Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy

We have recorded dose-fractionated electron cryo-microscope images of thin films of pure flash-frozen amorphous ice and pre-irradiated amorphous carbon on a Falcon II direct electron detector using 300 keV electrons. We observe Thon rings [1] in both the power spectrum of the summed frames and the sum of power spectra from the individual frames. The Thon rings from amorphous carbon images are always more visible in the power spectrum of the summed frames whereas those of amorphous ice are more visible in the sum of power spectra from the individual frames. This difference indicates that while pre-irradiated carbon behaves like a solid during the exposure, amorphous ice behaves like a fluid with the individual water molecules undergoing beam-induced motion. Using the measured variation in the power spectra amplitude with number of electrons per image we deduce that water molecules are randomly displaced by a mean squared distance of ∼1.1 Å² for every incident 300 keV e⁻/Ų. The induced motion leads to an optimal exposure with 300 keV electrons of 4.0 e⁻/Ų per image with which to observe Thon rings centred around the strong 3.7 Å scattering peak from amorphous ice. The beam-induced movement of the water molecules generates pseudo-Brownian motion of embedded macromolecules. The resulting blurring of single particle images contributes an additional term, on top of that from radiation damage, to the minimum achievable B-factor for macromolecular structure determination.

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Thon rings can be seen from amorphous ice.

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Radiation damage to amorphous ice randomly displaces water molecules.

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Each incident 300 keV e⁻/Ų displaces water molecules on average by ∼1 Å.

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Macromolecules embedded in amorphous ice undergo beam induced Brownian motion.

Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres

In brain regions containing crossing fibre bundles, voxel-average diffusion MRI measures such as fractional anisotropy (FA) are difficult to interpret, and lack within-voxel single fibre population specificity. Recent work has focused on the development of more interpretable quantitative measures that can be associated with a specific fibre population within a voxel containing crossing fibres (herein we use fixel to refer to a specific fibre population within a single voxel). Unfortunately, traditional 3D methods for smoothing and cluster-based statistical inference cannot be used for voxel-based analysis of these measures, since the local neighbourhood for smoothing and cluster formation can be ambiguous when adjacent voxels may have different numbers of fixels, or ill-defined when they belong to different tracts. Here we introduce a novel statistical method to perform whole-brain fixel-based analysis called connectivity-based fixel enhancement (CFE). CFE uses probabilistic tractography to identify structurally connected fixels that are likely to share underlying anatomy and pathology. Probabilistic connectivity information is then used for tract-specific smoothing (prior to the statistical analysis) and enhancement of the statistical map (using a threshold-free cluster enhancement-like approach). To investigate the characteristics of the CFE method, we assessed sensitivity and specificity using a large number of combinations of CFE enhancement parameters and smoothing extents, using simulated pathology generated with a range of test-statistic signal-to-noise ratios in five different white matter regions (chosen to cover a broad range of fibre bundle features). The results suggest that CFE input parameters are relatively insensitive to the characteristics of the simulated pathology. We therefore recommend a single set of CFE parameters that should give near optimal results in future studies where the group effect is unknown. We then demonstrate the proposed method by comparing apparent fibre density between motor neurone disease (MND) patients with control subjects. The MND results illustrate the benefit of fixel-specific statistical inference in white matter regions that contain crossing fibres.

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We introduce the fixel—a specific fibre population within a voxel.

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A novel method for whole-brain fixel-based analysis of diffusion MRI is presented.

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Structural connectivity between fixels is derived from template-based tractography.

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Connectivity information is used for tract-specific smoothing and enhancement.

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Quantitative assessment and an in vivo demonstration is performed.

Group A streptococcal endophthalmitis complicating a sore throat in a 2-year-old child

A previously well 2-year-old presented to her general practitioner after 5 days of fever, lethargy, sore throat and a slightly red eye. A viral infection was diagnosed. Two days later, she re-presented with a swollen right eyelid and a moderately red eye. Oral amoxicillin and chloramphenicol eye drops were prescribed. The next day, marked periorbital swelling developed. She was admitted to hospital and parenteral ceftriaxone was started. Examination under anaesthetic showed injected globe diffuse corneal clouding and peripheral corneal opacities; ultrasound and CT suggested endophthalmitis. On transfer to a tertiary centre, intraocular vancomycin and subconjunctival cefuroxime were given. Aqueous fluid samples were positive for group A Streptococcus (GAS) by PCR, so parenteral clindamycin was added. GAS endophthalmitis was confirmed 1 day later from the positive intraocular fluid culture results. Visual evoked potentials revealed complete loss of vision. The eye was removed to limit potential spread. She made a good recovery postoperatively and was discharged on oral antibiotics.

256 × 2 SPAD line sensor for time resolved fluorescence spectroscopy

We present a CMOS chip 256 × 2 single photon avalanche diode (SPAD) line sensor, 23.78 µm pitch, 43.7% fill factor, custom designed for time resolved emission spectroscopy (TRES). Integrating time-to-digital converters (TDCs) implement on-chip mono-exponential fluorescence lifetime pre-calculation allowing timing of 65k photons/pixel at 200 Hz line rate at 40 ps resolution using centre-of-mass method (CMM). Per pixel time-correlated single-photon counting (TCSPC) histograms can also be generated with 320 ps bin resolution. We characterize performance in terms of dark count rate, instrument response function and lifetime uniformity for a set of fluorophores with lifetimes ranging from 4 ns to 6 ns. Lastly, we present fluorescence lifetime spectra of multicolor microspheres and skin autofluorescence acquired using a custom built spectrometer. In TCSPC mode, time-resolved spectra are acquired within 5 minutes whilst in CMM mode spectral lifetime signatures are acquired within 2 ms for fluorophore in cuvette and 200 ms for skin autofluorescence. We demonstrate CMOS line sensors to be a versatile tool for time-resolved fluorescence spectroscopy by providing parallelized and flexible spectral detection of fluorescence decay.

Novel integrative genomic tool for interrogating lithium response in bipolar disorder

We developed a novel integrative genomic tool called GRANITE (Genetic Regulatory Analysis of Networks Investigational Tool Environment) that can effectively analyze large complex data sets to generate interactive networks. GRANITE is an open-source tool and invaluable resource for a variety of genomic fields. Although our analysis is confined to static expression data, GRANITE has the capability of evaluating time-course data and generating interactive networks that may shed light on acute versus chronic treatment, as well as evaluating dose response and providing insight into mechanisms that underlie therapeutic versus sub-therapeutic doses or toxic doses. As a proof-of-concept study, we investigated lithium (Li) response in bipolar disorder (BD). BD is a severe mood disorder marked by cycles of mania and depression. Li is one of the most commonly prescribed and decidedly effective treatments for many patients (responders), although its mode of action is not yet fully understood, nor is it effective in every patient (non-responders). In an in vitro study, we compared vehicle versus chronic Li treatment in patient-derived lymphoblastoid cells (LCLs) (derived from either responders or non-responders) using both microRNA (miRNA) and messenger RNA gene expression profiling. We present both Li responder and non-responder network visualizations created by our GRANITE analysis in BD. We identified by network visualization that the Let-7 family is consistently downregulated by Li in both groups where this miRNA family has been implicated in neurodegeneration, cell survival and synaptic development. We discuss the potential of this analysis for investigating treatment response and even providing clinicians with a tool for predicting treatment response in their patients, as well as for providing the industry with a tool for identifying network nodes as targets for novel drug discovery.

The Health Quality and Safety Commission: making good health care better

New Zealand has one of the best value health care systems in the world, but as a proportion of GDP our spending on health care has increased every year since 1999. Further, there are issues of quality and safety in our system we must address, including rates of adverse events. The Health Quality and Safety Commission was formed in 2010 as a crown agent to influence, encourage, guide and support improvement in health care practice in New Zealand. The New Zealand Triple Aim has been defined as: improved quality, safety and experience of care; improved health and equity for all populations; and best value for public health system resources. The Commission is pursuing the Triple Aim via two fundamental objectives: doing the right thing by providing care supported by the best evidence available, focused on what matters to each individual patient, and doing the right thing right, first time, by making sure health care is safe and of the highest quality possible. Improvement efforts must be supported by robust but economical measurements. New Zealand has a strong culture of quality, so the Commission's role is to work with our colleagues to make good health care better.

Fractional flow reserve vs. angiography in guiding management to optimize outcomes in non-ST-segment elevation myocardial infarction: the British Heart Foundation FAMOUS-NSTEMI randomized trial

AIM

We assessed the management and outcomes of non-ST segment elevation myocardial infarction (NSTEMI) patients randomly assigned to fractional flow reserve (FFR)-guided management or angiography-guided standard care.

METHODS AND RESULTS

We conducted a prospective, multicentre, parallel group, 1 : 1 randomized, controlled trial in 350 NSTEMI patients with ≥1 coronary stenosis ≥30% of the lumen diameter assessed visually (threshold for FFR measurement) (NCT01764334). Enrolment took place in six UK hospitals from October 2011 to May 2013. Fractional flow reserve was disclosed to the operator in the FFR-guided group (n = 176). Fractional flow reserve was measured but not disclosed in the angiography-guided group (n = 174). Fractional flow reserve ≤0.80 was an indication for revascularization by percutaneous coronary intervention (PCI) or coronary artery bypass surgery (CABG). The median (IQR) time from the index episode of myocardial ischaemia to angiography was 3 (2, 5) days. For the primary outcome, the proportion of patients treated initially by medical therapy was higher in the FFR-guided group than in the angiography-guided group [40 (22.7%) vs. 23 (13.2%), difference 95% (95% CI: 1.4%, 17.7%), P = 0.022]. Fractional flow reserve disclosure resulted in a change in treatment between medical therapy, PCI or CABG in 38 (21.6%) patients. At 12 months, revascularization remained lower in the FFR-guided group [79.0 vs. 86.8%, difference 7.8% (-0.2%, 15.8%), P = 0.054]. There were no statistically significant differences in health outcomes and quality of life between the groups.

CONCLUSION

In NSTEMI patients, angiography-guided management was associated with higher rates of coronary revascularization compared with FFR-guided management. A larger trial is necessary to assess health outcomes and cost-effectiveness.

Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy

Low dose electron imaging applications such as electron cryo-microscopy are now benefitting from the improved performance and flexibility of recently introduced electron imaging detectors in which electrons are directly incident on backthinned CMOS sensors. There are currently three commercially available detectors of this type: the Direct Electron DE-20, the FEI Falcon II and the Gatan K2 Summit. These have different characteristics and so it is important to compare their imaging properties carefully with a view to optimise how each is used. Results at 300 keV for both the modulation transfer function (MTF) and the detective quantum efficiency (DQE) are presented. Of these, the DQE is the most important in the study of radiation sensitive samples where detector performance is crucial. We find that all three detectors have a better DQE than film. The K2 Summit has the best DQE at low spatial frequencies but with increasing spatial frequency its DQE falls below that of the Falcon II.

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Three direct electron detectors offer better DQE than film at 300 keV.

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Recorded 300 keV electron events on the detectors have very similar Landau distributions.

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The Gatan K2 Summit detector has the highest DQE at low spatial frequency.

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The FEI Falcon II detector has the highest DQE beyond one half the Nyquist frequency.

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The Direct Electron DE-20 detector has the fastest data acquisition rate.

The effects of Crew Resource Management (CRM) training on flight attendants' safety attitudes

INTRODUCTION

A number of well-known incidents and accidents had led the aviation industry to introduce Crew Resource Management (CRM) training designed specifically for flight attendants, and joint (pilot and flight attendant) CRM training as a way to improve teamwork and communication. The development of these new CRM training programs during the 1990s highlighted the growing need for programs to be evaluated using research tools that had been validated for the flight attendant population.

METHOD

The FSAQ (Flight Safety Attitudes Questionnaire-Flight Attendants) was designed specifically to obtain safety attitude data from flight attendants working for an Asia-Pacific airline. Flight attendants volunteered to participate in a study before receiving CRM training (N=563) and again (N=526) after CRM training.

RESULTS

Almost half (13) of the items from the 36-item FSAQ showed highly significant changes following CRM training. Years of experience, crew position, seniority, leadership roles, flight attendant crew size, and length of route flown were all predictive of safety attitudes.

PRACTICAL APPLICATIONS

CRM training for flight attendants is a valuable tool for increasing positive teamwork behaviors between the flight attendant and pilot sub-groups. Joint training sessions, where flight attendants and pilots work together to find solutions to in-flight emergency scenarios, provide a particularly useful strategy in breaking down communication barriers between the two sub-groups.

Molecular analysis of intragenic recombination at the tryptophan synthetase locus in Neurospora crassa

Fifteen different classically generated and mapped mutations at the tryptophan synthetase locus in Neurospora crassa have been characterized to the level of the primary sequence of the gene. This sequence analysis has demonstrated that intragenic recombination is accurate to order mutations within one open reading frame. While classic genetic analysis correctly ordered the mutations, the position of mutations characterized by gene sequence analysis was more accurate. A leaky mutation was found to have a wild-type primary sequence. The presence of unique polymorphisms in the primary sequence of the trp-3 gene from strain 861 confirms that it has a unique history relative to the other strains studied. Most strains that were previously shown to be immunologically nonreactive with antibody preparations raised against tryptophan synthetase protein were shown to have nonsense mutations. This work defines 14 alleles of the N. crassa trp-3 gene.

A homozygous mutation in the TUB gene associated with retinal dystrophy and obesity

Inherited retinal dystrophies are a major cause of childhood blindness. Here, we describe the identification of a homozygous frameshift mutation (c.1194_1195delAG, p.Arg398Serfs*9) in TUB in a child from a consanguineous UK Caucasian family investigated using autozygosity mapping and whole-exome sequencing. The proband presented with obesity, night blindness, decreased visual acuity, and electrophysiological features of a rod cone dystrophy. The mutation was also found in two of the proband's siblings with retinal dystrophy and resulted in mislocalization of the truncated protein. In contrast to known forms of retinal dystrophy, including those caused by mutations in the tubby-like protein TULP-1, loss of function of TUB in the proband and two affected family members was associated with early-onset obesity, consistent with an additional role for TUB in energy homeostasis.

Patent foramen ovale closure with the Gore septal occluder: initial UK experience

OBJECTIVES

To report procedural outcome and short-term follow-up data for the Gore septal occluder (GSO), a new device for closure of patent foramen ovale (PFO).

BACKGROUND

Transcatheter closure of PFO is an established treatment modality but no current device provides a perfect solution. The GSO has a number of design features, which make it potentially attractive for closure of defects in the atrial septum.

METHODS

Data from 9 centers in the United Kingdom implanting the GSO device, submitted to an electronic registry for evaluation.

RESULTS

Two hundred twenty-nine patients undergoing PFO closure from June 2011 to October 2012 were included. Indications for closure were secondary prevention of paradoxical cerebral emboli (83.4%), migraine (2.1%), platypnoea orthodeoxia (3.9%), and other (10.5%). Median PFO size was 8 mm and 34 and 39%, respectively, had long tunnel anatomy or atrial septal aneurysms. A GSO was successfully implanted in all cases. A single device was used in 98% but in 4 patients the initial device was removed and a second device required. Procedural complications occurred in 3% and later complications (e.g., atrial fibrillation, atrial ectopics, and device thrombus) in 5.7% of cases. All patients have undergone clinical and echocardiographic follow-up and all devices remain in position. Early bubble studies (median 0 months) with Valsalva maneuver in 67.2% were negative in 89%.

CONCLUSIONS

The GSO is an effective occlusion device for closure of PFO of all types. Longer-term follow-up particularly to document later closure rates are required.