National Tuberculosis Genotyping and Surveillance Network: Design and Methods

The National Tuberculosis Genotyping and Surveillance Network was established in 1996 to perform a 5-year, prospective study of the usefulness of genotyping Mycobacterium tuberculosis isolates to tuberculosis control programs. Seven sentinel sites identified all new cases of tuberculosis, collected information on patients and contacts, and obtained patient isolates. Seven genotyping laboratories performed DNA fingerprinting analysis by the international standard IS6110 method. BioImage Whole Band Analyzer software was used to analyze patterns, and distinct patterns were assigned unique designations. Isolates with six or fewer bands on IS6110 patterns were also spoligotyped. Patient data and genotyping designations were entered in a relational database and merged with selected variables from the national surveillance database. In two related databases, we compiled the results of routine contact investigations and the results of investigations of the relationships of patients who had isolates with matching genotypes. We describe the methods used in the study

ATLAS flavour-tagging algorithms for the LHC Run 2 pp collision dataset

The flavour-tagging algorithms developed by the ATLAS Collaboration and used to analyse its dataset of √s = 13 TeV pp collisions from Run 2 of the Large Hadron Collider are presented. These new tagging algorithms are based on recurrent and deep neural networks, and their performance is evaluated in simulated collision events. These developments yield considerable improvements over previous jet-flavour identification strategies. At the 77% b-jet identification efficiency operating point, light-jet (charm-jet) rejection factors of 170 (5) are achieved in a sample of simulated Standard Model tt¯ events; similarly, at a c-jet identification efficiency of 30%, a light-jet (b-jet) rejection factor of 70 (9) is obtained

In-Depth Molecular Characterization of Mycobacterium tuberculosis from New Delhi – Predominance of Drug Resistant Isolates of the ‘Modern’ (TbD1−) Type

BACKGROUND: India has the highest estimated burden of tuberculosis in the world, accounting for 21% of all tuberculosis cases world-wide. However, due to lack of systematic analysis using multiple markers the available information on the genomic diversity of Mycobacterium tuberculosis in India is limited. METHODOLOGY/PRINCIPAL FINDINGS: Thus, 65 M. tuberculosis isolates from New Delhi, India were analyzed by spoligotyping, MIRU-VNTR, large deletion PCR typing and single nucleotide polymorphism analysis (SNP). The Central Asian (CAS) 1 _DELHI sub-lineage was the most prevalent sub-lineage comprising 46.2% (n = 30) of all isolates, with shared-type (ST) 26 being the most dominant genotype comprising 24.6% (n = 16) of all isolates. Other sub-lineages observed were: East-African Indian (EAI)-5 (9.2%, n = 6), EAI6_BGD1 (6.2%, n = 4), EAI3_IND, CAS and T1 with 6.2% each (n = 4 each), Beijing (4.6%, n = 3), CAS2 (3.1%, n = 2), and X1 and X2 with 1 isolate each. Genotyping results from five isolates (7.7%) did not match any existing spoligopatterns, and one isolate, ST124, belonged to an undefined lineage. Twenty-six percent of the isolates belonged to the TbD1+ PGG1 genogroup. SNP analysis of the pncA gene revealed a CAS-lineage specific silent mutation, S65S, which was observed for all CAS-lineage isolates (except two ST26 isolates) and in 1 orphan. Mutations in the pncA gene, conferring resistance to pyrazinamide, were observed in 15.4% of all isolates. Collectively, mutations in the rpoB gene, the katG gene and in both rpoB and katG genes, conferring resistance to rifampicin and isoniazid, respectively, were more frequent in CAS1_DELHI isolates compared to non-CAS_DELHI isolates (OR: 3.1, CI95% [1.11, 8.70], P = 0.045). The increased frequency of drug-resistance could not be linked to the patients' history of previous anti-tuberculosis treatment (OR: 1.156, CI95% [0.40, 3.36], P = 0.79). Fifty-six percent of all new tuberculosis patients had mutations in either the katG gene or the rpoB gene, or in both katG and rpoB genes. CONCLUSION: CAS1_DELHI isolates circulating in New Delhi, India have a high frequency of mutations in the rpoB and katG genes. A silent mutation (S65S) in the pncA gene can be used as a putative genetic marker for CAS-lineage isolates

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

Synthesis and Characterization of a Porphyrin Dyad

The sun is a bountiful source of energy for our planet. .With the advent of photovoltaic cells, man has begun harnessing the sun\u27s radiant energy, turning it into a form more directly useful: electricity. Commercially available solar cells currently operate at about 13% efficiency, sufficiently high to make them a viable source of electrical energy. It is of great interest, however, to improve their conversion efficiency, and to lower the cost of production so as to make them more economical, and thereby reduce our dependence upon traditional dirty sources of energy such as coal and oil. It has been found that an electrode coated with a thin film of nanocrystalline titanium dioxide, a very inexpensive and commonly available semiconductor, can be sensitized with a strong light-absorbing dye which can absorb the energy of sunlight and then transfer this energy as electronic charge into the electrode. A cell containing such an electrode is capable of producing a photocurrent at an appreciable voltage. The search is on to find the best sensitizing dye. It must absorb as much of the incident sunlight as possible, be capable of strong adsorption onto Ti02 so as to promote electron injection into the semiconductor, be relatively cheap and easy to synthesize, and be photochemically stable. It was the intent of this research to synthesize and test such a dye, a porphyrin dyad. The dyad was to be made from an electron donating moiety, meso-tetrakis(4-aminophenyl)porphyrin (TAPP), linked by an amide bond to an electron acceptor, meso-tetrakis(4-carboxyphenyl)porphyrin (TCPP). This material eluded attempts at synthesis, due to the poor reactivity of the aminoporphyrin and to the difficulty in ensuring that only one amide bond formed. Characterization of the monomers was carried out, and conditions for their chromatographic separation were determined. Recommendations for successful synthesis of the dyad are given

On the Unusual Synclinal Conformations of Hexafluorobutadiene and Structurally Similar Molecules

An explanation is presented for the unusual conformations of some molecules that contain the CC–CC core, namely, butadienes, biphenyls, and styrenes. Small substituents often induce a synclinal conformation, which brings the substituents into close proximity, and sometimes, there is no anticlinal minimum at all. This would not be predicted from steric repulsion arguments nor would it be expected that atoms that are nonbonded in a Lewis structure would approach closer than the sum of their van der Waals radii. Atomic energies calculated according to the quantum theory of atoms in molecules (QTAIM) do not show a consistent pattern for these structurally similar molecules, nor are intersubstituent bond paths consistently found, nor favorable diatomic interaction energies calculated using the interacting quantum atoms (IQA) scheme. Instead, the synclinal conformations are found to be driven by the attraction energy of the electron distribution of the carbon atoms and the nuclei of the molecule