Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database

ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database are resources of curated chemistry-to-protein relationships widely used in the chemogenomic arena. In this work we have extended an earlier analysis (PMID 22821596) by comparing chemistry and protein target content between 2010 and 2013. For the former, details are presented for overlaps and differences, statistics of stereochemistry as well as stereo representation and MW profiles between the four databases. For 2013 our results indicate quality improvements, major expansion, increased achiral structures and changes in MW distributions. An orthogonal comparison of chemical content with different sources inside PubChem highlights further interpretable differences. Expansion of protein content by UniProt IDs is also recorded for 2013 and Gene Ontology comparisons for human-only sets indicate differences. These emphasise the expanding complementarity of chemistry-to-protein relationships between sources, although different criteria are used for their capture

Near-field iron and carbon chemistry of non-buoyant hydrothermal plume particles, Southern East Pacific Rise 15°S

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Chemistry 201 (2018): 183-197, doi:10.1016/j.marchem.2018.01.011.Iron (Fe)-poor surface waters limit phytoplankton growth and their ability to remove carbon (C) from the atmosphere and surface ocean. Over the past few decades, research has focused on constraining the global Fe cycle and its impacts on the global C cycle. Hydrothermal vents have become a highly debated potential source of Fe to the surface ocean. Two main mechanisms for transport of Fe over long distances have been proposed: Fe-bearing nanoparticles and organic C complexation with Fe in the dissolved (dFe) and particulate (pFe) pools. However, the ubiquity and importance of these processes is unknown at present, and very few vents have been investigated for Fe-Corg interactions or the transport of such materials away from the vent. Here we describe the near-field contributions (first ~100 km from ridge) of pFe and Corg to the Southern East Pacific Rise (SEPR) plume, one of the largest known hydrothermal plume features in the global ocean. Plume particles (> 0.2 μm) were collected as part of the U.S. GEOTRACES Eastern Pacific Zonal Transect cruise (GP16) by in-situ filtration. Sediment cores were also collected to investigate the properties of settling particles. In this study, X-ray absorption near edge structure (XANES) spectroscopy was used in two complementary X-ray synchrotron approaches, scanning transmission X-ray microscopy (STXM) and X-ray microprobe, to investigate the Fe and C speciation of particles within the near-field non-buoyant SEPR plume. When used in concert, STXM and X-ray microprobe provide fine-scale and representative information on particle morphology, elemental co-location, and chemical speciation. Bulk chemistry depth profiles for particulate Corg (POC), particulate manganese (pMn), and pFe indicated that the source of these materials to the non-buoyant plume is hydrothermal in origin. The plume particles at stations within the first ~100 km down-stream of the ridge were composites of mineral (oxidized Fe) and biological materials (organic C, Corg). Iron chemistry in the plume and in the core-top suspended sediment fluff layer were both dominated by Fe(III) phases, such as Fe(III) oxyhydroxides and Fe(III) phyllosilicates. Particulate sulfur (pS) was a rare component of our plume and sediment samples. When pS was detected, it was in the form of an Fe sulfide mineral phase, composing ≤ 0.4% of the Fe on a per atom basis. The resuspended sediment fluff layer contained a mixture of inorganic (coccolith fragments) and Corg bearing (lipid-rich biofilm-like) materials. The particle morphology and co-location of C and Fe in the sediment was different from that in plume particles. This indicates that if the Fe-Corg composite particles settle rapidly to the sediments, then they experience strong alteration during settling and/or within the sediments. Overall, our observations indicate that the particles within the first ~ 100 km of the laterally advected plume are S-depleted, Fe(III)-Corg composites indicative of a chemically oxidizing plume with strong biological modification. These findings confirm that the Fe-Corg relationships observed for non-buoyant plume particles within ~ 100 m of the vent site are representative of particles within this region of the non-buoyant plume (~100 km). These findings also point to dynamic alteration of Fe-Corg bearing particles during transport and settling. The specific biogeochemical processes at play, and the implications for nutrient cycling in the ocean are currently unknown and represent an area of future investigation

A computationally efficient method for hand–eye calibration

Purpose: Surgical robots with cooperative control and semiautonomous features have shown increasing clinical potential, particularly for repetitive tasks under imaging and vision guidance. Effective performance of an autonomous task requires accurate hand–eye calibration so that the transformation between the robot coordinate frame and the camera coordinates is well defined. In practice, due to changes in surgical instruments, online hand–eye calibration must be performed regularly. In order to ensure seamless execution of the surgical procedure without affecting the normal surgical workflow, it is important to derive fast and efficient hand–eye calibration methods. Methods: We present a computationally efficient iterative method for hand–eye calibration. In this method, dual quaternion is introduced to represent the rigid transformation, and a two-step iterative method is proposed to recover the real and dual parts of the dual quaternion simultaneously, and thus the estimation of rotation and translation of the transformation. Results: The proposed method was applied to determine the rigid transformation between the stereo laparoscope and the robot manipulator. Promising experimental and simulation results have shown significant convergence speed improvement to 3 iterations from larger than 30 with regard to standard optimization method, which illustrates the effectiveness and efficiency of the proposed method

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected

Alertness and visuospatial attention in clinical depression

<p>Abstract</p> <p>Background</p> <p>Cognitive deficits are a substantial burden in clinical depression. The present study considered dysfunction in the right-hemispheric attention network in depression, examining alertness and visuospatial attention.</p> <p>Methods</p> <p>Three computerized visuospatial attention tests and an alertness test were administered to 16 depressive patients and 16 matched healthy controls.</p> <p>Results</p> <p>Although no significant group effect was observed, alertness predicted reduced visuospatial performance in the left hemifield. Furthermore, sad mood showed a trend towards predicting left visual field omissions.</p> <p>Conclusions</p> <p>Decreased alertness may lead to lower left hemifield visuospatial attention; this mechanism may be responsible for a spatial bias to the right side in depression, even though treatment of depression and anxiety may reduce this cognitive deficit.</p

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Measurement of the cross-section of high transverse momentum vector bosons reconstructed as single jets and studies of jet substructure in pp collisions at √s = 7 TeV with the ATLAS detector

This paper presents a measurement of the cross-section for high transverse momentum W and Z bosons produced in pp collisions and decaying to all-hadronic final states. The data used in the analysis were recorded by the ATLAS detector at the CERN Large Hadron Collider at a centre-of-mass energy of √s = 7 TeV;{\rm Te}{\rm V}$and correspond to an integrated luminosity of$4.6\;{\rm f}{{{\rm b}}^{-1}}$. The measurement is performed by reconstructing the boosted W or Z bosons in single jets. The reconstructed jet mass is used to identify the W and Z bosons, and a jet substructure method based on energy cluster information in the jet centre-of-mass frame is used to suppress the large multi-jet background. The cross-section for events with a hadronically decaying W or Z boson, with transverse momentum${{p}_{{\rm T}}}\gt 320\;{\rm Ge}{\rm V}$and pseudorapidity$|\eta |\lt 1.9$, is measured to be${{\sigma }_{W+Z}}=8.5\pm 1.7$ pb and is compared to next-to-leading-order calculations. The selected events are further used to study jet grooming techniques

Search for pair-produced long-lived neutral particles decaying to jets in the ATLAS hadronic calorimeter in ppcollisions at √s=8TeV

The ATLAS detector at the Large Hadron Collider at CERN is used to search for the decay of a scalar boson to a pair of long-lived particles, neutral under the Standard Model gauge group, in 20.3fb−1of data collected in proton–proton collisions at √s=8TeV. This search is sensitive to long-lived particles that decay to Standard Model particles producing jets at the outer edge of the ATLAS electromagnetic calorimeter or inside the hadronic calorimeter. No significant excess of events is observed. Limits are reported on the product of the scalar boson production cross section times branching ratio into long-lived neutral particles as a function of the proper lifetime of the particles. Limits are reported for boson masses from 100 GeVto 900 GeV, and a long-lived neutral particle mass from 10 GeVto 150 GeV

Search for direct pair production of the top squark in all-hadronic final states in proton-proton collisions at s√=8 TeV with the ATLAS detector

The results of a search for direct pair production of the scalar partner to the top quark using an integrated luminosity of 20.1fb−1 of proton–proton collision data at √s = 8 TeV recorded with the ATLAS detector at the LHC are reported. The top squark is assumed to decay via t˜→tχ˜01 or t˜→ bχ˜±1 →bW(∗)χ˜01 , where χ˜01 (χ˜±1 ) denotes the lightest neutralino (chargino) in supersymmetric models. The search targets a fully-hadronic final state in events with four or more jets and large missing transverse momentum. No significant excess over the Standard Model background prediction is observed, and exclusion limits are reported in terms of the top squark and neutralino masses and as a function of the branching fraction of t˜ → tχ˜01 . For a branching fraction of 100%, top squark masses in the range 270–645 GeV are excluded for χ˜01 masses below 30 GeV. For a branching fraction of 50% to either t˜ → tχ˜01 or t˜ → bχ˜±1 , and assuming the χ˜±1 mass to be twice the χ˜01 mass, top squark masses in the range 250–550 GeV are excluded for χ˜01 masses below 60 GeV

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration