sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. Results: This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. Conclusions: The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMapComment: 3 pages, 1 table, 1 eps figur

Introducing lignin as a binder material for the aqueous production of NMC111 cathodes for Li-ion batteries

By enabling water-based cathode processing, the energy-intensive N-methyl-2-pyrrolidone (NMP) recovery step can be eliminated, reducing the cost and environmental impact of LIBs. Aqueous processing of high capacity Ni-containing LiNixMn1−x−yCoyO2 (NMC) cathodes is problematic due to lithium-ion(Li+) leaching, corrosion of the aluminum (Al) current collector, and the lack of aqueous soluble bio-derived binders. The present study investigates the potential of substituting and fully replacing the commonly used polyvinylidene fluoride (PVDF) and carboxymethyl cellulose (CMC) binders with abundant, bio-derived kraft lignin. This paper gives a holistic overview of the optimal conditions when employing these binders. For the first time, we demonstrate that NMC111 cathodes of comparable specific capacities to NMP/PVDF-based ones over 100 cycles or at high C-rates (5C) can be formulated in water using lignin or CMC/lignin as binder materials. Cyclic voltammetry (CV) revealed that kraft lignin undergoes a redox reaction with the electrolyte between 2.8 and 4.5 V, which diminishes upon subsequent cycles. Differential scanning calorimetry (DSC) revealed that lignin is thermally stable up to 152 °C. Rheology measurements showed that replacing NMP with water allows for a solvent reduction. The cathodes fabricated using an aqueous slurry should be dried at 50 °C, as extensive surface cracks detected using scanning electron microscopy (SEM) diminish. Li+ leaching from NMC111 and NaOH species from kraft lignin caused an increase in pH during aqueous slurry fabrication. A carbon-coated Al foil (C-Al) prevented Al corrosion and increased the lignin cathode's mechanical strength revealing lignin's exceptional binding abilities to carbon. The electrolyte wettability decreased for calendered lignin-containing cathodes with low porosity and a large carbon black/lignin matrix

Lateral spreading effects on VLBI radio images of neutron star merger jets

Very long baseline interferometry radio images recently proved to be essential in breaking the degeneracy in the ejecta model for the neutron star merger GW170817. We discuss the properties of synthetic radio images of merger jet afterglows by using semi-analytical models of laterally spreading or non-spreading jets. The image centroid initially moves away from the explosion point in the sky with apparent superluminal velocity. After reaching a maximum displacement, its motion is reversed. This behaviour is in line with that found in full hydrodynamic simulations. We show that the evolution of the centroid shift and the image size are significantly different when lateral spreading is considered. For Gaussian jet models with plausible model parameters, the morphology of the laterally spreading jet images is much closer to circular. The maximum displacement of the centroid shift and its occurrence time are smaller/earlier by a factor of a few for spreading jets. Our results indicate that it is crucial to include lateral spreading effects when analysing radio images of neutron star merger jets. We also obtain the viewing angle θobs by using the centroid shift of radio images provided the ratio of the jet core size θc and θobs is determined by afterglow light curves. We show that a simple method based on a point-source approximation provides reasonable angular estimates (⁠10−20 per cent errors at most). By taking a sample of laterally spreading structured Gaussian jets, we obtain θobs ∼ 0.32 for GW170817, consistent with previous studies

Structured aqueous processed lignin-based NMC cathodes for energy-dense LIBs with improved rate capability

The cost and environmental impact of lithium-ion batteries (LIBs) can be reduced substantially by enabling the aqueous processing of cathode materials. For the first time, we fabricate high-density, thick NMC111 cathode coatings using water as a solvent, and bio-derived kraft lignin as a binder material. The performance deterioration at high discharge currents is amplified by high mass loading and low bulk porosity. At porosities higher than 60%, the electronic conductivity limits the rate capability of the cathode, while for porosities lower than 30%, ionic conduction causes significant ionic polarization and consequently diminishes rate performance. The underlying lithium-ion diffusion limitation at current densities higher than 0.2 C is mitigated by creating line structures on the surface of the cathode. Structuring the half-dried cathode surface with ceramic blades is preferred over a stamp-like silicon wafer, and the line structures are easier to produce with high mechanical stability in comparison to pit structures. The lignin/water cells investigated herein restore after undergoing rate capability tests (5C), except those with pit structures or ultra-high thickness (>200 μm), due to the extensive crack formation during water evaporation which causes poor mechanical stability. Mechanical and laser structuring methods are compared on the surface of a PVDF/NMP-based cathode. Concerning the implementation in a large-scale battery factory, mechanical structuring is currently considered a processing of choice as it has no surface residuals or waste material. However, laser structuring with ultra-short pulses technique has the potential of outperforming mechanical structuring if the process is optimized to high precision to reduce residual and waste material, due to reproducibility and lower operational costs

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was a novel concept and innovative tool first introduced by Lamb et al to connect small molecules, genes, and diseases using genomic signatures [Lamb et al (2006), Science 313, 1929-1935]. However, the Connectivity Map had some limitations, particularly there was no effective safeguard against false connections if the observed connections were considered on an individual-by-individual basis. Further when several connections to the same small-molecule compound were viewed as a set, the implicit null hypothesis tested was not the most relevant one for the discovery of real connections. Here we propose a simple and robust method for constructing the reference gene-expression profiles and a new connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with the two example gene-signatures (HDAC inhibitors and Estrogens) used by Lamb et al and also a new gene signature of immunosuppressive drugs. Our testing with this new method shows that it achieves a higher level of specificity and sensitivity than the original method. For example, our method successfully identified raloxifene and tamoxifen as having significant anti-estrogen effects, while Lamb et al's Connectivity Map failed to identify these. With these properties our new method has potential use in drug development for the recognition of pharmacological and toxicological properties in new drug candidates.Comment: 8 pages, 2 figures, and 2 tables; supplementary data supplied as a ZIP fil

GRB jet structure and the jet break

We investigate the shape of the jet break in within-beam gamma-ray burst (GRB) optical afterglows for various lateral jet structure profiles. We consider cases with and without lateral spreading and a range of inclinations within the jet core half-opening angle, θc. We fit model and observed afterglow light curves with a smoothly-broken power-law function with a free-parameter κ that describes the sharpness of the break. We find that the jet break is sharper (κ is greater) when lateral spreading is included than in the absence of lateral spreading. For profiles with a sharp-edged core, the sharpness parameter has a broad range of 0.1 ≲ κ ≲ 4.6, whereas profiles with a smooth-edged core have a narrower range of 0.1 ≲ κ ≲ 2.2 when models both with and without lateral spreading are included. For sharp-edged jets, the jet break sharpness depends strongly on the inclination of the system within θc, whereas for smooth-edged jets, κ is more strongly dependent on the size of θc. Using a sample of 20 GRBs, we find 9 candidate smooth-edged jet structures and 8 candidate sharp-edged jet structures, while the remaining 3 are consistent with either. The shape of the jet break, as measured by the sharpness parameter κ, can be used as an initial check for the presence of lateral structure in within-beam GRBs where the afterglow is well-sampled at and around the jet-break time

Search algorithms as a framework for the optimization of drug combinations

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms, originally developed for digital communication, modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs with only one third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6-9 interventions in 80-90% of tests, compared with 15-30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution.Comment: 36 pages, 10 figures, revised versio

Superluminal motion of a relativistic jet in the neutron star merger GW170817

The binary neutron star merger GW170817 was accompanied by radiation across the electromagnetic spectrum and localized to the galaxy NGC 4993 at a distance of 41+/-3 Mpc. The radio and X-ray afterglows of GW170817 exhibited delayed onset, a gradual rise in the emission with time as t^0.8, a peak at about 150 days post-merger, followed by a relatively rapid decline. To date, various models have been proposed to explain the afterglow emission, including a choked-jet cocoon and a successful-jet cocoon (a.k.a. structured jet). However, the observational data have remained inconclusive as to whether GW170817 launched a successful relativistic jet. Here we show, through Very Long Baseline Interferometry, that the compact radio source associated with GW170817 exhibits superluminal motion between two epochs at 75 and 230 days post-merger. This measurement breaks the degeneracy between the models and indicates that, while the early-time radio emission was powered by a wider-angle outflow (cocoon), the late-time emission was most likely dominated by an energetic and narrowly-collimated jet, with an opening angle of <5 degrees, and observed from a viewing angle of about 20 degrees. The imaging of a collimated relativistic outflow emerging from GW170817 adds substantial weight to the growing evidence linking binary neutron star mergers and short gamma-ray bursts.Comment: 42 pages, 4 figures (main text), 2 figures (supplementary text), 2 tables. Referee and editor comments incorporate

Prophylactic and therapeutic activity of fully human monoclonal antibodies directed against Influenza A M2 protein

Influenza virus infection is a prevalent disease in humans. Antibodies against hemagglutinin have been shown to prevent infection and hence hemagglutinin is the major constituent of current vaccines. Antibodies directed against the highly conserved extracellular domain of M2 have also been shown to mediate protection against Influenza A infection in various animal models. Active vaccination is generally considered the best approach to combat viral diseases. However, passive immunization is an attractive alternative, particularly in acutely exposed or immune compromized individuals, young children and the elderly. We recently described a novel method for the rapid isolation of natural human antibodies by mammalian cell display. Here we used this approach to isolate human monoclonal antibodies directed against the highly conserved extracellular domain of the Influenza A M2 protein. The identified antibodies bound M2 peptide with high affinities, recognized native cell-surface expressed M2 and protected mice from a lethal influenza virus challenge. Moreover, therapeutic treatment up to 2 days after infection was effective, suggesting that M2-specific monoclonals have a great potential as immunotherapeutic agents against Influenza infection

Characterization of AKT independent effects of the synthetic AKT inhibitors SH-5 and SH-6 using an integrated approach combining transcriptomic profiling and signaling pathway perturbations

<p>Abstract</p> <p>Background</p> <p>Signal transduction processes mediated by phosphatidyl inositol phosphates affect a broad range of cellular processes such as cell cycle progression, migration and cell survival. The protein kinase AKT is one of the major effectors in this signaling network. Chronic AKT activation contributes to oncogenic transformation and tumor development. Therefore, analogs of phosphatidyl inositol phosphates (PIAs) were designed as new small drugs to block AKT activity for cancer treatment. Here we characterize the biological effects of the PIAs SH-5 and SH-6 in colorectal cancer cell lines.</p> <p>Methods</p> <p>Serum-starved or serum-supplemented human colorectal cancer cell lines SW480, HT29 and HCT116 were exposed to SH-5 and SH-6. AKT activation was determined by western blotting. Cell viability was assessed using a colorimetric XTT-based assay, apoptosis and cell cycle changes were monitored by FACS analysis. The dynamics of cell morphology alterations was evaluated by confocal and time-lapse microscopy. Transcriptional changes due to inhibitor treatment were analyzed using Affymetrix HG-U133A microarrays and RT-PCR.</p> <p>Results</p> <p>While the PIAs clearly reduce AKT phosphorylation in serum starved cells, we did not observe a significant reduction under serum supplemented conditions, giving us the opportunity to analyze AKT independent effects of these compounds. Both inhibitors induce broadly the same morphological alterations, in particular changes in cell shape and formation of intracellular vesicles. Moreover, we observed the induction of binucleated cells specifically in the SW480 cell line. Gene expression analysis revealed transcriptional alterations, which are mostly cell line specific. In accordance to the phenotype we found a gene group associated with mitosis and spindle organization down regulated in SW480 cells, but not in the other cell lines. A bioinformatics analysis using the Connectivity Map linked the gene expression pattern of the inhibitor treated SW480 cells to PKC signaling. Using confocal laser scanning microscopy and time lapse recording we identified a specific defect in the last step of the cytokinesis as responsible for the binucleation.</p> <p>Conclusions</p> <p>The PIAs SH-5 and SH-6 impinge on additional cellular targets apart from AKT in colorectal cancer cells. The effects are mostly cell line specific and have an influence at the outcome of the treatment. In view of potential clinical trials it will be necessary to take these diverse effects into consideration to optimize patient treatment.</p