 1.95; 95% CI 1.19-3.21) or excluded (aHR 1.96; 95% CI 1.02-2.85) from the analysis.Cervico-vaginal HPV infection was associated with an increased risk of HIV acquisition in women, and specific HPV types were implicated in this association. The observational nature of our study precludes establishment of causation between HPV infection and HIV acquisition. However, given the high prevalence of HPV infection in women, further investigation of the role of HPV in HIV transmission is warranted

Ocean forests: breakthrough yields for macroalgae

The US Department of Energy Advanced Research Projects Agency - Energy (ARPA-E) MacroAlgae Research Inspiring Novel Energy Research (MARINER) program is encouraging technologies for the sustainable harvest of large funding research of macroalgae for biofuels at less than $80 per dry metric ton (DMT). The Ocean Forests team, led by the University of Southern Mississippi, is developing a complete managed ecosystem where nutrients are transformed and recycled. The team’s designs address major bottlenecks in profitability of offshore aquaculture systems including economical moored structures that can withstand storms, efficient planting, managing and harvesting systems, and sustainable nutrient supply. The work is inspired by Lapointe who reported yields of Gracilaria tikvahiae equivalent to 127 DMT per hectare per year (compared with standard aquaculture systems in the range of 20 to 40 DMT/ha/yr). This approach offers the potential for breakthrough yields for many macroalgae species. Moreover, mini-ecosystems in offshore waters create communities of macroalgae, shellfish, and penned finfish, supplemented by visiting free-range fish that can increase productivity, produce quality products, and create jobs and income for aquafarmers. Additional benefits include reduced disease in fish pens, cleaning contaminated coastal waters, and maximizing nutrient recycling. Cost projections for a successful, intensive, scaled system are competitive with current prices for fossil fuels

Tracking the Impact of Excisional Cervical Treatment on the Cervix using Biospectroscopy

Local excisional treatment for cervical intra-epithelial neoplasia (CIN) is linked to significant adverse sequelae including preterm birth, with cone depth and radicality of treatment correlating to the frequency and severity of adverse events. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy can detect underlying cervical disease more accurately than conventional cytology. The chemical profile of cells pre- and post-treatment may differ as a result of altered biochemical processes due to excision, or treatment of the disease. Since pre-treatment cervical length varies amongst women, the percentage of cervix excised may correlate more accurately to risk than absolute dimensions. We show that treatment for CIN significantly alters the biochemistry of the cervix, compared with women who have not had treatment; this is due to the removal of cervical tissue rather than the removal of the disease. However, the spectra do not seem to correlate to the cone depth or proportion of cervical length excised. Future research should aim to explore the impact of treatment in a larger cohort

The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions

Emerging evidence suggests associations between the vaginal microbiota (VMB) composition, human papillomavirus (HPV) infection, and cervical intraepithelial neoplasia (CIN); however, causal inference remains uncertain. Here, we use bacterial DNA sequencing from serially collected vaginal samples from a cohort of 87 adolescent and young women aged 16–26 years with histologically confirmed, untreated CIN2 lesions to determine whether VMB composition affects rates of regression over 24 months. We show that women with a Lactobacillus-dominant microbiome at baseline are more likely to have regressive disease at 12 months. Lactobacillus spp. depletion and presence of specific anaerobic taxa including Megasphaera, Prevotella timonensis and Gardnerella vaginalis are associated with CIN2 persistence and slower regression. These findings suggest that VMB composition may be a future useful biomarker in predicting disease outcome and tailoring surveillance, whilst it may offer rational targets for the development of new prevention and treatment strategies

Reduced expression of tissue factor pathway inhibitor-2 contributes to apoptosis and angiogenesis in cervical cancer

<p>Abstract</p> <p>Background</p> <p>Tissue factor pathway inhibitor-2 (TFPI-2) is an extracellular matrix associated broad-spectrum Kunitz-type serine proteinase inhibitor. Recently, down regulation of TFPI-2 was suggested to be involved in tumor invasion and metastasis in some cancers.</p> <p>Methods</p> <p>This study involved 12 normal cervical squamous epithelia, 48 cervical intraepithelial neoplasia (CIN), and 68 cervical cancer. The expression of TFPI-2, Ki-67 and vascular endothelial growth factor (VEGF) were investigated by immunohistochemistry staining. The apoptolic index(AI) was determined with an in situ end-labeling assay(TUNEL). And the marker of CD34 staining was used as an indicator of microvessel density (MVD).</p> <p>Results</p> <p>TFPI-2 expression has a decreasing trend with the progression of cervical cancer and was significantly correlated with FIGO stage, lymph node metastasis and HPV infection. In addition, there were significant positive correlations between the grading of TFPI-2 expression and AI(P = 0.004). In contrast, the expression of TFPI-2 and VEGF or MVD was negatively correlated (both p < 0.001). However, we did not establish any significant correlation between Ki-67 and TFPI-2 expression in cervical cancer.</p> <p>Conclusions</p> <p>The results suggested that the expression of TFPI-2 had a decreasing trend with tumor progression of cervical cancer. There was a close association between the expression of TFPI-2 and tumor cell apoptosis and angiogenesis in patients with cervical cancer. TFPI-2 may play an inhibitive role during the development of cervical cancer.</p

Comparison of vaginal microbiota sampling techniques: Cytobrush versus swab

© 2017 The Author(s). Evidence suggests the vaginal microbiota (VM) may influence risk of persistent Human Papillomavirus (HPV) infection and cervical carcinogenesis. Established cytology biobanks, typically collected with a cytobrush, constitute a unique resource to study such associations longitudinally. It is plausible that compared to rayon swabs; the most commonly used sampling devices, cytobrushes may disrupt biofilms leading to variation in VM composition. Cervico-vaginal samples were collected with cytobrush and rayon swabs from 30 women with high-grade cervical precancer. Quantitative PCR was used to compare bacterial load and Illumina MiSeq sequencing of the V1-V3 regions of the 16S rRNA gene used to compare VM composition. Cytobrushes collected a higher total bacterial load. Relative abundance of bacterial species was highly comparable between sampling devices (R 2 = 0.993). However, in women with a Lactobacillus-depleted, high-diversity VM, significantly less correlation in relative species abundance was observed between devices when compared to those with a Lactobacillus species-dominant VM (p = 0.0049). Cytobrush and swab sampling provide a comparable VM composition. In a small proportion of cases the cytobrush was able to detect underlying high-diversity community structure, not realized with swab sampling. This study highlights the need to consider sampling devices as potential confounders when comparing multiple studies and datasets