Estimating the quantity of transferred DNA in primary and secondary transfers.

We conducted experiments to characterize the quantity of DNA recovered on surfaces using 6 donors with a view to help assigning probabilities to the observation of given quantities of DNA under different transfer scenarios. The donors were asked to conduct a total of 120 simulations involving primary transfer on a knife handle. With 2 selected donors, 60 associated experiments involving secondary transfer were also carried out. DNA recovered on COPAN’s FLOQSwab™ was extracted, quantified and profiled using standard commercial kits. DNA mixtures were subsequently deconvoluted using STRmix™ to obtain the proportion corresponding to the person of interest (POI). The transfer proportion between the quantity of DNA on the bare hands and the amounts recovered on the touched surfaces was also measured and studied. For a given activity, each donor left varying amounts of DNA amounting to distributions that can be characterized by their means and standard deviations. The quantity of transferred DNA is dependent on the donor and on the type of transfer. Typically, our “best” donor left an average of 0.84ng (SD = 1.23) on a knife handle compared to a mean of 0.07ng (SD = 0.09) for the least “prone to leave DNA” donor. For secondary transfer, we recorded a mean of 0.04ng (SD = 0.11) for the first donor and of 0.002 (SD = 0.01, max = 0.04ng) for the second. Linked to the above is the observation that the transfer proportion (i.e. the ratio of the quantity of DNA on an hand to the amount of DNA recovered following a transfer) depends also on the donor and on the type of the transfer. Hence the amount of DNA obtained on a given touched surface cannot simply be deduced from the quantity of DNA available on a donor’s hand. Given these sources of variability, it is not advised to use a single and fixed label, such as “good “or “bad” regardless of the circumstances, to describe a donor’s ability to leave DNA. To properly evaluate the probability of finding a given quantity of DNA the whole variation of DNA quantity should be accounted for. This can be done by using or measuring empirically the appropriate underpinning distribution for that quantity. Note however that it will be conditioned upon the donor, the receiving surface and the transfer mechanism. We also explored the potential benefit of deconvoluting mixtures to better characterize the quantity of DNA left by the POI as opposed to the total quantity of DNA measured by quantification. Our results show that such deconvolution is beneficial when low quantities of POI’s DNA may be mixed with larger quantities such as in secondary transfer scenarios. For primary transfers on clean surfaces, the touching person will dominate in the recovered DNA and the deconvolution is not critical

Activity profiles of fourteen selected medicinal plants from Rural Venda communities in South Africa against fifteen clinical bacterial species

Fourteen plants used in traditional medicine in the Venda region of South Africa were screened for activity against fifteen bacterial species. Methanol, acetone and hexane extracts and in some cases essential oils were tested using the disc diffusion and the microdilution methods. Most of the extractswere active against at least one bacterial species. Methanol and acetone extracts were the most active while Gram positive bacteria were the most sensitive as compared to Gram negative bacteria. This study has revealed the strong in vitro activity of Syzigium cordatum, Peltophorum africanum,Rhoicissus tridentata, Bridelia micrantha and Ximenia caffra against Gram positive and Gram negative bacteria. Essential oils of Lippia javanica was also effective against most of the bacterial species studied. However, Pouzolzia mixta and Mucuna coriaceae showed less activity. Some plants were more active than commercial antibiotics. This study is the first to test the activity of the selected plants from the Venda region against such number of bacterial isolates and justifies their use by local traditional healers. The identification of the active components of the plants and the determination of the effect of these plants on the immune system will give more information on their activity. Finally, these results may be of importance in identifying candidate plants and essential oils for eventual drug design and other therapeutic purposes, respectively

Oops: Optimizing operation-mode selection for IoT edge devices

The massive increase of IoT devices and their collected data raises the question of how to analyze all that data. Edge computing provides a suitable compromise, but the question remains: How much processing should be done locally vs. offloaded to other devices? The diverse application requirements and limited resources at the edge extend the challenges. We propose Oops , an optimization framework to adapt the resource management at runtime distributedly. It orchestrates the IoT devices and adapts their operation mode with respect to their constraints and the gateway’s limited shared resources. Oops reduces runtime overhead significantly while increasing user utility compared to state-of-the-art. </jats:p

Helping to distinguish primary from secondary transfer events for trace DNA.

DNA is routinely recovered in criminal investigations. The sensitivity of laboratory equipment and DNA profiling kits means that it is possible to generate DNA profiles from very small amounts of cellular material. As a consequence, it has been shown that DNA we detect may not have arisen from a direct contact with an item, but rather through one or more intermediaries. Naturally the questions arising in court, particularly when considering trace DNA, are of how DNA may have come to be on an item. While scientists cannot directly answer this question, forensic biological results can help in discriminating between alleged activities. Much experimental research has been published showing the transfer and persistence of DNA under varying conditions, but as of yet the results of these studies have not been combined to deal with broad questions about transfer mechanisms. In this work we use published data and Bayesian networks to develop a statistical logical framework by which questions of transfer mechanism can be approached probabilistically. We also identify a number of areas where further work could be carried out in order to improve our knowledge base when helping to address questions about transfer mechanisms. Finally, we apply the constructed Bayesian network to ground truth known data to determine if, with current knowledge, there is any power in DNA quantities to distinguish primary and secondary transfer events

A simplified protocol for the detection of blood, saliva, and semen from a single biological trace using immunochromatographic tests.

The detection of body fluids (e.g., blood, saliva or semen) provides information that is important both for the investigation and for the choice of the analytical protocols. Because of their sensitivity, specificity, as well as their simplicity of use, immunochromatographic tests are widely applied. These tests target different body fluids and generally require specific buffer solutions. If one needs to investigate whether the material is of a specific nature (e.g., blood), this is fine. However, if the material can also contain other material (e.g., saliva or semen) then the use of different tests can be problematic. Indeed, if the different tests require different buffers, it will not be possible to perform all tests on the exact same specimen.In this study, we assess the use of the RSID™-universal buffer to perform three immunochromatographic tests (HEXAGON OBTI, RSID-saliva, and PSA Semiquant) as well as spermatozoa detection. We use the same eluate for the detection of all three body fluids. The proposed protocol provides similar results to those obtained when each test is conducted independently. Furthermore, it does not affect the quality of the DNA profiles. The main advantage of this protocol is that the results of the presumptive test(s) and of the DNA analyses are representative of the exact same specimen

Prevalence of Intestinal Parasitic and Bacterial Pathogens in Diarrhoeal and Non-diarroeal Human Stools from Vhembe District, South Africa

In the present study, a cross-sectional survey of intestinal parasitic and bacterial infections in relation to diarrhoea in Vhembe district and the antimicrobial susceptibility profiles of isolated bacterial pathogens was conducted. Stool samples were collected from 528 patients attending major public hospitals and 295 children attending two public primary schools and were analyzed by standard microbiological and parasitological techniques. Entamoeba histolytica/E. dispar (34.2%) and Cryptosporidium spp. (25.5%) were the most common parasitic causes of diarrhoea among the hospital attendees while Giardia lamblia (12.8%) was the most common cause of diarrhoea among the primary school children (p<0.05). Schistosoma mansoni (14.4%) was more common in non-diarrhoeal samples at both hospitals (16.9%) and schools (17.6%). Campylobacter spp. (24.9%), Aeromonas spp. (20.8%), and Shigella spp. (8.5%) were the most common bacterial causes of diarrhoea among the hospital attendees while Campylobacter (12.8%) and Aeromonas spp. (12.8%) were most common in diarrhoeal samples from school children. Vibrio spp. was less common (3% in the hospitals) and were all associated with diarrhoea. Antimicrobial resistance was common among the bacterial isolates but ceftriaxone (91%) and ciprofloxacin (88.6%) showed stronger activities against all the organisms. The present study has demonstrated that E. histolytica/dispar, Cryptosporidium, Giardia, and Cyclospora are common parasitic causes of diarrhoea in Vhembe district while Campylobacter spp. and Aeromonas are the most common bacterial causes of diarrhoea in Vhembe district of South Africa

SABRE: A bio-inspired fault-tolerant electronic architecture

As electronic devices become increasingly complex, ensuring their reliable, fault-free operation is becoming correspondingly more challenging. It can be observed that, in spite of their complexity, biological systems are highly reliable and fault tolerant. Hence, we are motivated to take inspiration for biological systems in the design of electronic ones. In SABRE (self-healing cellular architectures for biologically inspired highly reliable electronic systems), we have designed a bio-inspired fault-tolerant hierarchical architecture for this purpose. As in biology, the foundation for the whole system is cellular in nature, with each cell able to detect faults in its operation and trigger intra-cellular or extra-cellular repair as required. At the next level in the hierarchy, arrays of cells are configured and controlled as function units in a transport triggered architecture (TTA), which is able to perform partial-dynamic reconfiguration to rectify problems that cannot be solved at the cellular level. Each TTA is, in turn, part of a larger multi-processor system which employs coarser grain reconfiguration to tolerate faults that cause a processor to fail. In this paper, we describe the details of operation of each layer of the SABRE hierarchy, and how these layers interact to provide a high systemic level of fault tolerance. © 2013 IOP Publishing Ltd

Antibiotic resistance patterns and beta-lactamase identification in Escherichia coli isolated from young children in rural Limpopo Province, South Africa: The MAL-ED cohort

Background. Antibiotic resistance is a growing problem worldwide. Mechanisms of resistance vary, and some can confer resistance to multiple classes of antibiotics.Objective. To characterise the antibiotic resistance profiles of Escherichia coli isolates obtained from stool samples of young rural children exposed or unexposed to antibiotics.Methodology. The samples were collected from children aged 4 - 12 months who were participants in the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) project at the South Africa research site. We isolated 87 E. coli samples (clones) from 65 individual participants, all of which were subjected to disc diffusion assay to determine resistance. We characterised the minimum inhibitory concentration of antibiotics in a subset of strains as well as the mechanism by which these strains were resistant to beta-lactam antibiotics.Results. Our results revealed high resistance rates to co-trimoxazole (54.0%), penicillin (47.1%) and tetracycline (44.8%) in our isolates, and indicated that the beta-lactamase TEM-1 is a prevalent source of beta-lactam resistance. We also identified two isolates with the extended-spectrum beta-lactamase CTX-M-14.Conclusions. This study identified antibiotic-resistant E. coli in children with and without prior exposure to antibiotics, with some isolates showing resistance to multiple classes of antibiotics. Clinicians should bear in mind that transmission of extended-spectrum beta-lactamase-resistant E. coli exists at the community level, and that children as young as 2 years may be harbouring these resistant phenotypes

Antibiotic resistance patterns and beta-lactamase identification in Escherichia coli isolated from young children in rural Limpopo Province, South Africa: The MAL-ED cohort

Background. Antibiotic resistance is a growing problem worldwide. Mechanisms of resistance vary, and some can confer resistance to multiple classes of antibiotics. Objective. To characterise the antibiotic resistance profiles of Escherichia coli isolates obtained from stool samples of young rural children exposed or unexposed to antibiotics. Methodology. The samples were collected from children aged 4 - 12 months who were participants in the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) project at the South Africa research site. We isolated 87 E. coli samples (clones) from 65 individual participants, all of which were subjected to disc diffusion assay to determine resistance. We characterised the minimum inhibitory concentration of antibiotics in a subset of strains as well as the mechanism by which these strains were resistant to beta-lactam antibiotics. Results. Our results revealed high resistance rates to co-trimoxazole (54.0%), penicillin (47.1%) and tetracycline (44.8%) in our isolates, and indicated that the beta-lactamase TEM-1 is a prevalent source of beta-lactam resistance. We also identified two isolates with the extended-spectrum beta-lactamase CTX-M-14. Conclusions. This study identified antibiotic-resistant E. coli in children with and without prior exposure to antibiotics, with some isolates showing resistance to multiple classes of antibiotics. Clinicians should bear in mind that transmission of extended-spectrum beta-lactamase-resistant E. coli exists at the community level, and that children as young as 2 years may be harbouring these resistant phenotypes