Scalable structural index construction for json analytics

JavaScript Object Notation ( JSON) and its variants have gained great popularity in recent years. Unfortunately, the performance of their analytics is often dragged down by the expensive JSON parsing. To address this, recent work has shown that building bitwise indices on JSON data, called structural indices, can greatly accelerate querying. Despite its promise, the existing structural index construction does not scale well as records become larger and more complex, due to its (inherently) sequential construction process and the involvement of costly memory copies that grow as the nesting level increases. To address the above issues, this work introduces Pison – a more memory-efficient structural index constructor with supports of intra-record parallelism. First, Pison features a redesign of the bottleneck step in the existing solution. The new design is not only simpler but more memory-efficient. More importantly, Pison is able to build structural indices for a single bulky record in parallel, enabled by a group of customized parallelization techniques. Finally, Pison is also optimized for better data locality, which is especially critical in the scenario of bulky record processing. Our evaluation using real-world JSON datasets shows that Pison achieves 9.8X speedup (on average) over the existing structural index construction solution for bulky records and 4.6X speedup (on average) of end-to-end performance (indexing plus querying) over a state-of-the-art SIMD-based JSON parser on a 16-core machine

Manganese coordination chemistry of bis(imino)phenoxide derived [2 + 2] Schiff-base macrocyclic ligands

The [2 + 2] Schiff base macrocycles [2,2'-(CH₂CH₂)(C₆H₄N)₂-2,6-(4-RC₆H₃OH)]₂ (IʳH₂), upon reaction with MnCl₂ (two equivalents) afforded the bimetallic complex [Cl₃Mn(NCMe)][MnCl(IᵗᵇᵘH₂)] (2). Under similar conditions, use of the related [2 + 2] oxy-bridged macrocycle [2,2'-O(C₆H₄N=CH)₂4-RC₆H₃OH] (IIʳH₂), afforded the bimetallic complexes [(MnCl)₂IIʳ] (R = Me 3, tBu 4), whilst the macrocycle derived from 1,2-diaminobenzene and 5,5'-di-tert-butyl-2,2'-dihydroxy-3,3'-methylenedibenzaldehyde (IIIH₄) afforded the complex [(MnCl)₂(III)]·2MeCN (5·2MeCN). For comparative studies, the salt complexes [2,6-(ArNHCH)₂-4-MeC₆H₂O][MnCl₃(NCMe)] (Ar = 2,4-Me₂C₆H₃, 6) and {[2,6-(ArNHCH)₂-4-MeC₆H₂O][MnCl}₂[MnCl₄]·8CH₂Cl₂ (Ar = 4-MeC₆H₄, 7·8CH₂Cl₂) were prepared. The crystal structures of 1 - 7 are reported (synchrotron radiation was necessary for complexes 1, 3 and 5). Complexes 1 - 7 (not 5) were screened for their potential to act as pre-catalysts for the ring opening polymerization (ROP) of ε-caprolactone; 3, 4 and 6, 7 were inactive, whilst 1 and 2 exhibited only poor activity low conversion (<15 %) at temperatures above 60 °C

A pyrene-functionalized triazole-linked hexahomotrioxacalix[3]arene as a fluorescent chemosensor for Zn²⁺ ions

A new pyrenyl appended hexahomotrioxacalix[3]arene L featuring 1,2,3-triazole linkers was synthesized as a fluorescent chemosensor for Zn²⁺ in mixed aqueous media. It exhibited high affinity toward Zn²⁺, and the monomer and excimer emission of the pyrene moieties could be adjusted. The binding stoichiometry of the L·Zn²⁺ complex was determined to be 1:1, and the association constant (Ka) was found to be 7.05 × 10⁴ M⁻¹. The binding behavior with Zn²⁺ has been confirmed by ¹H NMR spectroscopic analysis

A readily accessible multifunctional probe: simultaneous recognition of the cation ZN²⁺ and the anion F⁻ via distinguishable wavelengths

The probe 1 was readily prepared via condensation of 8-formyl-7-hydroxy-coumarin and carbonic dihydrazide in a one-step procedure. Probe 1 exhibited high sensitivity and selectivity towards Zn²⁺ and F⁻ through a “turn-on” fluorescence response and/or ratiometric colorimetric response with low detection limits of the order of 10-8 M. The complex behaviour was fully investigated by spectral titration, isothermal titration calorimetry, 1H NMR spectroscopic titration and mass spectrometry. Interestingly, probe 1 not only recognizes the cation Zn²⁺ and the anion F⁻, but can also distinguish between these two ions via the max wavelength in their UV-vis spectra (360 nm for 1-Zn²⁺ versus 400 nm for 1-F⁻ complex) or their fluorescent spectra (λₑₓ / λₑm = 360 nm/ 454 nm for 1-Zn²⁺ versus λₑₓ / λₑm = 400 nm/ 475 nm for 1-F⁻ complex) due to their differing red-shifts. Additionally, probe 1 has been further explored in the detection of Zn²⁺ in living cells

A multichannel thiacalix[4]arene-based fluorescent chemosensor for Zn²⁺, F⁻ ions and imaging of living cells

The fluorescent sensor (3) based on the 1,3-alternate conformation of the thiacalix[4]arene bearing the coumarin fluorophore, appended via an imino group, has been synthesised. Sensing properties were evaluated in terms of a colorimetric and fluorescence sensor for Zn 2+ and F - . High selectivity and excellent sensitivity were exhibited, and off-on optical behaviour in different media was observed. All changes were visible to the naked eye, whilst the presence of the Zn 2+ and F - induces fluorescence enhancement and the formation of a 1:1 complex with 3. In addition, 3 exhibits low cytotoxicity and good cell permeability and can readily be employed for assessing the change of intracellular levels of Zn 2+ and F -

Synthesis and evaluation of a novel fluorescent sensor based on hexahomotrioxacalix[3]arene for Zn²+ and Cd²+

A novel type of selective and sensitive fluorescent sensor having triazole rings as the binding sites on the lower rim of a hexahomotrioxacalix[3]arene scaffold in a cone conformation is reported. This sensor has desirable properties for practical applications, including selectivity for detecting Zn²⁺ and Cd²⁺ in the presence of excess competing metal ions at low ion concentration or as a fluorescence enhancement type chemosensor due to the cavity of calixarene changing from a ‘flattened-cone’ to a more-upright form and inhibition of PET. In contrast, the results suggested that receptor 1 is highly sensitive and selective for Cu²⁺ and Fe³⁺ as a fluorescence quenching type chemosensor due to the photoinduced electron transfer (PET) or heavy atom effect

Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta.

Amyloid protein aggregates are associated with dozens of devastating diseases including Alzheimer's, Parkinson's, ALS, and diabetes type 2. While structure-based discovery of compounds has been effective in combating numerous infectious and metabolic diseases, ignorance of amyloid structure has hindered similar approaches to amyloid disease. Here we show that knowledge of the atomic structure of one of the adhesive, steric-zipper segments of the amyloid-beta (Aβ) protein of Alzheimer's disease, when coupled with computational methods, identifies eight diverse but mainly flat compounds and three compound derivatives that reduce Aβ cytotoxicity against mammalian cells by up to 90%. Although these compounds bind to Aβ fibers, they do not reduce fiber formation of Aβ. Structure-activity relationship studies of the fiber-binding compounds and their derivatives suggest that compound binding increases fiber stability and decreases fiber toxicity, perhaps by shifting the equilibrium of Aβ from oligomers to fibers. DOI:http://dx.doi.org/10.7554/eLife.00857.001

Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data.

Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification