637 research outputs found
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
Prediction of the ballistic limit of an aluminium sandwich panel
This paper presents research on modelling the impact of a 150g projectile on a 35mm thick aluminium sandwich panel. The objective of the work is a predictive modelling capability for the ballistic limit of the panel. A predictive modelling capability supports the design of capture and deorbit missions for large items of space debris such as satellites and rocket upper stages. A detailed explicit finite element model was built using the LSDYNA software and results were compared with experimental data for the projectile exit velocity to establish key parameters. The primary parameters influencing the model behaviour were the strength and failure of the aluminium face sheets and the friction between projectile and panel. The model results showed good agreement with experimental results for ogive nose projectiles, but overestimated the exit velocity for flat nose projectiles.This work was funded by the European Space Agency under a contract with Airbus Defence and Space
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
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 International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods
An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term âfermentedâ led the panel to define fermented foods and beverages as âfoods made through desired microbial growth and enzymatic conversions of food componentsâ. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines
The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods
An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term âfermentedâ led the panel to define fermented foods and beverages as âfoods made through desired microbial growth and enzymatic conversions of food componentsâ. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines
Different cervical cancer screening approaches in a Chinese multicentre study
To evaluate alternative cervical cancer screening methods, digital colposcopy and collection of cervical exfoliated cells for liquid-based cytology (LBC) and hybrid capture 2 (HC2) testing were performed among 2562 women aged 15â59 years in three study sites in the People's Republic of China (rural Shanxi province, Shenyang city in Liaoning province and Shenzhen city in Guangdong province). Visual inspection with acetic acid (VIA) was also evaluated independently from colposcopy. A total of 74 cases of histologically confirmed cervical intraepithelial neoplasia grade 2 or worse (CIN2+) were identified, and 16 CIN2+ cases were imputed among unbiopsied women to correct for verification bias. Corrected sensitivity for CIN2+ was 37% for VIA, 54% for colposcopy, 87% for LBC with a threshold of atypical cells of undetermined significance (LBCâ©ŸASCUS), 90% for HC2, 84% for LBC using HC2 to triage ASCUS and 96% for positivity to LBCâ©ŸASCUS or HC2. For VIA, sensitivity was much lower among women â©Ÿ40 years (12%) than those aged â©œ39 years (50%). Specificity varied from 77% for positivity to LBCâ©ŸASCUS or HC2, up to 94% for LBC using HC2 to triage ASCUS. In conclusion, LBC, HC2 and their combinations performed well, whereas VIA missed a majority of CIN2+, particularly in older women. Digital colposcopy performed better than VIA, but still missed nearly half of CIN2+ in this study
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