Monitoring of liquid flow through microtubes using a micropressure sensor

The pressure-driven liquid flow through microtubes was studied in a range of very low Reynolds numbers (<0.15) by monitoring the pressure change in situ. Cylindrical microtubes with diameters ranging from 50 ?m to 500 ?m were examined and two types of tube material, namely PEEK polymer and fused silica were compared. A good linear relation for the pressure drop versus flow rate was obtained. Apparent deviations between the measured slopes with those calculated using conventional theory were attributed to uncertainties in the calculated values which are dominated by the uncertainties in the microtube diameters. It was found that a period of stabilisation time was required for reaching a steady flow after the syringe pump was switched on/off or to a different flow rate. The stabilisation time was likely due to the compressibility of the fluid. Insignificant difference between PEEK polymer and fused silica microtubes in terms of flow resistance was observed. The in-situ measurement of pressure drops provides a convenient approach for monitoring fluid flow through microtubes and detecting dimensional changes within microchannels in Lab-on-a-Chip and microreactor systems

An Example of Eskers Formed in Stagnant Ice

Study of stratified glacial deposits near Farmington, New Hampshire reveals that the retreat of Late Wisconsin ice in this area proceeded by means of ice-marginal stagnation. Eskers in t his area were formed within localized ice masses a t or near the base of thin ice by streams which had dendritic patterns and were subaerially exposed

Targeted fluorescent optical nanosensors for imaging and measuring function in intracellular microdomains

Nanosensors offer the opportunity to measure intracellular domains with minimal chemical or physical perturbation. Typically only 60 nm in diameter and synthesised from polymer matrices they entrap chemical sensing elements and can be surface functionalised allowing for further chemical modification. Upon intracellular localisation the cellular environment can be monitored using conventional techniques such as confocal laser scanning microscopy. Reported here is one use of nanosensors to investigate the mechanisms of intracellular delivery mediated via the cell penetrating peptide, Tat. It is shown that information obtained from the nanosensors reveals that the post-delivery environment is representative of a lysosome in terms of both pH and morphology. The delivery mechanism of Tat, however, is shown to be dependent upon the cargo being delivered, corresponding to the absence or presence of a body of polymer matrix; thus nanosensors have been used to further the understanding of the cell penetrating mechanisms of Tat peptide. Technological aspects of nanosensor development have been investigated including polymer matrix modification and different methods of incorporating fluorophores into the nanosensor body. Addressing nanosensors located in an intracellular domain has historically been achieved with epi-fluorescent and confocal microscopy acquiring data from individual or low numbers of cells only. Reported here is the combination of nanosensors with flow cytometry as a technique for en masse investigation into entire cell populations

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification.

BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq. RESULTS: Our optimized bioinformatics pipeline for PacBio sequence analysis was able to achieve an error rate of 0.007% on the Staphylococcus aureus full-length 16S rRNA gene. Capillary sequencing of the full-length bacterial 16S rRNA gene from the pool of 50 colonies from stool identified 40 bacterial species of which up to 80% could be identified by PacBio full-length bacterial 16S rRNA gene sequencing. Analysis of the human vaginal microbiome using the bacterial 16S rRNA V1V2 gene region on MiSeq generated 129 operational taxonomic units (OTUs) from which 70 species could be identified. For the PacBio, 36,000 sequences from over 58,000 raw reads could be assigned to a barcode, and the in silico selected bacterial 16S rRNA V1V2 gene region generated 154 OTUs grouped into 63 species, of which 62% were shared with the MiSeq dataset. The PacBio full-length bacterial 16S rRNA gene datasets generated 261 OTUs, which were grouped into 52 species, of which 54% were shared with the MiSeq dataset. Alpha diversity index reported a higher diversity in the MiSeq dataset. CONCLUSION: The PacBio sequencing error rate is now in the same range of the previously widely used Roche 454 sequencing platform and current MiSeq platform. Species-level microbiome analysis revealed some inconsistencies between the full-length bacterial 16S rRNA gene capillary sequencing and PacBio sequencing

Diversification of bacterial genome content through distinct mechanisms over different timescales

Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages

Validation of a home safety questionnaire used in a series of case-control studies

© 2014 BMJ Publishing Group. All rights reserved. Conclusions This study found that the validity of selfreports varied with safety practice. Questions with a high specificity will be useful for practitioners for identifying households who may benefit from home safety interventions and will be useful for researchers as measures of exposures or outcomes.Objective To measure the validity of safety behaviours, safety equipment use and hazards reported on a questionnaire by parents/carers with children aged under 5 years participating in a series of home safety casecontrol studies.Methods The questionnaire measured safety behaviours, safety equipment use and hazards being used as exposures in five case-control studies. Responses to questions were compared with observations made during a home visit. The researchers making observations were blind to questionnaire responses.Results In total, 162 families participated in the study. Overall agreement between reported and observed values of the safety practices ranged from 48.5% to 97.3%. Only 3 safety practices (stair gate at the top of stairs, stair gate at the bottom of stairs, stairs are carpeted) had substantial agreement based on the κ statistic (k=0.65, 0.72, 0.74, respectively). Sensitivity was high (≥70%) for 19 of the 30 safety practices, and specificity was high (≥70%) for 20 of the 30 practices. Overall for 24 safety practices, a higher proportion of respondents over-reported than under-reported safe practice (negative predictive value>positive predictive value). For six safety practices, a higher proportion of respondents under-reported than over-reported safe practice (negative predictive valu

Modifiable risk factors for scald injury in children under 5 years of age: a multi-centre case–control study

Objective: To determine the relationship between a range of modifiable risk factors and medically attended scalds in children under the age of 5 years. Methods: Multicentre matched case-control study in acute hospitals, minor injury units and GP practices in four study centres in England. Cases comprised 338 children under 5 presenting with a scald, and 1438 control participants matched on age, sex, date of event and study centre. Parents/caregivers completed questionnaires on safety practices, safety equipment use, home hazards and potential confounders. Odds ratios were estimated using conditional logistic regression. Results: Parents of cases were significantly more likely than parents of controls to have left hot drinks within reach of their child (adjusted odds ratio (AOR) 2.33, 95%CI 1.63, 3.31; population attributable fraction (PAF) 31%). They were more likely not to have taught children rules about climbing on kitchen objects (AOR 1.66, 95%CI 1.12, 2.47; PAF 20%); what to do or not do when parents are cooking (AOR 1.95, 95%CI 1.33, 2.85; PAF 26%); and about hot things in the kitchen (AOR 1.89, 95%CI 1.30, 2.75; PAF 26%). Conclusions: Some scald injuries may be prevented by parents keeping hot drinks out of reach of children and by teaching children rules about not climbing on objects in the kitchen, what to do or not do whilst parents are cooking using the top of the cooker and about hot objects in the kitchen. Further studies, providing a more sophisticated exploration of the immediate antecedents of scalds are required to quantify associations between other hazards and behaviours and scalds in young children