Critical Assessment of Metagenome Interpretation: the second round of challenges

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.

Weight loss and African-American women: a systematic review of the behavioural weight loss intervention literature

The excess burden of obesity among African-American women is well documented. However, the behavioural weight loss intervention literature often does not report results by ethnic group or gender. The purpose of this article is to conduct a systematic review of all behavioural weight loss intervention trials published between 1990 and 2010 that included and reported results separately for African-American women. The criteria for inclusion included (i) participants age ≥18 years; (ii) a behavioural weight loss intervention; (iii) weight as an outcome variable; (iv) inclusion of African-American women; and (v) weight loss results reported separately by ethnicity and gender. The literature search identified 25 studies that met inclusion criteria. Our findings suggest that more intensive randomized behavioural weight loss trials with medically at-risk populations yield better results. Well-designed and more intensive multi-site trials with medically at-risk populations currently offer the most promising results for African-American women. Still, African-American women lose less weight than other subgroups in behavioural weight loss interventions. It is now critical to expand on individual-level approaches and incorporate the biological, social and environmental factors that influence obesity. This will help enable the adoption of healthier behaviours for this group of women disproportionately affected by obesity.

Dogger Bank itch in the eastern English Channel: a newly described geographical distribution of an old problem

Dogger Bank itch is an allergic contact dermatitis to the (2-hydroxyethyl) dimethylsulphoxonium ion, a metabolite produced by the marine Bryozoan Alcyonidium diaphanum. The condition may become disabling in affected individuals, who are chiefly fishermen and dock labourers. It involves regions of skin directly exposed to sea water and areas where water may course. As A. diaphanum is common in the coastal waters of Britain, Ireland and neighbouring mainland Europe, it is important for dermatologists to be aware of Dogger Bank itch. Data published in 1966 suggested that 7% of trawler-men at the UK port of Lowestoft had the condition. The current epidemiology is unknown, but the disease still occurs despite shrinkage of the fishing industry, and the condition is not confined to North Sea trawler-men as had been thought previously. It has been reported in trawler-men from Le Havre and shell fishermen from Cornwall, and we report it here in a fisherman using fixed nets in the eastern English Channel.

Comparison of three different loading doses to establish epidural analgesia in labour

Women requesting epidural analgesia were randomized to receive one of three loading doses. Group 1 received a single dose of bupivacaine 9.375 mg (15 ml of 0.0625%) containing fentanyl 37.5 microg and adrenaline 37.5 microg group 2 received a single dose of bupivacaine 15 mg (15 ml of 0.1%) containing fentanyl 30 microg and adrenaline 30 microg and group 3 received a test dose of bupivacaine 10 mg (4 ml of 0.25% - test) followed 5 min later by bupivacaine 20 mg (8 ml of 0.25% - loading). All groups received an infusion of bupivacaine 0.0625% with fentanyl 0.00025% and adrenaline 0.00025% at 10-12 ml/h started 15 min after the loading dose. Speed of onset of analgesia was the same in all three groups, with the majority of women achieving satisfactory analgesia by 20 min. Motor block was significantly increased in group 3 at 30 min, but by 1 h there was no difference in motor block between the groups.

The influence of epidural administration of fentanyl infusion on gastric emptying in labour

The effect of epidural infusions containing fentanyl on maternal gastric emptying in labour was examined using the rate of paracetamol absorption. Women were randomly allocated to receive one of two epidural infusions, bupivacaine 0.125% alone or bupivacaine 0.0625% with fentanyl 2.5 micrograms.ml-1 at a rate of 10-12 ml.h-1. Paracetamol 1.5 g was given orally to women after either 30 ml of the infusion solution had been given (mean time 2.5 h, study A) or 40-50 ml (mean time 4.5 h. study B). Six venous blood samples were taken over the next 90 min for measurement of plasma paracetamol concentration. There were no significant differences in maximum plasma paracetamol concentration, time to maximum paracetamol concentration and area under the concentration-time curve between the two groups for study A. In study B the time to maximum plasma paracetamol concentration was significantly delayed in women receiving > 100 micrograms fentanyl compared with controls (p < 0.05). We conclude that the dose of fentanyl that may delay gastric emptying when given by epidural infusion is greater than 100 micrograms.

The effect of epidural opioids on maternal oxygenation during labour and delivery

The effects of epidural fentanyl on the incidence of maternal hypoxaemia during labour and on neonatal welfare were examined. Women were randomly allocated to receive one of two epidural infusions, bupivacaine 0.125% alone or bupivacaine 0.0625% with 2.5 micrograms.ml-1 fentanyl, and maternal arterial oxygen saturation was monitored continuously until delivery. The median incidence of desaturation (SpO2 < 95%) during the active phase of the second stage of labour was significantly greater in the fentanyl group than in controls (2.9 versus 0.6 min.h-1, p = 0.02). Similarly, the incidence of desaturation to SpO2 < or = 90% was greater in the fentanyl group than in controls (p = 0.02). There was no correlation between maternal oxygenation or plasma fentanyl concentration and neonatal welfare as measured by umbilical arterial and venous blood gas and acid base status, Apgar score and Neurologic and Adaptive Capacity Score.

Quantitative measurements of membrane potential in Escherichia coli

By use of giant cells of Escherichia coli induced by growth in the presence of 6-amidinopenicillanic acid, membrane potentials have been measured by two completely independent techniques: directly with intracellular microelectrodes and indirectly from the steady-state distribution of [3H]tetraphenylphosphonium. Under a variety of conditions, the two methods yield values that agree very closely. Thus, with both techniques, the membrane potential approximates -85 mV (interior negative) at pH 5.0 and -142 mV at pH 8.0, with an average slope of -22 mV/pH unit over the range pH 5.0-7.0. A parallel study of membrane vesicles prepared from giant cells was undertaken using tetraphenylphosphonium distribution alone as a measure of membrane potential. The vesicles were found to exhibit a much smaller slope of membrane potential vs. extracellular pH (about -6 mV/pH unit) than intact giant cells. The results indicate that distribution studies with these lipophilic cations provide an excellent measure of membrane potential and are discussed in relation to calculations of H+/substrate stoichiometry for protonsymport systems in E. coli.

Prosthecae of Asticcacaulis biprosthecum: system for the study of membrane transport

Prosthecae removed from cells of Asticcacaulis biprosthecum were examined for their ability to accumulate proline, alanine, aspartate, glutamate, and glucose against a concentration gradient. The transport of all of these compounds into prosthecae was stimulated by the nonphysiological electron donors phenazine methosulfate and N,N,N',N'-tetramethyl-p-phenylene diamine dihydrochloride. Reduced pyridine nucleotides caused very slight stimulation of transport of proline and glucose. Other physiological electron donors did not stimulate uptake. Evidence is presented indicating that the failure of certain potential electron donors to drive respiratory chain-linked transport is due to the inabilityof these compounds to enter prosthecae rather than to the absence of enzymes for their oxidation in prosthecae. Inhibition of respiration and uncouplers of oxidative phosphorylation, with the exception of arsenate, inhibit active transport systems of prosthecae.