Patient Independent Interictal Epileptiform Discharge Detection.

Epilepsy is a highly prevalent brain condition with many serious complications arising from it. The majority of patients which present to a clinic and undergo electroencephalogram (EEG) monitoring would be unlikely to experience seizures during the examination period, thus the presence of interictal epileptiform discharges (IEDs) become effective markers for the diagnosis of epilepsy. Furthermore, IED shapes and patterns are highly variable across individuals, yet trained experts are still able to identify them through EEG recordings - meaning that commonalities exist across IEDs that an algorithm can be trained on to detect and generalise to the larger population. This research proposes an IED detection system for the binary classification of epilepsy using scalp EEG recordings. The proposed system features an ensemble based deep learning method to boost the performance of a residual convolutional neural network, and a bidirectional long short-term memory network. This is implemented using raw EEG data, sourced from Temple University Hospital's EEG Epilepsy Corpus, and is found to outperform the current state of the art model for IED detection across the same dataset. The achieved accuracy and Area Under Curve (AUC) of 94.92% and 97.45% demonstrates the effectiveness of an ensemble method, and that IED detection can be achieved with high performance using raw scalp EEG data, thus showing promise for the proposed approach in clinical settings.

The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation.

Netrin-1 is a bifunctional chemotropic guidance cue that plays key roles in diverse cellular processes including axon pathfinding, cell migration, adhesion, differentiation, and survival. Here, we present a molecular understanding of netrin-1 mediated interactions with glycosaminoglycan chains of diverse heparan sulfate proteoglycans (HSPGs) and short heparin oligosaccharides. Whereas interactions with HSPGs act as platform to co-localise netrin-1 close to the cell surface, heparin oligosaccharides have a significant impact on the highly dynamic behaviour of netrin-1. Remarkably, the monomer-dimer equilibrium of netrin-1 in solution is abolished in the presence of heparin oligosaccharides and replaced with highly hierarchical and distinct super assemblies leading to unique, yet unknown netrin-1 filament formation. In our integrated approach we provide a molecular mechanism for the filament assembly which opens fresh paths towards a molecular understanding of netrin-1 functions.

Boron rich nanotube drug carrier system is suited for boron neutron capture therapy.

Boron neutron capture therapy (BNCT) is a two-step therapeutic process that utilizes Boron-10 in combination with low energy neutrons to effectively eliminate targeted cells. This therapy is primarily used for difficult to treat head and neck carcinomas; recent advances have expanded this method to cover a broader range of carcinomas. However, it still remains an unconventional therapy where one of the barriers for widespread adoption is the adequate delivery of Boron-10 to target cells. In an effort to address this issue, we examined a unique nanoparticle drug delivery system based on a highly stable and modular proteinaceous nanotube. Initially, we confirmed and structurally analyzed ortho-carborane binding into the cavities of the nanotube. The high ratio of Boron to proteinaceous mass and excellent thermal stability suggest the nanotube system as a suitable candidate for drug delivery into cancer cells. The full physicochemical characterization of the nanotube then allowed for further mechanistic molecular dynamic studies of the ortho-carborane uptake and calculations of corresponding energy profiles. Visualization of the binding event highlighted the protein dynamics and the importance of the interhelical channel formation to allow movement of the boron cluster into the nanotube. Additionally, cell assays showed that the nanotube can penetrate outer membranes of cancer cells followed by localization around the cells' nuclei. This work uses an integrative approach combining experimental data from structural, molecular dynamics simulations and biological experiments to thoroughly present an alternative drug delivery device for BNCT which offers additional benefits over current delivery methods.

Proteinaceous Nano container Encapsulate Polycyclic Aromatic Hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) are toxic, mutagenic and among the most damaging chemical compounds with regard to living organisms. Because of their persistence and wide distribution removal from the environment is an important challenge. Here we report a new Nano container matrix based on the deep sea archaea-derived RHCC-Nanotube (RHCC-NT), which rapidly and preferentially binds low molecular weight PAHs. Under controlled-laboratory conditions and using fluorescence spectroscopy in combination with X-ray crystallography and MD simulations, we quantified the real-time binding of low molecular weight PAHs (2-4 rings) to our substrate. Binding coefficients ranged from 5.4 ± 1.6 (fluorene) to 32 ± 7.0 µM (acenaphthylene) and a binding capacity of 85 pmoles PAH per mg RHCC-NT, or 2.12 µmoles in a standard 25 mg sampler. The uptake rate of pyrene was calculated to be 1.59 nmol/hr∙mol RHCC-NT (at 10  C). Our results clearly show that RHCC-NT is uniquely suited as a monitoring matrix for low molecular weight PAHs.

Reductive power of the archaea right-handed coiled coil nanotube (RHCC-NT) and incorporation of mercury clusters inside protein cages.

Coiled coils are well described as powerful oligomerization motifs and exhibit a large diversity of functions, including gene regulation, cell division, membrane fusion and drug extrusion. The archaea S-layer originated right-handed coiled coil -RHCC-NT- is characterized by extreme stability and is free of cysteine and histidine moieties. In the current study, we have followed a multidisciplinary approach to investigate the capacity of RHCC-NT to bind a variety of ionic complex metal ions. At the outside of the RHCC-NT, one mercury ion forms an electrostatic interaction with the S-methyl moiety of the single methionine residue present in each coil. We demonstrate that RHCC-NT is reducing and incorporating metallic mercury in the large-sized interior cavities which are lined up along the tetrameric channel.

Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge.

The identification of four-stranded G-quadruplexes (G4s) has highlighted the fact that DNA has additional spatial organisations at its disposal other than double-stranded helices. Recently, it became clear that the formation of G4s is not limited to the traditional G3+NL1G3+NL2G3+NL3G3+ sequence motif. Instead, the G3 triplets can be interrupted by deoxythymidylate (DNA) or uridylate (RNA) where the base forms a bulge that loops out from the G-quadruplex core. Here, we report the first high-resolution X-ray structure of a unique unimolecular DNA G4 with a cytosine bulge. The G4 forms a dimer that is stacked via its 5'-tetrads. Analytical ultracentrifugation, static light scattering and small angle X-ray scattering confirmed that the G4 adapts a predominantly dimeric structure in solution. We provide a comprehensive comparison of previously published G4 structures containing bulges and report a special γ torsion angle range preferentially populated by the G4 core guanylates adjacent to bulges. Since the penalty for introducing bulges appears to be negligible, it should be possible to functionalize G4s by introducing artificial or modified nucleotides at such positions. The presence of the bulge alters the surface of the DNA, providing an opportunity to develop drugs that can specifically target individual G4s.

Absorption of polycyclic aromatic hydrocarbons by a highly absorptive polymeric medium.

The efficacy of a lightly cross-linked polymeric bead to absorb polycyclic aromatic hydrocarbons (PAHs) from the surface of fresh- and salt-water in a simulated oil-spill scenario was assessed in this study. A layer of PAHs at the water surface was created by first preparing the PAHs in hexane and then carefully spiking this mixture onto the surface of water. Beads were then applied to the surface of the organic phase and the amount of hydrocarbons absorbed by the beads was examined at prescribed time intervals and at different temperatures. Absorption of PAHs into the beads was exhaustive with ∼86 ±â€¯4% being selectively removed from the organic phase by 120 s. First order reaction rates best described the uptake kinetics and absorption rates ranged from 0.0085 (naphthalene) to 0.0325 s-1 (dibenzo[a,h]anthracene). Absorption of PAHs into the beads was driven by molecular volume (A3). Uptake rates increased markedly for PAHs with molecular volumes between 130 A3 and 190 A3. Beyond this molecular volume there was no apparent change in the rate of uptake. This study shows that these polymeric beads have a high affinity for PAHs and can be used under various environmental conditions with negligible difference in absorptive efficacy.

Archaea S-layer nanotube from a "black smoker" in complex with cyclo-octasulfur (S8 ) rings.

Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion. Comparisons with earlier MD studies of the free energy of hydration as a function of water occupancy in the same cavity of archaeal tetrabrachion show that the sulfur ring is energetically favored over water.

Correction: Dramatic and concerted conformational changes enable rhodocetin to block α2ß1 integrin selectively.

[This corrects the article DOI: 10.1371/journal.pbio.2001492.].

Dramatic and concerted conformational changes enable rhodocetin to block α2ß1 integrin selectively.

The collagen binding integrin α2ß1 plays a crucial role in hemostasis, fibrosis, and cancer progression amongst others. It is specifically inhibited by rhodocetin (RC), a C-type lectin-related protein (CLRP) found in Malayan pit viper (Calloselasma rhodostoma) venom. The structure of RC alone reveals a heterotetramer arranged as an αß and γδ subunit in a cruciform shape. RC specifically binds to the collagen binding A-domain of the integrin α2 subunit, thereby blocking collagen-induced platelet aggregation. However, until now, the molecular basis for this interaction has remained unclear. Here, we present the molecular structure of the RCγδ-α2A complex solved to 3.0 Å resolution. Our findings show that RC undergoes a dramatic structural reorganization upon binding to α2ß1 integrin. Besides the release of the nonbinding RCαß tandem, the RCγ subunit interacts with loop 2 of the α2A domain as result of a dramatic conformational change. The RCδ subunit contacts the integrin α2A domain in the "closed" conformation through its helix C. Combined with epitope-mapped antibodies, conformationally locked α2A domain mutants, point mutations within the α2A loop 2, and chemical modifications of the purified toxin protein, this molecular structure of RCγδ-α2A complex explains the inhibitory mechanism and specificity of RC for α2ß1 integrin.

Inhibition of glycosylation on a camelid antibody uniquely affects its FcγRI binding activity.

Glycoengineering of mAbs has become common practice in attempts to generate the ideal mAb candidate for a wide range of therapeutic applications. The effects of these glycan modifications on the binding affinity of IgG mAbs for FcγRIIIa and their cytotoxicity are well known. However, little is understood about the effect that these modifications have on binding to the high affinity FcγRI receptor. This study analyzed the effect of variable N-glycosylation on a human-llama hybrid mAb (EG2-hFc, 80kDa) binding to FcγRI including a comparison to a full-sized IgG1 (DP-12, 150kDa). This was achieved by the addition of three glycosylation inhibitors (swainsonine, castanospermine, and kifunensine) independently to Chinese hamster ovary (CHO) cell cultures to generate hybrid and high mannose glycan structures. Biophysical analysis by circular dichroism, dynamic light scattering and analytical ultra-centrifugation confirmed that the solution-behaviour of the mAbs remained constant over multiple concentrations and glycan treatments. However, changes were observed when studying the interaction of FcγRI with variously glycosylated mAbs. Both mAbs were observed to have a decreased binding affinity upon treatment with swainsonine which produced hybrid glycans. Following de-glycosylation the binding affinity for EG2-hFc was only marginally reduced (6-fold) compared to a drastic (118-fold) decrease for DP-12. In summary, our data suggest that the relatively low molecular weight of chimeric EG2-hFc may contribute to its enhanced stability against glycan changes making it a highly suitable mAb candidate for therapeutic applications.

Structural decoding of netrin-4 reveals a regulatory function towards mature basement membranes.

Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies with netrin-1, netrin-4 was also proposed to play a role in neuronal outgrowth and developmental/pathological angiogenesis via interactions with netrin-1 receptors. Here, we present the high-resolution structure of netrin-4, which shows unique features in comparison with netrin-1, and show that it does not bind directly to any of the known netrin-1 receptors. We show that netrin-4 disrupts laminin networks and basement membranes (BMs) through high-affinity binding to the laminin γ1 chain. We hypothesize that this laminin-related function is essential for the previously described effects on axon growth promotion and angiogenesis. Our study unveils netrin-4 as a non-enzymatic extracellular matrix protein actively disrupting pre-existing BMs.

The effect of social networking sites on the relationship between perceived social support and depression.

This study examined whether Social Networking Sites (SNSs) have a negative moderator effect on the established relationship between perceived social support and depression in psychiatric inpatients. Survey instruments assessing for depression, perceived social support, and SNS use, were filled out by 301 psychiatric inpatients. Additional data on age, gender, and primary psychiatric diagnosis were collected. A step-wise multiple regression analysis was performed to determine significant interactions. There was no significant interaction of SNS use on the relationship between perceived social support and depression when measured by Social Media Use Integration Scale or by hours of SNS use per day. There was a significant negative relationship between perceived social support and depression, and a significant positive relationship between hours of SNS use per day and depression, measured by the Beck Depression Inventory-II. Limitations include a gender discrepancy among participants, generalizability, recall bias, and SNS measurement. This is the first study to look at SNS use and depression in psychiatric inpatients. SNS use did not affect perceived social support or the protective relationship between perceived social support and depression. Hours of SNS use per day were correlated with depression scores. Future studies between SNS use and depression should quantify daily SNS use.

Increased Activity in Unstructured Versus Structured Gym Time in an After-School Program.

BACKGROUND: More than 10 million American youth engage in after-school programs that provide an opportunity to increase physical activity. The purpose of this study was to test the hypothesis that children in unstructured gym time (free) would have greater activity than both structured gym time (structured) and when increased screen time was available. METHODS: Three interventions were compared in a nested design, with each two-week intervention preceded and followed by a two-week control period. Seventy-four children aged 6 to 12 years were enrolled and wore pedometers during the interventions. RESULTS: Mean pedometer counts were higher during free than structured gym time (p=0.01), which was more apparent in boys (p=0.02) than girls (p=0.24). Neither age nor habitual activity was associated with pedometer counts. Body mass index (BMI) was inversely correlated with counts during free gym time (r=-0.314) in boys and girls combined. Accident rates did not differ among interventions. CONCLUSIONS: After-school programs may be appropriate environments to increase activity levels, but greatest increases were observed in children with the lowest BMIs and may not be as effective in girls as boys. Future research should focus on identifying where children at risk of overweight spend their time and how to implement a program designed at increasing activity levels within those spaces.

Platinum (IV) coiled coil nanotubes selectively kill human glioblastoma cells.

Malignant glioma are often fatal and pose a significant therapeutic challenge. Here we have employed α-helical right handed coiled coils (RHCC) which self-assemble into tetrameric nanotubes that stably associate with platinum (Pt) (IV) compound. This Pt(IV)-RHCC complex showed superior in vitro and in vivo toxicity in human malignant glioma cells at up to 5 fold lower platinum concentrations when compared to free Pt(IV). Pt(IV)-RHCC nanotubes activated multiple cell death pathways in GB cells without affecting astrocytes in vitro or causing damage to normal mouse brain. This Pt(IV)-RHCC nanotubes may serve as a promising new therapeutic tool for low dose Pt(IV) prodrug application for highly efficient and selective treatment of human brain tumors. FROM THE CLINICAL EDITOR: The prognosis of malignant glioma remains poor despite medical advances. Platinum, one of the chemotherapeutic agents used, has significant systemic side effects. In this article, the authors employed α-helical right handed coiled coil (RHCC) protein nanotubes as a carrier for cisplatin. It was shown that the new compound achieved higher tumor kill rate but lower toxicity to normal cells and thus may hold promise to be a highly efficient treatment for the future.