Proposed best practice for projects that involve modelling and simulation

Modelling and simulation has been used in many ways when developing new treatments. To be useful and credible, it is generally agreed that modelling and simulation should be undertaken according to some kind of best practice. A number of authors have suggested elements required for best practice in modelling and simulation. Elements that have been suggested include the pre-specification of goals, assumptions, methods, and outputs. However, a project that involves modelling and simulation could be simple or complex and could be of relatively low or high importance to the project. It has been argued that the level of detail and the strictness of pre-specification should be allowed to vary, depending on the complexity and importance of the project. This best practice document does not prescribe how to develop a statistical model. Rather, it describes the elements required for the specification of a project and requires that the practitioner justify in the specification the omission of any of the elements and, in addition, justify the level of detail provided about each element. This document is an initiative of the Special Interest Group for modelling and simulation. The Special Interest Group for modelling and simulation is a body open to members of Statisticians in the Pharmaceutical Industry and the European Federation of Statisticians in the Pharmaceutical Industry. Examples of a very detailed specification and a less detailed specification are included as appendices

Visualizing genetic constraints

Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, evolutionary biologists gain important insights from these low variation directions. Specifically, they are interested in directions of low genetic variability that are biologically interpretable. These directions are called genetic constraints and indicate directions in which a trait cannot evolve through selection. Here, we propose studying the subspace spanned by low variance principal components by determining vectors in this subspace that are simplest. Our method and accompanying graphical displays enhance the biologist's ability to visualize the subspace and identify interpretable directions of low genetic variability that align with simple directions.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS603 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A paperfluidic platform to detect Neisseria gonorrhoeae in clinical samples

Globally, the microbe Neisseria gonorrhoeae (NG) causes 106 million newly documented sexually transmitted infections each year. Once appropriately diagnosed, NG infections can be readily treated with antibiotics, but high-risk patients often do not return to the clinic for treatment if results are not provided at the point of care. A rapid, sensitive molecular diagnostic would help increase NG treatment and reduce the prevalence of this sexually transmitted disease. Here, we report on the design and development of a rapid, highly sensitive, paperfluidic device for point-of-care diagnosis of NG. The device integrates patient swab sample lysis, nucleic acid extraction, thermophilic helicase-dependent amplification (tHDA), an internal amplification control (NGIC), and visual lateral flow detection within an 80 min run time. Limits of NG detection for the NG/NGIC multiplex tHDA assay were determined within the device, and clinical performance was validated retroactively against qPCR-quantified patient samples in a proof-of-concept study. This paperfluidic diagnostic has a clinically relevant limit of detection of 500 NG cells per device with analytical sensitivity down to 10 NG cells per device. In triplicate testing of 40 total urethral and vaginal swab samples, the device had 95% overall sensitivity and 100% specificity, approaching current laboratory-based molecular NG diagnostics. This diagnostic platform could increase access to accurate NG diagnoses to those most in need.This work was funded by the National Institute of Health National Institute of Allergy and Infectious Diseases award number R01 AI113927 to Boston University and the NIH National Institute of Biomedical and Bioengineering award number U54 EB007958 to Johns Hopkins University. (R01 AI113927 - National Institute of Health National Institute of Allergy and Infectious Diseases; U54 EB007958 - NIH National Institute of Biomedical and Bioengineering)Accepted manuscrip

Prevalence and correlates of Trichomonas vaginalis infection among female US federal prison inmates

BACKGROUND: Previous studies have observed high prevalences of Trichomonas vaginalis infection among women entering US jails and state prisons (22%–47%). We sought to determine the prevalence among women incarcerated in 2 US female-only federal prisons. METHODS: Female inmates were recruited at 2 prisons (n = 624). Participants completed a self-administered questionnaire and provided self-collected first-catch urine and vaginal swab specimens. Specimens were tested for T. vaginalis DNA. RESULTS: Approximately 8.5% of participants at the first prison, and 8.3% at the second prison had a positive urine result, vaginal swab result or both, for a combined prevalence of 8.5%. Using positivity in either specimen as the reference standard, urine polymerase chain reaction had a sensitivity of 66.7% and vaginal swab polymerase chain reaction had a sensitivity of 84.4%. The only significant positive correlate of T. vaginalis infection was lower household income before arrest. Other variables nonsignificantly positively correlated with T. vaginalis were being employed at the time of arrest, having experienced sexual, physical, or emotional abuse by a family member, having a parent who had not had a drug or alcohol addiction, never exchanging sex for money or drugs, ever being pregnant, having abnormal vaginal bleeding/spotting, and having concurrent chlamydia or gonorrhea. CONCLUSIONS: Although not as high as in other studies of women entering US jails and state prisons, our observed T. vaginalis prevalence of 8.5% was much higher than in the general US population. Therefore, screening for T. vaginalis infection may be warranted at federal prison entry, as well as sexual health education during prison stay

Longitudinal Analysis of Antibody Responses to Trachoma Antigens Before and After Mass Drug Administration.

Blinding trachoma, caused by the bacteria Chlamydia trachomatis, is a neglected tropical disease targeted for elimination by 2020. A major component of the elimination strategy is mass drug administration (MDA) with azithromycin. Currently, program decisions are made based on clinical signs of ocular infection, but we have been investigating the use of antibody responses for post-MDA surveillance. In a previous study, IgG responses were detected in children lacking clinical evidence of trachoma, suggesting that IgG responses represented historical infection. To explore the utility of serology for program evaluation, we compared IgG and IgA responses to trachoma antigens and examined changes in IgG and IgA post-drug treatment. Dried blood spots and ocular swabs were collected with parental consent from 264 1-6 year olds in a single village of Kongwa District, central Tanzania. Each child also received an ocular exam for detection of clinical signs of trachoma. MDA was given, and six months later an additional blood spot was taken from these same children. Ocular swabs were analyzed for C. trachomatis DNA and antibody responses for IgA and total IgG were measured in dried bloods spots. Baseline antibody responses showed an increase in antibody levels with age. By age 6, the percentage positive for IgG (96.0%) was much higher than for IgA (74.2%). Antibody responses to trachoma antigens declined significantly six months after drug treatment for most age groups. The percentage decrease in IgA response was much greater than for IgG. However, no instances of seroreversion were observed. Data presented here suggest that focusing on concordant antibody responses in children will provide the best serological surveillance strategy for evaluation of trachoma control programs

Screening of Chlamydia trachomatis urogenital infections among the male and female population of the Republic of Macedonia

Noninvasive urine screening for Chlamydia trachomatis infections offers a valuable public health tool, that could be of vast importance in Chlamydia control programs. The goal was to determine the prevalence of C. trachomatis infections among a sexually active population, to define the epidemiological factors associated with it, and to develop potential selective screening strategies among asymptomatic individuals in the Republic of Macedonia, using a highly sensitive and specific DNA amplification method for C. trachomatis. A total of 1435 urine samples, divided into two main groups: asymptomatic individuals (n = 1210) and symptomatic patients (n = 225), were tested. Samples from the asymptomatic group were collected during routine screening programs, while the symptomatic group consisted of patients with symptoms of urogenital tract infection, attending sexually transmitted diseases (STD) clinics. The presence of C. trachomatis was determined using commercial AMPLICOR C. trachomatis Assay (Roche Diagnostic Systems, Inc., Branchburg, NJ, USA). The prevalence of C. trachomatis infections among different groups was: recruits 0%, soldiers 0.4%, policemen 3.5%, clerks 4.6%, pregnant women 4%, and students 4.4%. The average prevalence for both groups (asymptomatic and symptomatic) was 2.3%[95% confidence interval (CI): 1.5-3.1%]. The average prevalence for the asymptomatic group was 1.6% (95% CI: 0.8-2.4%), while the average prevalence for the symptomatic group was 6.2% (95% CI: 3.1-9.3%) which were significantly different (P = 0.00003). Testing first void urine specimens by AMPLICOR C. trachomatis assay is a highly sensitive and specific method for diagnosing C. trachomatis infections in men and women. This method provides health care workers and public health officials with a new molecular amplification assay that uses noninvasive urine specimens for population-based screening purposes. The prevalence of C. trachomatis was relatively low among asymptomatic individuals. However, selective screening strategies are highly recommended for testing the student population in the Republic of Macedonia. Journal of the European Academy of Dermatology and Venereology 08/2005; 19(4):427-30. • 2.69 Impact Facto

Use of the X-Band Radar to Support the Detection of In-Flight Icing Hazards by the NASA Icing Remote Sensing System

The Alliance Icing Research Study-II (AIRS-II) field program was conducted near Montreal, Canada during the winter of 2003. The NASA Icing Remote Detection System (NIRSS) was deployed to detect in-flight icing hazards and consisted of a vertically pointing multichannel radiometer, a ceilometer and an x-band cloud radar. The radiometer was used to derive atmospheric temperature soundings and integrated liquid water, while the ceilometer and radar were used only to define cloud boundaries. The purpose of this study is to show that the radar reflectivity profiles from AIRS-II case studies could be used to provide a qualitative icing hazard

Genotypic determinants of fluoroquinolone and macrolide resistance in Neisseria gonorrhoeae.

Background:High rates of antimicrobial resistance (AMR) in Neisseria gonorrhoeae hinder effective treatment, but molecular AMR diagnostics may help address the challenge. This study aimed to appraise the literature for resistance-associated genotypic markers linked to fluoroquinolones and macrolides, to identify and review their use in diagnostics. Methods: Medline and EMBASE databases were searched and data pooled to evaluate associations between genotype and phenotypic resistance. The minimum inhibitory concentration (MIC) cut-offs were ≤ 0.06 mg L-1 for non-resistance to ciprofloxacin and ≤ 0.5 mg L-1 for non-resistance to azithromycin. Results: Diagnostic accuracy estimates were limited by data availability and reporting. It was found that: 1) S91 and D95 mutations in the GyrA protein independently predicted ciprofloxacin resistance and, used together, gave 98.6% (95% confidence interval (CI) 98.0-99.0%) sensitivity and 91.4% (95%CI 88.6-93.7%) specificity; 2) the number of 23S rRNA gene alleles with C2611T or A2059G mutations was highly correlated with azithromycin resistance, with mutation in any allele giving a sensitivity and specificity of 66.1% (95%CI 62.1-70.0%) and 98.9% (95%CI 97.5-99.5%) respectively. Estimated negative (NPV) and positive predictive values (PPV) for a 23S rRNA diagnostic were 98.6% (95%CI 96.8-99.4%) and 71.5% (95%CI 68.0-74.8%) respectively; 3) mutation at amino acid position G45 in the MtrR protein independently predicted azithromycin resistance; however, when combined with 23S rRNA, did not improve the PPV or NPV. Conclusions: Viable candidates for markers of resistance detection for incorporation into diagnostics were demonstrated. Such tests may enhance antibiotic stewardship and treatment options

Rapid and point-of-care tests for the diagnosis of Trichomonas vaginalis in women and men.

BACKGROUND: Trichomonasvaginalis (TV) is a highly prevalent parasitic infection worldwide. It is associated with many adverse reproductive health outcomes. Many infections are asymptomatic and syndromic management leads to underdetection of TV. Traditional methods of TV detection such as wet preparation are insensitive. New rapid, point-of-care (POC) tests can enhance the diagnosis of trichomoniasis. METHODS: The authors reviewed the literature and discuss older POC tests for TV detection, as well as the OSOM lateral flow test, the AmpliVue test, the Solana test and the GeneXpert test as well as the limitations of wet preparation and culture for detection of TV. RESULTS: The OSOM test is easy to perform, compared with other POC tests, and is Clinical Laboratory Improvement Amendments (CLIA)-waived, equipment-free, has sensitivities of 83%-86% compared with nucleic acid amplification tests (NAATs) and can be performed in 15 min. The AmpliVue and the Solana tests are not CLIA waived and require small pieces of equipment. They are molecular amplified assays and can be completed in <1 hour. AmpliVue demonstrated a sensitivity for vaginal swabs of 100% compared with wet preparation/culture and 90.7% compared with NAATs. Solana demonstrated a sensitivity of 98.6%-100% for vaginal swabs and 92.9%-98% for female urines, compared with wet preparation/culture. Compared with other NAATs, the sensitivity for Solana was 89.7% for swabs and 100% for urine. The GeneXpert TV test for women and men is a moderately complex test, requires a small platform and can be performed in <1 hour. The sensitivity compared with wet preparation/culture for self-collected vaginal swabs was 96.4%, 98.9% for endocervical specimens and 98.4% for female urine. For men, sensitivity for urines was excellent (97.2%). The specificity for all assays was excellent. CONCLUSIONS: Several rapid POC tests have the potential to rapidly diagnose trichomoniasis in women and one is available for detection of TV in men

Accurate PCR detection of influenza A/B and respiratory syncytial viruses by use of Cepheid Xpert Flu+RSV Xpress Assay in point-of-care settings: Comparison to Prodesse ProFlu+

ABSTRACT The Xpert Flu+RSV Xpress Assay is a fast, automated in vitro diagnostic test for qualitative detection and differentiation of influenza A and B viruses and respiratory syncytial virus (RSV) performed on the Cepheid GeneXpert Xpress System. The objective of this study was to establish performance characteristics of the Xpert Flu+RSV Xpress Assay compared to those of the Prodesse ProFlu+ real-time reverse transcription-PCR (RT-PCR) assay (ProFlu+) for the detection of influenza A and B viruses as well as RSV in a Clinical Laboratory Improvement Amendments (CLIA)-waived (CW) setting. Overall, the assay, using fresh and frozen nasopharyngeal (NP) swabs, demonstrated high concordance with results of the ProFlu+ assay in the combined CW and non-CW settings with positive percent agreements (PPA) (100%, 100%, and 97.1%) and negative percent agreements (NPA) (95.2%, 99.5%, and 99.6%) for influenza A and B viruses and RSV, respectively. In conclusion, this multicenter study using the Cepheid Xpert Flu+RSV Xpress Assay demonstrated high sensitivities and specificities for influenza A and B viruses and RSV in ∼60 min for use at the point-of-care in the CW setting. </jats:p