Twisted [(R3P)PdX] groups above dicarbaborane ligands: 4-dimethylsulfido-3-iodo-3-triphenylphosphine-closo-3-pallada-1,2-dicarbadodecaborane and 3-dimethylphenylphosphine-3-chloro-4-dimethylsulfido-closo-3-pallada-1,2-dicarbadodecaborane

The structural analyses of [3-(PPh₃)-3-I-4-(SMe₂)-closo-3,1,2-PdC₂B₉H₁₀] or [Pd(C₄H₁₆B₉S)I(C₁₈H₁₅P)], (I), and [3-(PPhMe₂)-3-Cl-4-(SMe₂)-closo-3,1,2-PdC₂B₉H₁₀] or [Pd(C₄H₁₆B₉S)Cl(C₈H₁₁P)], (II), show that in comparison with [3-(PR₃)2-closo-3,1,2-PdC₂B₉H₁₁] the presence of the 4-SMe₂ group causes the [PdX(PR₃)] unit (X = halogen) to twist about an axis passing through the Pd atom and the directly opposite B atom of the carbaborane ligand. The halogen atoms are located almost directly above a C atom in the C₂B₃ face, and the conformations of the [PdX(PR₃)] units above the C₂B₃ faces are not those predicted from molecular orbital calculations of the closo-3,1,2-PdC₂B₉ system. The fact that the variation from the predicted conformation is greater in the case of (I) than in (II) may be ascribed to the greater steric interactions induced by the I atom in (I) compared with the Cl atom in (II)

An improved mosquito electrocuting trap that safely reproduces epidemiologically relevant metrics of mosquito human-feeding behaviours as determined by human landing catch

Background: Reliable quantification of mosquito host—seeking behaviours is required to determine the efficacy of vector control methods. For malaria, the gold standard approach remains the risky human landing catch (HLC). Here compare the performance of an improved prototype of the mosquito electrocuting grid trap (MET) as a safer alternative with HLC for measuring malaria vector behaviour in Dar es Salaam, Tanzania. Methods: Mosquito trapping was conducted at three sites within Dar es Salaam representing a range of urbanicity over a 7-month period (December 2012–July 2013, 168 sampling nights). At each site, sampling was conducted in a block of four houses, with two houses being allocated to HLC and the other to MET on each night of study. Sampling was conducted both indoors and outdoors (from 19:00 to 06:00 each night) at all houses, with trapping method (HLC and MET) being exchanged between pairs of houses at each site using a crossover design. Results: The MET caught significantly more Anopheles gambiae sensu lato than the HLC, both indoors (RR [95 % confidence interval (CI)]) = 1.47 [1.23–1.76], P < 0.0001 and outdoors = 1.38 [1.14–1.67], P < 0.0001). The sensitivity of MET compared with HLC did not detectably change over the course of night for either An. gambiae s.l. (OR [CI]) = 1.01 [0.94–1.02], P = 0.27) or Culex spp. (OR [CI]) = 0.99 [0.99–1.0], P = 0.17) indoors and declined only slightly outdoors: An. gambiae s.l. (OR [CI]) = 0.92 [0.86–0.99], P = 0.04), and Culex spp. (OR [CI]) = 0.99 [0.98–0.99], P = 0.03). MET-based estimates of the proportions of mosquitoes caught indoors (P i ) or during sleeping hours (P fl ), as well as the proportion of human exposure to bites that would otherwise occurs indoors (π i ), were statistically indistinguishable from those based on HLC for An. gambiae s.l. (P = 0.43, 0.07 and 0.48, respectively) and Culex spp. (P = 0.76, 0.24 and 0.55, respectively). Conclusions: This improved MET prototype is highly sensitive tool that accurately quantifies epidemiologically-relevant metrics of mosquito biting densities, behaviours and human exposure distribution

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

Positive Clinical Psychology and Schema Therapy (ST): the development of the Young Positive Schema Questionnaire (YPSQ) to complement the Young Schema Questionnaire 3 Short Form (YSQ-S3)

Negative schemas have been widely recognized as being linked to psychopathology and mental health, and they are central to the Schema Therapy (ST) model. This study is the first to report on the psychometric properties of the Young Positive Schema Questionnaire (YPSQ). In a combined community sample (Manila, Philippines, n = 559; Bangalore, India, n = 350; Singapore, n = 628), we identified a 56-item 14-factor solution for the YPSQ. Confirmatory factor analysis supported the 14-factor model for data from the Singapore sample as well as 2 other samples; an Eastern sample from Kuala Lumpur, Malaysia (n =229) and a Western sample from the United States (n = 214). Construct validity was demonstrated with the Young Schema Questionnaire 3 Short Form (YSQ-S3) that measures negative schemas and divergent validity was demonstrated for 11 of the YPSQ subscales with their respective negative schema counterparts. Convergent validity of the 14 subscales of YPSQ was demonstrated with measures of personality dispositions, emotional distress, well-being, trait gratitude, and humor styles. Positive schemas also showed incremental validity over and above negative schemas for these same measures thus demonstrating that both positive and negative schemas are separate constructs that relate in unique ways to mental health. Implications for using both the YPSQ and the YSQ-S3 scales in tandem in ST as well as cultural nuances from the use of Asian samples were discussed

Oxygen Vacancies in LiAlO\u3csub\u3e2\u3c/sub\u3e Crystals

Singly ionized oxygen vacancies are produced in LiAlO2 crystals by direct displacement events during a neutron irradiation. These vacancies, with one trapped electron, are referred to as V+O centers. They are identified and characterized using electron paramagnetic resonance (EPR) and optical absorption. The EPR spectrum from the V+O centers is best monitored near 100 K with low microwave power. When the magnetic field is along the [001] direction, this spectrum has a g value of 2.0030 and well-resolved hyperfine interactions of 310 and 240 MHz with the two 27Al nuclei that are adjacent to the oxygen vacancy. A second EPR spectrum, also showing hyperfine interactions with two 27Al nuclei, is attributed to a metastable state of the V+O center. An optical absorption band peaking near 238 nm is assigned to V+O centers. Bleaching light from a Hg lamp converts a portion of the V+O centers to V0O centers (these latter centers are oxygen vacancies with two trapped electrons). The V0O centers have an absorption band peaking near 272 nm, a photoluminescence band peaking near 416 nm, and a photoluminescence excitation band peaking near 277 nm. Besides the oxygen-vacancy EPR spectra, a holelike spectrum with a resolved, but smaller, hyperfine interaction with one 27Al nucleus is present in LiAlO2 after the neutron irradiation. This spectrum is tentatively assigned to doubly ionized aluminum vacancies

Similarity to peroxisomal-membrane protein family reveals that Sinorhizobium and Brucella BacA affect lipid-A fatty acids

Sinorhizobium meliloti, a legume symbiont, and Brucella abortus, a phylogenetically related mammalian pathogen, both require the bacterial-encoded BacA protein to establish chronic intracellular infections in their respective hosts. We found that the bacterial BacA proteins share sequence similarity with a family of eukaryotic peroxisomal-membrane proteins, including the human adrenoleukodystrophy protein, required for the efficient transport of verylong- chain fatty acids out of the cytoplasm. This insight, along with the increased sensitivity of BacA-deficient mutants to detergents and cell envelope-disrupting agents, led us to discover that BacA affects the very-long-chain fatty acid (27-OHC28:0 and 29-OHC30:0) content of both Sinorhizobium and Brucella lipid A. We discuss models for how BacA function affects the lipid-A fatty-acid content and why this activity could be important for the establishment of chronic intracellular infections. Originally published Proceedings of the National Academy of Sciences, Vol. 101, No. 14, Apr 200

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design. To address this challenge, our group has developed a computational model, rooted in physics, that aims to predict the fitness landscape of HIV-1 proteins in order to design vaccine immunogens that lead to impaired viral fitness, thus blocking viable escape routes. Here, we advance the computational models to address previous limitations, and directly test model predictions against in vitro fitness measurements of HIV-1 strains containing multiple Gag mutations. We incorporated regularization into the model fitting procedure to address finite sampling. Further, we developed a model that accounts for the specific identity of mutant amino acids (Potts model), generalizing our previous approach (Ising model) that is unable to distinguish between different mutant amino acids. Gag mutation combinations (17 pairs, 1 triple and 25 single mutations within these) predicted to be either harmful to HIV-1 viability or fitness-neutral were introduced into HIV-1 NL4-3 by site-directed mutagenesis and replication capacities of these mutants were assayed in vitro. The predicted and measured fitness of the corresponding mutants for the original Ising model (r = −0.74, p = 3.6×10−6) are strongly correlated, and this was further strengthened in the regularized Ising model (r = −0.83, p = 3.7×10−12). Performance of the Potts model (r = −0.73, p = 9.7×10−9) was similar to that of the Ising model, indicating that the binary approximation is sufficient for capturing fitness effects of common mutants at sites of low amino acid diversity. However, we show that the Potts model is expected to improve predictive power for more variable proteins. Overall, our results support the ability of the computational models to robustly predict the relative fitness of mutant viral strains, and indicate the potential value of this approach for understanding viral immune evasion, and harnessing this knowledge for immunogen design

High Redshift Supernova Rates

We use a sample of 42 supernovae detected with the Advanced Camera for Surveys on-board the Hubble Space Telescope as part of the Great Observatories Origins Deep Survey to measure the rate of core collapse supernovae to z~0.7 and type Ia supernovae to z~1.6. This significantly increases the redshift range where supernova rates have been estimated from observations. The rate of core collapse supernovae can be used as an independent probe of the cosmic star formation rate. Based on the observations of 17 core collapse supernovae, we measure an increase in the core collapse supernova rate by a factor of 1.6 in the range 0.3<z<0.7, and an overall increase by a factor of 7 to z~0.7 in comparison to the local core collapse supernova rate. The increase in the rate in this redshift range in consistent with recent measurements of the star formation rate derived from UV-luminosity densities and IR datasets. Based on 25 type Ia supernovae, we find a SN Ia rate that is a factor 3-5 higher at z~1 compared to earlier estimates at lower redshifts (z<0.5), implying that the type Ia supernova rate traces a higher star formation rate at redshifts z>1 compared to low redshift. At higher redshift (z>1), we find a suggested decrease in the type Ia rate with redshift. This evolution of the Ia rate with redshift is consistent with a type Ia progenitor model where there is a substantial delay between the formation of the progenitor star and the explosion of the supernova. Assuming that the type Ia progenitor stars have initial main sequence masses 3-8 M_Sun, we find that 5-7% of the available progenitors explode as type Ia supernovae.Comment: 16 pages, 3 figures, accepted for publication in the Astrophysical Journa

Low-temperature gas opacity - AESOPUS: a versatile and quick computational tool

We introduce a new tool - AESOPUS: Accurate Equation of State and OPacity Utility Software - for computing the equation of state and the Rosseland mean (RM) opacities of matter in the ideal gas phase. Results are given as a function of one pair of state variables, (i.e. temperature T in the range 3.2 <= log(T) <= 4.5, and parameter R= rho/(T/10^6 K)^3 in the range -8 <= log(R) <= 1), and arbitrary chemical mixture. The chemistry is presently solved for about 800 species, consisting of almost 300 atomic and 500 molecular species. The gas opacities account for many continuum and discrete sources, including atomic opacities, molecular absorption bands, and collision-induced absorption. Several tests made on AESOPUS have proved that the new opacity tool is accurate in the results,flexible in the management of the input prescriptions, and agile in terms of computational time requirement. We set up a web-interface (http://stev.oapd.inaf.it/aesopus) which enables the user to compute and shortly retrieve RM opacity tables according to his/her specific needs, allowing a full degree of freedom in specifying the chemical composition of the gas. Useful applications may regard RM opacities of gas mixtures with i) scaled-solar abundances of metals, choosing among various solar mixture compilations available in the literature; ii) varying CNO abundances, suitable for evolutionary models of red and asymptotic giant branch stars and massive stars in the Wolf-Rayet stages; iii) various degrees of enhancement in alpha-elements, and C-N, Na-O and Mg-Al abundance anti-correlations, necessary to properly describe the properties of stars in early-type galaxies and Galactic globular clusters; iv) zero-metal abundances appropriate for studies of gas opacity in primordial conditions.Comment: 32 pages, 34 postscript figures, A&A in press; new section 4.1.2 showing first tests with stellar models, sections 2.2, 2.2.2 and 5 expanded; interactive web-page at http://stev.oapd.inaf.it/aesopu