Constructing protein polyhedra via orthogonal chemical interactions.

Many proteins exist naturally as symmetrical homooligomers or homopolymers1. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in biomolecular design2-5. As synthesized by ribosomes, proteins are inherently asymmetric. Thus, they must acquire multiple surface patches that selectively associate to generate the different symmetry elements needed to form higher-order architectures1,6-a daunting task for protein design. Here we address this problem using an inorganic chemical approach, whereby multiple modes of protein-protein interactions and symmetry are simultaneously achieved by selective, 'one-pot' coordination of soft and hard metal ions. We show that a monomeric protein (protomer) appropriately modified with biologically inspired hydroxamate groups and zinc-binding motifs assembles through concurrent Fe3+ and Zn2+ coordination into discrete dodecameric and hexameric cages. Our cages closely resemble natural polyhedral protein architectures7,8 and are, to our knowledge, unique among designed systems9-13 in that they possess tightly packed shells devoid of large apertures. At the same time, they can assemble and disassemble in response to diverse stimuli, owing to their heterobimetallic construction on minimal interprotein-bonding footprints. With stoichiometries ranging from [2 Fe:9 Zn:6 protomers] to [8 Fe:21 Zn:12 protomers], these protein cages represent some of the compositionally most complex protein assemblies-or inorganic coordination complexes-obtained by design.

Selective area oxidation of copper derived from chemical vapor deposited graphene microstructure.

The barrier properties of graphene coating are highly correlated with its microstructure which is then determined by the chemical vapor deposition (CVD) growth history on metals. We demonstrate here an unrevealed selective area oxidation of copper under graphene, which is derived from the implicit-etching-controlled CVD growth mode of graphene. By charactering and analyzing the selective area patterns of Cu oxidation, an etched pattern trace with nano/microvoids during graphene growth has been proposed to account for this. Based on such selective oxidation of Cu, distributed galvanic corrosion will be triggered and proceed locally at the interface of graphene-Cu system to coalescence together under a continuous corrosion environment, eventually presenting a homogeneous oxidation of Cu and gradual decoupling of graphene-Cu system. This discovery will assist our understanding of the barrier properties of two-dimensional materials and can be extended to other applications related to quality monitoring of grown materials and defects-based chemical modifications.

Filovirus Filament Proteins.

Filoviruses are highly filamentous enveloped animal viruses that can cause severe haemorrhagic fevers. The filovirus ribonucleoprotein forms a highly organized double-layered helical nucleocapsid (NC) containing five different virally encoded proteins. The inner layer consists of NP, the RNA binding protein, complexed with the monopartite linear genome. A distinctive outer layer links individual NP subunits with bridges composed of VP24-VP35 heterodimers, which achieves condensation of the NP-RNA into tight helical coils. There are no vertical connections between the outer helical layers, explaining the flexibility of the NC and its ability to bend into tight curves without breaking the genomic RNA. These properties allow the formation of enveloped virions with varying polymorphisms, including single, linear, continuous, linked, comma-shaped and torroidal forms. Virion length is modular so that just one, or two or more genome copies may be present in each virion, producing polyploid particles. The matrix protein VP40, which drives budding and envelopment, is found in a layer adjacent to the inner cytoplasmic side of viral envelope and is arranged in a 5 nm lattice structure, but its exact symmetry is unclear. There is a constant low density gap between VP40 and the nucleocapsid, so that the latter is held rigidly centred on the long axis of the viral filament. This gap likely contains a region of flexible contacts between VP40 and the NC. The unique morphology of filoviruses may be related to high titre replication, their ease of transmission, and abilities to invade a wide range of host cells and tissues.

A Graphene-Edge Ferroelectric Molecular Switch.

We show that polar molecules (water, ammonia, and nitrogen dioxide) adsorbed solely at the exposed edges of an encapsulated graphene sheet exhibit ferroelectricity, collectively orienting and switching reproducibly between two available states in response to an external electric field. This ferroelectric molecular switching introduces drastic modifications to the graphene bulk conductivity and produces a large and ambipolar charge bistability in micrometer-size graphene devices. This system comprises an experimental realization of envisioned memory capacitive ("memcapacitive") devices whose capacitance is a function of their charging history, here conceived via confined and correlated polar molecules at the one-dimensional edge of a two-dimensional crystal.

Conductivity mapping of graphene on polymeric films by terahertz time-domain spectroscopy.

Fast inline characterization of the electrical properties of graphene on polymeric substrates is an essential requirement for quality control in industrial graphene production. Here we show that it is possible to measure the sheet conductivity of graphene on polymer films by terahertz time-domain spectroscopy (THz-TDS) when all internally reflected echoes in the substrate are taken into consideration. The conductivity measured by THz-TDS is comparable to values obtained from four point probe measurements. THz-TDS maps of 25x30 cm2 area graphene films were recorded and the DC conductivity and carrier scattering time were extracted from the measurements. Additionally, the THz-TDS conductivity maps highlight tears and holes in the graphene film, which are not easily visible by optical inspection.

MicroRNA abundance is altered in synaptoneurosomes during prion disease.

Discrepancy in synaptic structural plasticity is one of the earliest manifestations of the neurodegenerative state. In prion diseases, a reduction in synapses and dendritic spine densities is observed during preclinical disease in neurons of the cortex and hippocampus. The underlying molecular mechanisms of these alterations have not been identified but microRNAs (miRNAs), many of which are enriched at the synapse, likely regulate local protein synthesis in rapid response to stressors such as replicating prions. MiRNAs are therefore candidate regulators of these early neurodegenerative changes and may provide clues as to the molecular pathways involved. We therefore determined changes in mature miRNA abundance within synaptoneurosomes isolated from prion-infected, as compared to mock-infected animals, at asymptomatic and symptomatic stages of disease. During preclinical disease, miRNAs that are enriched in neurons including miR-124a-3p, miR-136-5p and miR-376a-3p were elevated. At later stages of disease we found increases in miRNAs that have previously been identified as deregulated in brain tissues of prion infected mice, as well as in Alzheimer's disease (AD) models. These include miR-146a-5p, miR-142-3p, miR-143-3p, miR-145a-5p, miR-451a, miR-let-7b, miR-320 and miR-150-5p. A number of miRNAs also decreased in abundance during clinical disease. These included almost all members of the related miR-200 family (miR-200a-3p, miR-200b-3p, miR-200c-3p, miR-141-3p, and miR-429-3p) and the 182 cluster (miR-182-5p and miR-183-5p).

Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome.

The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. Here we present the cryo-EM structure analysis of the small (28S) subunit (SSU) of the 55S mitoribosome. We find that the mito-specific extensions in homologous MRPs generally are involved in inter-MRP contacts and in contacts with mito-specific MRPs, suggesting a stepwise evolution of the current architecture of the mitoribosome. Although most of the mito-specific MRPs and extensions of homologous MRPs are situated on the peripheral regions, they also contribute significantly to the formation of linings of the mRNA and tRNA paths, suggesting a tailor-made structural organization of the mito-SSU for the recruitment of mito-specific mRNAs, most of which do not possess a 5' leader sequence. In addition, docking of previously published coordinates of the large (39S) subunit (LSU) into the cryo-EM map of the 55S mitoribosome reveals that mito-specific MRPs of both the SSU and LSU are involved directly in the formation of six of the 15 intersubunit bridges.

Non-accidental trauma: the role of radiology.

Non-accidental trauma is a significant source of morbidity and mortality in the pediatric population. Given the vulnerable state of the child, the radiologist can often provide valuable diagnostic information in the setting of suspected abuse. This review focuses on common findings of abusive trauma and serves as a guide to aid in clinical decision-making for providers of emergency medicine and pediatrics. Amid this discussion is an assessment of modern controversies regarding reported mimicking pathologies, recapitulation of the current state of evidence with respect to radiologic findings of abuse, and examination of the contribution that spine imaging may add to the diagnosis of possible abusive head trauma in the acutely injured child. Recommendations for avoiding pitfalls regarding the dating of intracranial injuries are discussed, and illustrated depictions of perpetrator-induced pathology are provided to aid in the understanding of these injuries. Through the use of the appropriate approach to imaging and evidence-based guidelines regarding radiologic findings, the role of radiology is to provide fundamental clues to diagnose and prevent recurrence of abusive injury in patients who cannot speak for themselves.

Nonrandomized comparison of neurofibromatosis type 1 and non-neurofibromatosis type 1 children who received carboplatin and vincristine for progressive low-grade glioma: A report from the Children's Oncology Group.

BACKGROUND: To evaluate tumor responses, event-free survival (EFS), overall survival (OS), and toxicity of chemotherapy, children with neurofibromatosis type 1 (NF1) and progressive low-grade glioma were enrolled into the Children's Oncology Group (COG) A9952 protocol and treated with carboplatin and vincristine (CV). METHODS: Non-NF1 patients were randomized to CV or thioguanine, procarbazine, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea, and vincristine in COG A9952. NF1 patients were assigned to CV only. NF1 patients and non-NF1 patients who were treated with CV were compared with respect to baseline characteristics, toxicity, tumor responses, EFS, and OS. RESULTS: A total of 127 eligible patients with NF1 were nonrandomly assigned to CV: 42 NF1 patients (33%) had events, and 6 (4.7%) died. The 5-year EFS rate was 69% ± 4% for the CV-NF1 group and 39% ± 4% for the CV-non-NF1 group (P < .001). In a univariate analysis, NF1 children had a significantly higher tumor response rate and superior EFS and OS in comparison with CV-treated children without NF1. NF1 patients and non-NF1 patients differed significantly in amount of residual tumor, extent of resection, tumor location, and pathology. According to a multivariate analysis, NF1 was independently associated with better EFS (P < .001) but not with OS. NF1 patients also had a decreased risk of grade 3 or 4 toxicities in comparison with non-NF1 patients. Three second malignant neoplasms occurred in NF1 patients receiving CV (CV-NF1 group) at a median of 7.8 years (range, 7.3-9.4 years) after enrollment, but there were none in the non-NF1 group. CONCLUSIONS: Children with NF1 tolerated CV well and had tumor response rates and EFS that were superior to those for children without NF1. Cancer 2016;122:1928-36. © 2016 American Cancer Society.

Electrically continuous graphene from single crystal copper verified by terahertz conductance spectroscopy and micro four-point probe.

The electrical performance of graphene synthesized by chemical vapor deposition and transferred to insulating surfaces may be compromised by extended defects, including for instance grain boundaries, cracks, wrinkles, and tears. In this study, we experimentally investigate and compare the nano- and microscale electrical continuity of single layer graphene grown on centimeter-sized single crystal copper with that of previously studied graphene films, grown on commercially available copper foil, after transfer to SiO2 surfaces. The electrical continuity of the graphene films is analyzed using two noninvasive conductance characterization methods: ultrabroadband terahertz time-domain spectroscopy and micro four-point probe, which probe the electrical properties of the graphene film on different length scales, 100 nm and 10 µm, respectively. Ultrabroadband terahertz time-domain spectroscopy allows for measurement of the complex conductance response in the frequency range 1-15 terahertz, covering the entire intraband conductance spectrum, and reveals that the conductance response for the graphene grown on single crystalline copper intimately follows the Drude model for a barrier-free conductor. In contrast, the graphene grown on commercial copper foil shows a distinctly non-Drude conductance spectrum that is better described by the Drude-Smith model, which incorporates the effect of preferential carrier backscattering associated with extended, electronic barriers with a typical separation on the order of 100 nm. Micro four-point probe resistance values measured on graphene grown on single crystalline copper in two different voltage-current configurations show close agreement with the expected distributions for a continuous 2D conductor, in contrast with previous observations on graphene grown on commercial copper foil. The terahertz and micro four-point probe conductance values of the graphene grown on single crystalline copper shows a close to unity correlation, in contrast with those of the graphene grown on commercial copper foil, which we explain by the absence of extended defects on the microscale in CVD graphene grown on single crystalline copper. The presented results demonstrate that the graphene grown on single crystal copper is electrically continuous on the nanoscopic, microscopic, as well as intermediate length scales.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

BACKGROUND: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. RESULTS: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. CONCLUSIONS: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

MRI of the petromastoid canal in children.

PURPOSE: To characterize the MRI features of the petromastoid canal in children with sensorineural hearing loss (SNHL) and in normal infants. MATERIALS AND METHODS: High resolution MRI examinations of 564 children who were evaluated for SNHL and brain MRI examinations of 112 infants who had normal studies were studied independently by two reviewers. RESULTS: In SNHL group, visibility of the PMC decreased for right and left PMC (P < 0.001). The width of the right PMC significantly decreased as age increased (P < 0.0001). There was no relation between abnormalities of membranous labyrinth and cochlear nerve and PMC visibility in children with SNHL (p > 0.05). In the normal group, the PMC visibility decreased with increasing age (right P = 0.0001, left P = 0.001). In the normal group also, as age increased, the PMC width decreased for both PMCs (right, P = 0.0006; left, P = 0.03). CONCLUSION: The PMC is more frequently visualized in young children. Its visibility and width are not associated with abnormalities of membranous labyrinth and cochlear nerves.

Directed self-assembled crystalline oligomer domains on graphene and graphite.

We observe the formation of thin films of fibre-like aggregates from the prototypical organic semiconductor molecule para-hexaphenylene (p-6P) on graphite thin flakes and on monolayer graphene. Using atomic force microscopy, scanning electron microscopy, x-ray diffraction, polarized fluorescence microscopy, and bireflectance microscopy, the molecular orientations on the surface are deduced and correlated to both the morphology as well as to the high-symmetry directions of the graphitic surface: the molecules align with their long axis at ±11° with respect to a high-symmetry direction. The results show that the graphene surface can be used as a growth substrate to direct the self-assembly of organic molecular thin films and nanofibres, both with and without lithographical processing.

Development of an augmented reality system for tracheal intubation guidance of airway management.

Tracheal intubation is a crucial procedure performed in airway management to sustain life during various procedures. However, difficult airways can make intubation challenging, which is associated with increased mortality and morbidity. This is particularly important for children who undergo intubation where the situation is difficult. Improved airway management will decrease incidences of repeated attempts, decrease hypoxic injuries in patients, and decrease hospital stays, resulting in better clinical outcomes and reduced costs. Currently, 3D printed models based on CT scans and ultrasound-guided intubation are being used or tested for device fitting and procedure guidance to increase the success rate of intubation, but both have limitations. Maintaining a 3D printing facility can be logistically inconvenient, and it can be time consuming and expensive. Ultrasound-guided intubation can be hindered by operator dependence, limited two-dimensional visualization, and potential artifacts. In this study, we developed an augmented reality (AR) system that allows the overlay of intubation tools and internal airways, providing real-time guidance during the procedure. A child manikin was used to develop and test the AR system. Three-dimensional CT images were acquired from the manikin. Different tissues were segmented to generate the 3D models that were imported into Unity to build the holograms. Phantom experiments demonstrated the AR-guided system for potential applications in tracheal intubation guidance.

Mapping nanoscale carrier confinement in polycrystalline graphene by terahertz spectroscopy.

Terahertz time-domain spectroscopy (THz-TDS) can be used to map spatial variations in electrical properties such as sheet conductivity, carrier density, and carrier mobility in graphene. Here, we consider wafer-scale graphene grown on germanium by chemical vapor deposition with non-uniformities and small domains due to reconstructions of the substrate during growth. The THz conductivity spectrum matches the predictions of the phenomenological Drude-Smith model for conductors with non-isotropic scattering caused by backscattering from boundaries and line defects. We compare the charge carrier mean free path determined by THz-TDS with the average defect distance assessed by Raman spectroscopy, and the grain boundary dimensions as determined by transmission electron microscopy. The results indicate that even small angle orientation variations below 5° within graphene grains influence the scattering behavior, consistent with significant backscattering contributions from grain boundaries.

Molecular mechanisms of toxicity of silver nanoparticles in zebrafish embryos.

Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk-, and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24 h of exposure, but with a recovery at 48 h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24 h, but not at 48 h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.

High-resolution 3-D T2-weighted imaging in the diagnosis of labyrinthitis ossificans: emphasis on subtle cochlear involvement.

BACKGROUND: Meningitis is the most common cause of acquired sensorineural hearing loss (SNHL) in children. Labyrinthitis ossificans develops in a significant number of patients with meningitis-related SNHL. Reduced T2 signal on MRI within the membranous labyrinth is often noted in the fibrous and ossifying stages of labyrinthitis ossificans. OBJECTIVE: The purpose of this study is to demonstrate the distribution and extent of involvement of the cochlea in children being evaluated for labyrinthitis ossificans; using high-resolution 3-D T2-weighted imaging, and to evaluate for subtle involvement of the scala tympani within the basal turn of the cochlea. MATERIALS AND METHODS: A retrospective review from 2002 to 2012 was performed using a cochlear implant database and PACS search function. Twenty-four patients were found to have MR findings consistent with labyrinthitis ossificans, 13 previously reported. Axial 3-D T2-weighted sequences were obtained in all patients. The presence of abnormal decreased T2 signal within the scala tympani and vestibuli of the cochlea was noted and graded according to the extent. The electronic medical record was reviewed for audiometry and risk factors as well as correlative operative findings. RESULTS: The average age at imaging was 4.2 years. M:F ratio = 5:1. Eighty-eight percent (21/24) of patients had bilateral SNHL. The most common risk factor for labyrinthitis ossificans was meningitis (19/24 or 79%). Eighteen (75%) patients had a history of bacterial meningitis. The mean age for the onset of labyrinthitis was 1.2 years with an average of 2.2-year interval to imaging. Nineteen patients (79%) underwent placement of a cochlear implant. Cochlear obstruction was documented in 83% (40/48) of the ears. Lower grade (1) cochlear obstruction was present in 14 ears and limited to the scala tympani. Statistical analysis was performed correlating MRI imaging and surgical findings. CONCLUSION: Subtle, isolated involvement of the scala tympani within the proximal basal turn is a common finding in labyrinthitis ossificans and history typical for meningitis is not uniformly present. The extent of cochlear obstruction is important and has surgical implications.

In situ TEM creation and electrical characterization of nanowire devices.

We demonstrate the observation and measurement of simple nanoscale devices over their complete lifecycle from creation to failure within a transmission electron microscope. Devices were formed by growing Si nanowires, using the vapor-liquid-solid method, to form bridges between Si cantilevers. We characterize the formation of the contact between the nanowire and the cantilever, showing that the nature of the connection depends on the flow of heat and electrical current during and after the moment of contact. We measure the electrical properties and high current failure characteristics of the resulting bridge devices in situ and relate these to the structure. We also describe processes to modify the contact and the nanowire surface after device formation. The technique we describe allows the direct analysis of the processes taking place during device formation and use, correlating specific nanoscale structural and electrical parameters on an individual device basis.

Congenital Cystic Neck Masses.

Congenital cystic masses are commonly encountered when imaging a patient presenting with a neck mass. Congenital cysts are present at birth; however, these cysts may not present until later in life with some growing slowly and others rapidly increasing in size due to hemorrhage of infection. A neonatal presentation is rare but when present may allow a narrower differential diagnosis. Imaging plays a significant role in defining a lesion as cystic, assessing location, and directing the next step in evaluation and or intervention.