Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model

While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb concerning oligo length, overall similarity, and continuous stretches, the final behavior is difficult to predict. The aim of this study was to investigate the effect of well-defined mismatches on hybridization specificity using CodeLink Activated Slides, and to study quantitatively the relation between hybridization intensity and Gibbs free energy (Delta G), taking the mismatches into account. Our data clearly showed a correlation between the hybridization intensity and Delta G of the oligos over three orders of magnitude for the hybridization intensity, which could be described by the Langmuir model. As Delta G was calculated according to the nearest-neighbor model, using values related to DNA hybridizations in solution, this study clearly shows that target-probe hybridizations on microarrays with a three-dimensional coating are in quantitative agreement with the corresponding reaction in solution. These results can be interesting for some practical applications. The correlation between intensity and Delta G can be used in quality control of microarray hybridizations by designing probes and corresponding RNA spikes with a range of Delta G values. Furthermore, this correlation might be of use to fine-tune oligonucleotide design algorithms in a way to improve the prediction of the influence of mismatching targets on microarray hybridizations.Comment: 32 pages on a single pdf fil

Transform-domain analysis of packet delay in network nodes with QoS-aware scheduling

In order to differentiate the perceived QoS between traffic classes in heterogeneous packet networks, equipment discriminates incoming packets based on their class, particularly in the way queued packets are scheduled for further transmission. We review a common stochastic modelling framework in which scheduling mechanisms can be evaluated, especially with regard to the resulting per-class delay distribution. For this, a discrete-time single-server queue is considered with two classes of packet arrivals, either delay-sensitive (1) or delay-tolerant (2). The steady-state analysis relies on the use of well-chosen supplementary variables and is mainly done in the transform domain. Secondly, we propose and analyse a new type of scheduling mechanism that allows precise control over the amount of delay differentiation between the classes. The idea is to introduce N reserved places in the queue, intended for future arrivals of class 1

Modelling of Strain Softening Materials Based on Equivalent Damage Force

The main aim of the work presented in this paper was addressing localisation problem observed in the analysis of strain softening materials using finite element methods (FEM) combined with local continuum damage mechanics (CDM) approach. Strain softening is typically observed in damaged quasi brittle materials such as fibre reinforced composites and application of the CDM approach with the classic FEM features a number of anomalies, including mathematical (change of the type of partial differential equations leading to ill-posed boundary value problem), numerical (pronounced mesh dependency) and physical (infinitely small softening zone with the zero dissipated energy). These features of the classic FEM solutions have been already demonstrated in (Vignjevic, Djordjevic et al. 2014). The model proposed here is still based on the local CDM approach, but introduces an alternative definition of damage effects in the system of equilibrium equations. The constitutive equation in the model is defined in terms of effective stress, whilst the damage effects in the conservation of momentum equation are calculated as equivalent damage force (EDF), which contributes to the equilibrium on the right hand side of the momentum equation. The main advantages of this model are that the problem remains well posed, as the type of partial differential equations remains unchanged when the material enters softening, numerical stability, which is preserved without a need for regularisation measures, and significantly reduced mesh dependency. In addition, the EDF model can be combined with existing local CDM damage evolution functions and does not violate symmetry of the stiffness tensor. The EDF model was implemented in in-house developed coupled FEM - MCM code, where explicit FEM (Liu 2004) is coupled with a stable TotalLagrange form of SPH (Vignjevic, Reveles et al. 2006, Vignjevic, Campbell et al. 2009). Its performance is demonstrated in the analysis of a dynamic one dimensional stress wave propagation problem, which was analytically solved in (Bazant, Belytschko 1985). For a range of loading rates that correspond to the material softening regime, the numerical results shown nonlocal character with a finite size of the damaged zone, controlled with the damage characteristic length, which can be experimentally determined and is an input parameter independent of the discretisation density.European Commissio

Comparison of pap smear, visual inspection with acetic acid, human papillomavirus DNA-PCR testing and cervicography

Objective: To assess the test qualities of four screening methods to detect cervical intra-epithelial neoplasia in an urban African setting. Method: Six hundred fiftythree women, attending a family planning clinic in Nairobi (Kenya), underwent four concurrent screening methods: pap smear, visual inspection with acetic acid (VIA), PCR for high risk human papillomavirus (HR HPV) and cervicography. The presence of cervical intra-epithelial neoplasia (CIN) was verified by colposcopy or biopsy. Result: Sensitivity (for CIN2 or higher) and specificity (to exclude any CIN or cancer) were 83.3% (95% CI [73.6, 93.0]) and 94.6% (95% CI [92.6, 96.5]), respectively, for pap smear; 73.3% (95% CI [61.8, 84.9]) and 80.0% (95% CI [76.6, 83.4]) for VIA; 94.4% (95% CI [84.6, 98.8]) and 73.9% (95% CI [69.7, 78.2]) for HR HPV; and 72.3% (95% CI [59.1, 85.6]) and 93.2% (95% CI [90.8, 95.7]) for cervicography. Conclusion: The pap smear had the highest specificity (94.6%) and HPV testing the highest sensitivity (94.4%). The visual methods, VIA and cervicography, were similar and showed an accuracy in between the former two tests

The impact of scaling up cervical cancer screening and treatment services among women living with HIV in Kenya: a modelling study

Introduction: We aimed to quantify health outcomes and programmatic implications of scaling up cervical cancer (CC) screening and treatment options for women living with HIV in care aged 18–65 in Kenya. Methods: Mathematical model comparing from 2020 to 2040: (1) visual inspection with acetic acid (VIA) and cryotherapy (Cryo); (2) VIA and Cryo or loop excision electrical procedure (LEEP), as indicated; (3) human papillomavirus (HPV)-DNA testing and Cryo or LEEP; and (4) enhanced screening technologies (either same-day HPV-DNA testing or digitally enhanced VIA) and Cryo or LEEP. Outcomes measured were annual number of CC cases, deaths, screening and treatment interventions, and engaged in care (numbers screened, treated and cured) and five yearly age-standardised incidence. Results: All options will reduce CC cases and deaths compared with no scale-up. Options 1–3 will perform similarly, averting approximately 28 000 (33%) CC cases and 7700 (27%) deaths. That is, VIA screening would yield minimal losses to follow-up (LTFU). Conversely, LTFU associated with HPV-DNA testing will yield a lower care engagement, despite better diagnostic performance. In contrast, option 4 would maximise health outcomes, averting 43 200 (50%) CC cases and 11 800 (40%) deaths, given greater care engagement. Yearly rescreening with either option will impose a substantial burden on the health system, which could be reduced by spacing out frequency to three yearly without undermining health gains. Conclusions: Beyond the specific choice of technologies to scale up, efficiently using available options will drive programmatic success. Addressing practical constraints around diagnostics’ performance and LTFU will be key to effectively avert CC cases and deaths

Residual disease and HPV persistence after cryotherapy for cervical intraepithelial neoplasia grade 2/3 in HIV positive women in Kenya

Objective: To assess residual cervical intraepithelial neoplasia (CIN) 2/3 disease and clearance of high-risk (hr) human papillomavirus (HPV) infections at 6 months after cryotherapy among HIV-positive women. Design: Follow-up study. Methods: 79 HIV-positive women received cryotherapy for CIN2/3 in Nairobi, Kenya, and underwent conventional cytology 6 months later. Biopsies were performed on high grade cytological lesions and hrHPV was assessed before (cervical cells and biopsy) and after cryotherapy (cells). Results: At 6 months after cryotherapy CIN2/3 had been eliminated in 61 women (77.2%; 95% Confidence Interval, (CI):66.4–85.9). 18 women (22.8%) had residual CIN2/3, and all these women had hrHPV at baseline. CD4 count and duration of combination antiretroviral therapy (cART) were not associated with residual CIN2/3. CIN3 instead of CIN2 was the only significant risk factor for residual disease (odds ratio, OR vs CIN2 = 4.3; 95% CI: 1.2–15.0) among hrHPV-positive women after adjustment for age and HPV16 infection. Persistence of hrHPV types previously detected in biopsies was found in 77.5% of women and was associated with residual CIN2/3 (OR = 8.1, 95% CI: 0.9–70). The sensitivity, specificity, and negative predictive value of hrHPV test in detecting residual CIN2/3 were 0.94, 0.36, and 0.96 respectively. Conclusions: Nearly one quarter of HIV-positive women had residual CIN2/3 disease at 6 months after cryotherapy, and the majority had persistent hrHPV. CD4 count and cART use were not associated with residual disease or hrHPV persistence. The value of hrHPV testing in the detection of residual CIN2/3 was hampered by a low specificity

Prevalence and determinants of human papillomavirus infection and cervical lesions in HIV-positive women in Kenya

Background: We assessed the association of human papillomavirus (HPV) infection and cervical intraepithelial neoplasia (CIN) with various characteristics, CD4 count and use of combination antiretroviral therapy (cART) among HIV-positive women. Methods: Cross-sectional study of 498 HIV-positive women who underwent HPV PCR-based testing, cytology, and systematic cervical biopsy. Results: In all, 68.7% of women were HPV-positive, 52.6% had high-risk (hr) HPV, and 40.2% multiple type infections. High-risk human papillomavirus-positivity did not vary significantly by age but it was negatively associated with education level. The most frequent types in 113 CIN2/3 were HPV16 (26.5%), HPV35 (19.5%), and HPV58 (12.4%). CD4 count was negatively associated with prevalence of hrHPV (Po0.001) and CIN2/3 among non-users of cART (P¼0.013). Combination antiretroviral therapies users (X2 year) had lower hrHPV prevalence (prevalence ratio (PR) vs non-users¼0.77, 95% confidence interval (CI): 0.61–0.96) and multiple infections (PR¼0.68, 95% CI: 0.53–0.88), but not fewer CIN2/3. The positive predictive value of hrHPV-positivity for CIN2/3 increased from 28.9% at age o35 years to 53.3% in X45 years. Conclusion: The burden of hrHPV and CIN2/3 was high and it was related to immunosuppression level. Combination antiretroviral therapies (X2 year) use had a favourable effect on hrHPV prevalence but cART in our population may have been started too late to prevent CIN2/3

Comparison of HPV DNA testing in cervical exfoliated cells and tissue biopsies among HIV-positive women in Kenya

HIV-positive women are infected with human papillomavirus (HPV) (especially with multiple types), and develop cervical intraepithelial neoplasia (CIN) and cervical cancer more frequently than HIV-negative women. We compared HPV DNA prevalence obtained using a GP5+/6+ PCR assay in cervical exfoliated cells to that in biopsies among 468 HIV-positive women from Nairobi, Kenya. HPV prevalence was higher in cells than biopsies and the difference was greatest in 94 women with a combination normal cytology/normal biopsy (prevalence ratio, PR = 3.7; 95% confidence interval, CI: 2.4-5.7). PR diminished with the increase in lesion severity (PR in 58 women with high-grade squamous intraepithelial lesions (HSIL)/CIN2-3 = 1.1; 95% CI: 1.0-1.2). When HPV-positive, cells contained 2.0- to 4.6-fold more multiple infections than biopsies. Complete or partial agreement between cells and biopsies in the detection of individual HPV types was found in 91% of double HPV-positive pairs. The attribution of CIN2/3 to HPV16 and/or 18 would decrease from 37.6%, when the presence of these types in either cells or biopsies was counted, to 20.2% when it was based on the presence of HPV16 and/or 18 (and no other types) in biopsies. In conclusion, testing HPV on biopsies instead of cells results in decreased detection but not elimination of multiple infections in HIV-positive women. The proportion of CIN2/3 attributable to HPV16 and/or 18 among HIV-positive women, which already appeared to be lower than that in HIV-negative, would then further decrease. The meaning of HPV detection in cells and random biopsy from HIV-positive women with no cervical abnormalities remains unclear. What\u27s new? Assignment of human papillomavirus (HPV) types to individual cervical lesions is essential for the understanding of the biology of different HPV types, efficacy of HPV vaccines, and design of detection assays. Such attribution is however hampered in HIV-positive women by the high proportion of multiple HPV infections. This study is the first to systematically compare HPV detection in paired cervical exfoliated cells and cervical tissue biopsies. HPV testing using biopsies instead of cells results in decreased detection of multiple infections in HIV-positive women. Exclusive reliance on biopsies also decreased the proportion of CIN2/3 attributable to vaccine-preventable HPV16 and/or 18 infection

Lagrangian analysis led design of a shock recovery plate impact experiment

Shock recovery techniques, such as the flyer-plate impact test, are used to examine a material that has been subjected to a single well-defined shock, followed by a single release wave. One of the key requirements of this type of technique is that the process should be such that any change found in the sample after recovery, can only be attributed to the shock process alone. Therefore, the principal problem for a test specimen-fixture assembly is that it is designed such that the loading history of the recovered specimen is known. This has motivated this research through the analysis led design of a shock recovery experiment. The choice of Lagrangian Finite Element Analysis for this design work was driven by the method's ability to accurately track history variables (for plastic deformation) and treat contact interactions which are crucial in this problem. Starting from an initial configuration, LS-Dyna has been used to analyse in detail the resulting wave propagation to ensure the generation of a uniaxial strain state in the specimen through Lagrangian distance-time diagrams. These iso-maps enabled the identification of potential shortcomings with the initial design, in terms of the transmission of contact and the influence of radial release waves at the different boundaries between specimen and supporting fixture rings. The benefits of using Lagrangian Finite Element Analysis for this design work are its ability to track history variables (for plastic deformation) and contact treatment. Based on these findings, a new configuration was developed, which consists of an array of concentric rings that support the specimen. During shock formation in the specimen, these rings progressively transfer the loading in the impact direction and radially away from the specimen, acting as momentum traps and preventing unwanted release waves from affecting the strain state experienced by the specimen. Comparing distance time diagrams between original and proposed configurations, a design sensitivity analysis was performed, where the new geometry resulted in a decrease of both the residual velocity (-38%) and radial displacement (-27%) of the target when compared to the original setup