Continuity properties of measurable group cohomology

A version of group cohomology for locally compact groups and Polish modules has previously been developed using a bar resolution restricted to measurable cochains. That theory was shown to enjoy analogs of most of the standard algebraic properties of group cohomology, but various analytic features of those cohomology groups were only partially understood. This paper re-examines some of those issues. At its heart is a simple dimension-shifting argument which enables one to `regularize' measurable cocycles, leading to some simplifications in the description of the cohomology groups. A range of consequences are then derived from this argument. First, we prove that for target modules that are Fr\'echet spaces, the cohomology groups agree with those defined using continuous cocycles, and hence they vanish in positive degrees when the acting group is compact. Using this, we then show that for Fr\'echet, discrete or toral modules the cohomology groups are continuous under forming inverse limits of compact base groups, and also under forming direct limits of discrete target modules. Lastly, these results together enable us to establish various circumstances under which the measurable-cochains cohomology groups coincide with others defined using sheaves on a semi-simplicial space associated to the underlying group, or sheaves on a classifying space for that group. We also prove in some cases that the natural quotient topologies on the measurable-cochains cohomology groups are Hausdorff.Comment: 52 pages. [Nov 22, 2011:] Major re-write with Calvin C. Moore as new co-author. Results from previous version strengthened and several new results added. [Nov 25, 2012:] Final version now available at springerlink.co

A de novo assembly of the common frog (Rana temporaria) transcriptome and comparison of transcription following exposure to Ranavirus and Batrachochytrium dendrobatidis

This is the final version. Available on open access from Public Library of Science via the DOI in this recordata Availability: All raw data is available through EMBL-EBI Array Express, accession number E-MTAB-3632Amphibians are experiencing global declines and extinctions, with infectious diseases representing a major factor. In this study we examined the transcriptional response of metamorphic hosts (common frog, Rana temporaria) to the two most important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus. We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens. We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus. This may reflect the higher mortality rates found in wild common frogs infected with Ranavirusas opposed to Bd. These data provide a valuable genomic resource for the amphibians, contribute insight into gene expression changes after pathogen exposure, and suggest potential candidate genes for future host-pathogen research.European UnionRoyal SocietyZoological Society of LondonEuropean Research Counci

Quantification of the SF₆ lifetime based on mesospheric loss measured in the stratospheric polar vortex

Sulfur hexafluoride (SF₆) is a greenhouse gas with one of the highest radiative efficiencies in the atmosphere as well as an important indicator of transport time scales in the stratosphere. The current widely used estimate of the atmospheric lifetime of SF₆ is 3200 years. In this study we use in situ measurements in the 2000 Arctic polar vortex that sampled air with up to 50% SF₆ loss to calculate an SF₆ lifetime. Comparison of these measurements with output from the Whole Atmosphere Community Climate Model (WACCM) shows that WACCM transport into the vortex is accurate and that an important SF₆ loss mechanism, believed to be electron attachment, is missing in the model. Based on the measurements and estimates of the size of the vortex, we calculate an SF₆ lifetime of 850 years with an uncertainty range of 580–1400 years. The amount of SF₆ loss is shown to be consistent with that of HFC‐227ea, which has a lifetime of 670–780 years, adding independent support to our new SF₆ lifetime estimate. Based on the revised lifetime the global warming potential of SF₆ will decrease only slightly for short time horizons (<100 years) but will decrease substantially for time horizons longer than 2000 years. Also, the use of SF6 measurements as an indicator of transport time scales in the stratosphere clearly must account for potential influence from polar vortex air

Pitfalls of haplotype phasing from amplicon-based long-read sequencing

This is the final version. Available on open access from Nature Research via the DOI in this recordThe long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and PacBio sequencing to phase two variants 9 kb apart in the RET gene. We also re-analysed data from a recent paper which had apparently successfully used ONT to phase clinically important haplotypes at the CYP2D6 and HLA loci. From these analyses, we demonstrate PCR-chimera formation during PCR amplification and reference alignment bias are pitfalls that need to be considered when attempting to phase variants using amplicon-based long-read sequencing technologies. These methodological pitfalls need to be avoided if the opportunities provided by long-read sequencers are to be fully exploited.Wellcome Trus

Assessment of Diet and Physical Activity in Paediatric Non-Alcoholic Fatty Liver Disease Patients: A United Kingdom Case Control Study

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in children, with prevalence rising alongside childhood obesity rates. This study aimed to characterise the habitual diet and activity behaviours of children with NAFLD compared to obese children without liver disease in the United Kingdom (UK). Twenty-four biopsy-proven paediatric NAFLD cases and eight obese controls without biochemical or radiological evidence of NAFLD completed a 24-h dietary recall, a Physical Activity Questionnaire (PAQ), a Dutch Eating Behavior Questionnaire (DEBQ) and a 7-day food and activity diary (FAD), in conjunction with wearing a pedometer. Groups were well matched for age and gender. Obese children had higher BMI z-scores (p = 0.006) and BMI centiles (p = 0.002) than participants with NAFLD. After adjusting for multiple hypotheses testing and controlling for differences in BMI, no differences in macro- or micronutrient intake were observed as assessed using either 24-h recall or 7-day FAD (p > 0.001). Under-reporting was prevalent (NAFLD 75%, Obese Control 87%: p = 0.15). Restrained eating behaviours were significantly higher in the NAFLD group (p = 0.005), who also recorded more steps per day than the obese controls (p = 0.01). In conclusion, this is the first study to assess dietary and activity patterns in a UK paediatric NAFLD population. Only a minority of cases and controls were meeting current dietary and physical activity recommendations. Our findings do not support development of specific dietary/ physical activity guidelines for children with NAFLD; promoting adherence with current general paediatric recommendations for health should remain the focus of clinical management

Palpitations following regular ibuprofen dosing in a 13-year-old girl: a case report

Abstract Introduction The sensation of palpitations may either be the initial or the only symptom of cardiac arrhythmia. We describe a case of an apparent clear temporal relationship between standard ibuprofen dosing and palpitations. A review of the medical literature revealed this to be, to the best of our knowledge, the first reported case of this type. Case presentation A 13-year-old Caucasian girl initially presented to our clinic with hamstring tendinitis. She was commenced on a medication regimen of paracetamol and ibuprofen. After the third ibuprofen dose, she experienced palpitations. These were associated with lower chest and/or upper abdominal discomfort, and a feeling of being hot and sweaty. Her symptoms ceased upon the cessation of ibuprofen therapy. Conclusion Cardiac arrhythmia is a potentially fatal disorder that may exhibit heart palpitations as its initial (or only) symptom. The prompt recognition of the cause of the symptom can reduce mortality and morbidity associated with any underlying pathological processes. There is a need to investigate cases of recurrent palpitations so as to exclude underlying structural cardiac pathology and/or abnormal cardiac rhythm.</p

Controlling collapse in Bose-Einstein condensates by temporal modulation of the scattering length

We consider, by means of the variational approximation (VA) and direct numerical simulations of the Gross-Pitaevskii (GP) equation, the dynamics of 2D and 3D condensates with a scattering length containing constant and harmonically varying parts, which can be achieved with an ac magnetic field tuned to the Feshbach resonance. For a rapid time modulation, we develop an approach based on the direct averaging of the GP equation,without using the VA. In the 2D case, both VA and direct simulations, as well as the averaging method, reveal the existence of stable self-confined condensates without an external trap, in agreement with qualitatively similar results recently reported for spatial solitons in nonlinear optics. In the 3D case, the VA again predicts the existence of a stable self-confined condensate without a trap. In this case, direct simulations demonstrate that the stability is limited in time, eventually switching into collapse, even though the constant part of the scattering length is positive (but not too large). Thus a spatially uniform ac magnetic field, resonantly tuned to control the scattering length, may play the role of an effective trap confining the condensate, and sometimes causing its collapse.Comment: 7 figure

Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of ß-tubulin. Our analysis identified one amino acid substitution—ß-tubulin F224—which was highly lineage specific. Investigation of ß-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the ß-tubulin Neighbor-Net and demonstrated a fundamental division between core ß-tubulins (plant-like) and divergent ß-tubulins (animal and fungal). F224 was almost completely restricted to the core ß-tubulins, while divergent ß-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of ß-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core ß-tubulins and Y-type, divergent ß-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins

Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV–vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV–vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate