Understanding the relationship between local environmental changes and the function of the pH Low Insertion Peptide

Cancer is the second leading cause of death in the US with over 1.7 million new cases each year. Current cancer treatments tend to also target healthy tissues due to similarities with cancerous ones, resulting in acute side effects. Early detection is the best approach towards defeating cancer, however, modern imaging techniques require sizeable samples, often implying a late stage in the disease. One common attribute of tumors is their acidic microenvironment, which can be taken advantage of. The pH Low Insertion Peptide (pHLIP) is a membrane-active peptide that can take advantage of the acidic microenvironment surrounding cancer cells. pHLIP can spontaneously fold and insert unidirectionally as a transmembrane into lipid membranes under acidic conditions. Thus, pHLIP is able to transport drugs across cancerous membranes and deliver it to the interior of the cell. Although the mechanism of insertion and exit of the peptide has been thoroughly studied through experimental and computational approaches, there are still elements of the peptide and its behavior that are not fully understood. This dissertation focuses on all-atoms molecular dynamics (MD) simulations to study the interactions between pHLIP and its environmental factors. Through High Performance Computing (HPC) at West Virginia University (WVU), we were able to map the initial stages of exit of pHLIP, determine the effect of peptide insertion on the dynamics of a complex lipid bilayer and provide new insights into the environmental factors affecting pHLIP in solution. The results reported in this dissertation will aid the future development of pHLIP-based early detection and targeting agents

The sexual attitudes and lifestyles of London's Eastern Europeans (SALLEE Project): design and methods.

BACKGROUND: Since May 2004, ten Central and Eastern European (CEE) countries have joined the European Union, leading to a large influx of CEE migrants to the United Kingdom (UK). The SALLEE project (sexual attitudes and lifestyles of London's Eastern Europeans) set out to establish an understanding of the sexual lifestyles and reproductive health risks of CEE migrants. CEE nationals make up a small minority of the population resident in the UK with no sampling frame from which to select a probability sample. There is also difficulty estimating the socio-demographic and geographical distribution of the population. In addition, measuring self-reported sexual behaviour which is generally found to be problematic, may be compounded among people from a range of different cultural and linguistic backgrounds. This paper will describe the methods adopted by the SALLEE project to address these challenges. METHODS: The research was undertaken using quantitative and qualitative methods: a cross-sectional survey of CEE migrants based on three convenience samples (recruited from community venues, sexual health clinics and from the Internet) and semi-structured in-depth interviews with a purposively selected sample of CEE migrants. A detailed social mapping exercise of the CEE community was conducted prior to commencement of the survey to identify places where CEE migrants could be recruited. A total of 3,005 respondents took part in the cross-sectional survey, including 2,276 respondents in the community sample, 357 in the clinic sample and 372 in the Internet sample. 40 in-depth qualitative interviews were undertaken with a range of individuals, as determined by the interview quota matrix. DISCUSSION: The SALLEE project has benefited from using quantitative research to provide generalisable data on a range of variables and qualitative research to add in-depth understanding and interpretation. The social mapping exercise successfully located a large number of CEE migrants for the community sample and is recommended for other migrant populations, especially when little or no official data are available for this purpose. The project has collected timely data that will help us to understand the sexual lifestyles, reproductive health risks and health service needs of CEE communities in the UK

The impact of migration on the sexual health, behaviours and attitudes of Central and East European gay/bisexual men in London

Extensive social psychological research emphasises the importance of groups in shaping individuals' thoughts and actions. Within the child sexual abuse (CSA) literature criminal organisation has been largely overlooked, with some key exceptions. This research was a novel collaboration between academia and the UK's Child Exploitation and Online Protection Centre (CEOP). Starting from the premise that the group is, in itself, a form of social situation affecting abuse, it offers the first systematic situational analysis of CSA groups. In-depth behavioural data from a small sample of convicted CSA group-offenders (n =3) were analysed qualitatively to identify factors and processes underpinning CSA groups' activities and associations: group formation, evolution, identity and resources. The results emphasise CSA groups' variability, fluidity and dynamism. The foundations of a general framework are proposed for researching and assessing CSA groups and designing effective interventions. It is hoped that this work will stimulate discussion and development in this long-neglected area of CSA, helping to build a coherent knowledge-base

Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure

Interdependence across time and length scales is common in biology, where atomic interactions can impact larger-scale phenomenon. Such dependence is especially true for a well-known cancer signaling pathway, where the membrane-bound RAS protein binds an effector protein called RAF. To capture the driving forces that bring RAS and RAF (represented as two domains, RBD and CRD) together on the plasma membrane, simulations with the ability to calculate atomic detail while having long time and large length- scales are needed. The Multiscale Machine-Learned Modeling Infrastructure (MuMMI) is able to resolve RAS/RAF protein-membrane interactions that identify specific lipid-protein fingerprints that enhance protein orientations viable for effector binding. MuMMI is a fully automated, ensemble-based multiscale approach connecting three resolution scales: (1) the coarsest scale is a continuum model able to simulate milliseconds of time for a 1 μm2 membrane, (2) the middle scale is a coarse-grained (CG) Martini bead model to explore protein-lipid interactions, and (3) the finest scale is an all-atom (AA) model capturing specific interactions between lipids and proteins. MuMMI dynamically couples adjacent scales in a pairwise manner using machine learning (ML). The dynamic coupling allows for better sampling of the refined scale from the adjacent coarse scale (forward) and on-the-fly feedback to improve the fidelity of the coarser scale from the adjacent refined scale (backward). MuMMI operates efficiently at any scale, from a few compute nodes to the largest supercomputers in the world, and is generalizable to simulate different systems. As computing resources continue to increase and multiscale methods continue to advance, fully automated multiscale simulations (like MuMMI) will be commonly used to address complex science questions

Central and East European migrant men who have sex with men in London: a comparison of recruitment methods

Background: Following the expansion of the European Union, there has been a large influx of Central and East European (CEE) migrants to the UK. CEE men who have sex with men (MSM) represent a small minority within this population that are none-the-less important to capture in sexual health research among the CEE migrant community. This paper examines the feasibility of recruiting CEE MSM for a survey of sexual behaviour in London using respondent driven sampling (RDS), via gay websites and in GUM clinics.Methods: We sought CEE MSM to start RDS chain referral among GUM clinic attendees, our personal contacts and at gay events and venues in central London. We recruited CEE MSM (n = 485) via two popular websites for gay men in Britain (March-May 2009) and at two central London GUM clinics (n = 51) (July 2008-March 2009).Results: We found seventeen men who knew other CEE MSM in London and agreed to recruit contacts into the study. These men recruited only three men into the study, none of whom recruited any further respondents, and RDS was abandoned after 7 months (July 2008-January 2009). Half of the men that we approached to participate in RDS did not know any other CEE MSM in London. Men who agreed to recruit contacts for RDS were rather more likely to have been in the UK for more than one year (94.1% vs 70.0%, p = 0.052). Men recruited through gay websites and from GUM clinics were similar.Conclusions: The Internet was the most successful method for collecting data on sexual risk behaviour among CEE MSM in London. CEE MSM in London were not well networked. RDS may also have failed because they did not fully understand the procedure and/or the financial incentive was not sufficient motivation to take part

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Sexual and HIV risk behaviour in central and eastern European migrants in London.

BACKGROUND: Accession of 10 Central and Eastern European (CEE) countries to the E.U. resulted in the largest migratory influx in peacetime British history. No information exists on the sexual behaviour of CEE migrants within the U.K. The aim of this study was to assess the sexual lifestyles and health service needs of these communities. METHODS: A survey, delivered electronically and available in 12 languages, of migrants from the 10 CEE accession countries recruited from community venues in London following extensive social mapping and via the Internet. Reported behaviours were compared with those from national probability survey data. RESULTS: 2648 CEE migrants completed the survey. Male CEE migrants reported higher rates of partner acquisition (adjusted OR (aOR) 2.1, 95% CI: 1.3 to 2.1) and paying for sex (aOR 3.2, 95% CI: 2.5 to 4.0), and both male and female CEE migrants reported more injecting drug use (men: aOR 2.2, 95% CI: 1.3 to 3.9; women: aOR 3.0, 95% CI 1.1 to 8.1), than the general population; however, CEE migrants were more likely to report more consistent condom use and lower reported diagnoses of sexually transmitted infections (STI). Just over 1% of respondents reported being HIV positive. Most men and a third of women were not registered for primary care in the U.K. DISCUSSION: CEE migrants to London report high rates of behaviours associated with increased risk of HIV/STI acquisition and transmission. These results should inform service planning, identify where STI and HIV interventions should be targeted, and provide baseline data to help evaluate the effectiveness of such interventions