Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER

Single particle analysis has become a key structural biology technique. Experimental images are extremely noisy, and during iterative refinement it is possible to stably incorporate noise into the reconstruction. Such “over-fitting” can lead to misinterpretation of the structure and flawed biological results. Several strategies are routinely used to prevent over-fitting, the most common being independent refinement of two sides of a split dataset. In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise, despite independent refinement of half datasets. We propose a modification of the refinement process through the application of a local signal-to-noise filter: SIDESPLITTER. We show that our approach can reduce over-fitting for both idealised and experimental data while maintaining independence between the two sides of a split refinement. SIDESPLITTER refinement leads to improved density, and can also lead to improvement of the final resolution in extreme cases where datasets are prone to severe over-fitting, such as small membrane proteins

Interactive narration with a child: impact of prosody and facial expressions

International audienceIntelligent Virtual Agents are suitable means for interactive sto-rytelling for children. The engagement level of child interaction with virtual agents is a challenging issue in this area. However, the characteristics of child-agent interaction received moderate to little attention in scientific studies whereas such knowledge may be crucial to design specific applications. This article proposes a Wizard of Oz platform for interactive narration. An experimental study in the context of interactive story-telling exploiting this platform is presented to evaluate the impact of agent prosody and facial expressions on child participation during storytelling. The results show that the use of the virtual agent with prosody and facial expression modalities improves the engagement of children in interaction during the narrative sessions

The development of a light-weight, long-life diphacinone rodent bait

Ross, J.G., Eason, C.T., Sam, S., Shapiro, L., Blackie, H., MacMorran, D., Aylett, P., Tucker, N., Razzaq, H

Methylphenidate treatment of attention deficit hyperactivity disorder in young people with learning disability and difficult-to-treat epilepsy: Evidence of clinical benefit.

To establish the efficacy and safety of methylphenidate (MPH) treatment for attention deficit hyperactivity disorder (ADHD) in a group of children and young people with learning disability and severe epilepsy

Optical properties of meteoric smoke analogues

Accurate determination of the optical properties of analogues for meteoric smoke particles (MSPs), which are thought to be composed of iron-rich oxides or silicates, is important for their observation and characterization in the atmosphere. In this study, a photochemical aerosol flow system (PAFS) has been used to measure the optical extinction of iron oxide MSP analogues in the wavelength range 325–675 nm. The particles were made photochemically and agglomerate into fractal-like particles with sizes on the order of 100 nm. Analysis using transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX) and electron energy loss spectroscopy (EELS) suggested the particles were most likely maghemite-like (γ-Fe2O3) in composition, though a magnetite-like composition could not be completely ruled out. Assuming a maghemite-like composition, the optical extinction coefficients measured using the PAFS were combined with maghemite absorption coefficients measured using a complementary experimental system (the MICE-TRAPS) to derive complex refractive indices that reproduce both the measured absorption and extinction

Structure of the bacteriophage PhiKZ non-virion RNA polymerase

Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a ‘nucleus’, erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β′ subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor

A life story in three parts: the use of triptychs to make sense of personal digital data

Many social media platforms support the curation of personal digital data, and, more recently, the use of that data for review and reflection. We explored the process of reflection by asking users to create a meaningful ‘triptych’ of photographs drawn from their Facebook accounts. In a first study, we asked participants to manually trawl their own accounts and select three relevant images, which we then framed and used as an interview probe. In a second study, we designed an automated triptych generation system and assessed participants’ experiences of using this system. We conducted qualitative analyses of participant interviews from both studies. Consistent with other ‘slow technology’ work, we found the act of creating a physical artefact from social media data gave that data new meaning, albeit with notable differences between manual vs automatically generated triptychs. We conclude by discussing possible improvements to the design of the automated triptych system

The impact of solar radiation on polar mesospheric ice particle formation

Mean temperatures in the polar summer mesopause can drop to 130&thinsp;K. The low temperatures in combination with water vapor mixing ratios of a few parts per million give rise to the formation of ice particles. These ice particles may be observed as polar mesospheric clouds. Mesospheric ice cloud formation is believed to initiate heterogeneously on small aerosol particles (r &lt; 2 nm) composed of recondensed meteoric material, so-called meteoric smoke particles (MSPs). Recently, we investigated the ice activation and growth behavior of MSP analogues under realistic mesopause conditions. Based on these measurements we presented a new activation model which largely reduced the uncertainties in describing ice particle formation. However, this activation model neglected the possibility that MSPs heat up in the low-density mesopause due to absorption of solar and terrestrial irradiation. Radiative heating of the particles may severely reduce their ice formation ability. In this study we expose MSP analogues (Fe2O3 and FexSi1 − xO3) to realistic mesopause temperatures and water vapor concentrations and investigate particle warming under the influence of variable intensities of visible light (405, 488, and 660&thinsp;nm). We show that Mie theory calculations using refractive indices of bulk material from the literature combined with an equilibrium temperature model presented in this work predict the particle warming very well. Additionally, we confirm that the absorption efficiency increases with the iron content of the MSP material. We apply our findings to mesopause conditions and conclude that the impact of solar and terrestrial radiation on ice particle formation is significantly lower than previously assumed.</p

Genotypic and phenotypic spectrum of pyridoxine-dependent epilepsy (ALDH7A1 deficiency)

Pyridoxine-dependent epilepsy was recently shown to be due to mutations in the ALDH7A1 gene, which encodes antiquitin, an enzyme that catalyses the nicotinamide adenine dinucleotide-dependent dehydrogenation of L-{alpha}-aminoadipic semialdehyde/L-{Delta}1-piperideine 6-carboxylate. However, whilst this is a highly treatable disorder, there is general uncertainty about when to consider this diagnosis and how to test for it. This study aimed to evaluate the use of measurement of urine L-{alpha}-aminoadipic semialdehyde/creatinine ratio and mutation analysis of ALDH7A1 (antiquitin) in investigation of patients with suspected or clinically proven pyridoxine-dependent epilepsy and to characterize further the phenotypic spectrum of antiquitin deficiency. Urinary L-{alpha}-aminoadipic semialdehyde concentration was determined by liquid chromatography tandem mass spectrometry. When this was above the normal range, DNA sequencing of the ALDH7A1 gene was performed. Clinicians were asked to complete questionnaires on clinical, biochemical, magnetic resonance imaging and electroencephalography features of patients. The clinical spectrum of antiquitin deficiency extended from ventriculomegaly detected on foetal ultrasound, through abnormal foetal movements and a multisystem neonatal disorder, to the onset of seizures and autistic features after the first year of life. Our relatively large series suggested that clinical diagnosis of pyridoxine dependent epilepsy can be challenging because: (i) there may be some response to antiepileptic drugs; (ii) in infants with multisystem pathology, the response to pyridoxine may not be instant and obvious; and (iii) structural brain abnormalities may co-exist and be considered sufficient cause of epilepsy, whereas the fits may be a consequence of antiquitin deficiency and are then responsive to pyridoxine. These findings support the use of biochemical and DNA tests for antiquitin deficiency and a clinical trial of pyridoxine in infants and children with epilepsy across a broad range of clinical scenarios

Diagnostic algorithm for children presenting with epilepsia partialis continua

Objective: To characterize a cohort of children with epilepsia partialis continua (EPC) and develop a diagnostic algorithm incorporating key differential diagnoses. / Methods: Children presenting with EPC to a tertiary pediatric neurology center between 2002 and 2019 were characterized. / Results: Fifty‐four children fulfilled EPC criteria. Median age at onset was 7 years (range 0.6‐15), with median follow‐up of 4.3 years (range 0.2‐16). The diagnosis was Rasmussen encephalitis (RE) in 30 of 54 (56%), a mitochondrial disorder in 12 of 54 (22.2%), and magnetic resonance imaging (MRI) lesion‐positive focal epilepsy in 6 of 54 (11.1%). No diagnosis was made in 5 of 54 (9%). Children with mitochondrial disorders developed EPC earlier; each additional year at presentation reduced the odds of a mitochondrial diagnosis by 26% (P = .02). Preceding developmental concerns (odds ratio [OR] 22, P < .001), no seizures prior to EPC (OR 22, P < .001), bilateral slowing on electroencephalogram (EEG) (OR 26, P < .001), and increased cerebrospinal fluid (CSF) protein level (OR 16) predicted a mitochondrial disorder. Asymmetry or hemiatrophy was evident on MRI at presentation with EPC in 18 of 30 (60%) children with RE, and in the remainder at a median of 6 months (range 3‐15) after EPC onset. The first diagnostic test is brain MRI. Hemiatrophy may permit a diagnosis of RE with unilateral clinical and EEG findings. For children in whom a diagnosis of RE cannot be made on first scan but the clinical and radiological presentation resembles RE, repeat imaging every 6 months is recommended to detect progressive unicortical hemiatrophy, and brain biopsy should be considered. Evidence of intrathecal inflammation (oligoclonal bands and raised neopterin) can be supportive. In children with bihemispheric EPC, rapid polymerase gamma testing is recommended and if negative, sequencing mtDNA and whole‐exome sequencing on blood‐derived DNA should be performed. / Significance: Children presenting with EPC due to a mitochondrial disorder show clinical features distinguishing them from RE and structural epilepsies. A diagnostic algorithm for children with EPC will allow targeted investigation and timely diagnosis