bluuebunny/crossref_metadata_2025 huggingface dataset:
A CRISPR-Cas9 Genome Engineering Platform in Primary CD4+ T Cells for the Interrogation of HIV Host Factors
Authors: Hultquist Judd F. , Hiatt Joseph , Schumann Kathrin , McGregor Michael J. , Roth Theodore L. , Haas Paige , Doudna Jennifer , Marson Alexander , Krogan Nevan J.
Published: October 2017

CRISPR-Cas9 gene editing strategies have revolutionized our ability to engineer the human genome for robust functional interrogation of complex biological processes. We have recently adapted this technology to primary human T cells to generate a high-throughput platform for analyzing the role of host factors in pathogen infection and lifecycle. Here, we describe applications of this system to investigate HIV pathogenesis in CD4+ T cells. Briefly, CRISPR-Cas9 ribonucleoproteins (crRNPs) are synthesized in vitro and delivered to activated primary human CD4+ T cells by nucleofection. These edited cells are then validated and expanded for use in downstream cellular, genetic, or protein-based assays. Our platform supports the arrayed generation of several gene manipulations in only a few hours’ time and is widely adaptable across culture conditions, infection protocols, and downstream applications. We present detailed protocols for crRNP synthesis, primary T cell culture, 96-well nucleofection, molecular validation, and HIV infection with additional considerations for guide and screen design as well as crRNP multiplexing.
Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)
Authors: Bayona-Vásquez Natalia J , Glenn Travis C , Kieran Troy J , Pierson Todd W , Hoffberg Sandra L , Scott Peter A , Bentley Kerin E , Finger John W , Louha Swarnali , Troendle Nicholas , Díaz-Jaimes Píndaro , Mauricio Rodney , Faircloth Brant C
Published: October 2017

Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially due to the inability to highly-multiplex samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that relies on adapters and primers designed inAdapterama I. Major features of our method include: 1) minimizing the number of processing steps; 2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; 3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; 4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; 5) interchangeable adapter designs; 6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; 7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, 8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
A molecular network of the aging brain implicatesINPPL1andPLXNB1in Alzheimer’s disease
Authors: Mostafavi S. , Gaiteri C. , Sullivan S. E. , White C.C. , Tasaki S. , Xu J. , Taga M. , Klein H. , Patrick E. , Komashko V. , McCabe C. , Smith R. , Bradshaw E.B. , Root D. , Regev A. , Yu L. , Chibnik L.B. , Schneider J.A. , Young-Pearse T. , Bennett D.A. , De Jager P.L.
Published: October 2017

The fact that only symptomatic therapies of small effect are available for Alzheimer’s disease (AD) today highlights the need for new therapeutic targets with which to prevent a major contributor to aging-related cognitive decline. Here, we report the construction and validation of a molecular network of the aging human frontal cortex. Using RNA sequence data from 478 individuals, we first identify the role of modules of coexpressed genes, and then confirm them in independent AD datasets. Then, we prioritize influential genes in AD-related modules and test our predictions in human model systems. We functionally validate two putative regulator genes in human astrocytes:INPPL1andPLXNB1, whose activity in AD may be related to semaphorin signalling and type II diabetes, which have both been implicated in AD. This arc of network identification followed by statistical and experimental validation provides specific new targets for therapeutic development and illustrates a network approach to a complex disease.

One sentence summary

Molecular network analysis of RNA sequencing data from the aging human cortex identifies new Alzheimer’s and cognitive decline genes.
Enhanced intestinal reabsorption due to reduced metabolism of ceftriaxone
Authors: Sar Tapas K , Samanta Indranil , Hansda Rabindra N , Buragohain Rinku , Mandal Tapan K
Published: October 2017

The polyherbal drug (Fibrosin®) is often used as supportive therapy with intramuscular ceftriaxone injection for treatment of mastitis. A single dose of ceftriaxone at 50 mg kg−1was administered intramuscularly in six healthy lactating goats and a single oral dose of Fibrosin®(1.9 gm) was given 1 hr prior to intramuscular ceftriaxone injection to study disposition of ceftriaxone. Plasma and urine samples were collected at predetermined time schedule and ceftriaxone/ceftizoxime was extracted and analyzed by HPLC. Ceftriaxone persisted for 3 hr in plasma of fibrosin treated healthy lactating goats. Mean t½K (distribution half life) following absorption phase and t½K′(elimination half life) following intestinal re-absorption phase were respectively, 0.091 ± 0.01 and 0.43 ± 0.03 hr with a re-absorption half life (t½Ka′) of 0.18 ± 0.003 hr.Ceftriaxone at a lower concentration (67.91 ± 9.42 μg ml−1) was recovered at 24 hr post dosing from urine. This is the first report of pharmacokinetic interaction of intramuscular ceftriaxone injection and the oral polyherbal drug (which was found to be a cytochrome P450inhibitor).
Multiple interactions between Scc1 and Scc2 activate cohesin’s DNA dependent ATPase and replace Pds5 during loading
Authors: Petela Naomi J , Gligoris Thomas G , Metson Jean , Lee Byung-Gil , Voulgaris Menelaos , Hu Bin , Kikuchi Sotaro , Chapard Christophe , Chen Wentao , Rajendra Eeson , Srinivisan Madhusudhan , Yu Hongtao , Löwe Jan , Nasmyth Kim A
Published: October 2017

In addition to sharing with condensin an ability to organize DNA into chromatids, cohesin regulates enhancer-promoter interactions and confers sister chromatid cohesion. Association with chromosomes is regulated by hook-shaped HEAT repeat proteins that Associate With its Kleisin (Scc1) subunit (HAWKs), namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently displaces Pds5 during loading. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesin’s ATPase activity, loading, and translocation while Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesin’s initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2’s association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states, one with Pds5 bound to Scc1 that is not able to hydrolyse ATP efficiently but is capable of release from chromosomes and another in which Scc2, transiently replacing Pds5, stimulates the ATP hydrolysis necessary for loading and translocation away from loading sites.
COPD lungs show an attached stratified mucus layer resembling the protective colonic mucus
Authors: Fernández-Blanco Joan Antoni , Arike Liisa , Ermund Anna , Fakih Dalia , Rodríguez-Piñeiro Ana M. , Martínez-Abad Beatriz , Skansebo Elin , Jackson Sonya , Root James , Singh Dave , McCrae Christopher , Evans Christopher M. , Åstrand Annika , Hansson Gunnar C.
Published: October 2017

The respiratory tract is normally kept essentially free of bacteria by cilia-mediated mucus transport, but in chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF) mucus accumulates due to goblet cell hyperplasia and mucin overexpression. To address mechanisms behind the mucus accumulation, the elastase-induced mouse model was utilized. The proteomes of bronchoalveolar lavage fluid from elastase-induced mice and COPD patients showed similarities to each other and to colonic mucus. Lung mucus showed a striated, laminated appearance in the elastase-induced mice, COPD and CF, resembling that observed for colonic mucus. Less mucus obstruction was observed in mice lacking the Muc5b mucin. The accumulated mucus plugs of the elastase-induced mice were possible to wash out, but a mucus layer covering the epithelium remained attached to the surface goblet cells also after hypertonic saline washings as widely used in CF therapy. The results suggest that the lung can convert its mucus system into an attached mucus layer that protects the epithelium, similarly to the colon.
Genetic analysis ofde novovariants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicatesMYRFas a candidate gene
Authors: Qi Hongjian , Yu Lan , Zhou Xueya , Kitaygorodsky Alexander , Wynn Julia , Zhu Na , Aspelund Gudrun , Lim Foong Yen , Crombleholme Timothy , Cusick Robert , Azarow Kenneth , Danko Melissa Ellen , Chung Dai , Warner Brad W. , Mychaliska George B. , Potoka Douglas , Wagner Amy J. , ElFiky Mahmoud , Nickerson Deborah A. , Bamshad Michael J. , Wilson Jay M. , High Frances A. , Longoni Mauro , Donahoe Patricia , Chung Wendy K. , Shen Yufeng
Published: October 2017

Congenital diaphragmatic hernia (CDH) is one of the most common and lethal birth defects. Previous studies using exome sequencing support a significant contribution of codingde novovariants in complex CDH cases with additional anomalies and likely gene-disrupting (LGD) variants in isolated CDH cases. To further investigate the genetic architecture of CDH, we performed exome or genome sequencing in 283 proband-parent trios. Combined with data from previous studies, we analyzed a total of 357 trios, including 148 complex and 209 isolated cases. Complex and isolated cases both have a significant burden of deleteriousde novocoding variants (1.7~fold, p= 1.2×10−5for complex, 1.5~fold, p= 9.0×10−5for isolated). Strikingly, in isolated CDH, almost all of the burden is carried by female cases (2.1~fold, p=0.004 for likely gene disrupting and 1.8~fold, p= 0.0008 for damaging missense variants); whereas in complex CDH, the burden is similar in females and males. Additionally,de novoLGD variants in complex cases are mostly enriched in genes highly expressed in developing diaphragm, but distributed in genes with a broad range of expression levels in isolated cases. Finally, we identified a new candidate risk geneMYRF(4de novovariants, p-value=2×10−10), a transcription factor intolerant of mutations. Patients withMYRFmutations have additional anomalies including congenital heart disease and genitourinary defects, likely representing a novel syndrome.
Human pluripotent reprogramming with CRISPR activators
Authors: Weltner Jere , Balboa Diego , Katayama Shintaro , Bespalov Maxim , Krjutškov Kaarel , Jouhilahti Eeva-Mari , Trokovic Ras , Kere Juha , Otonkoski Timo
Published: October 2017

CRISPR/Cas9 based gene activation (CRISPRa) is an attractive tool for cellular reprogramming applications due to its high multiplexing capacity and direct targeting of endogenous loci. Here we present the reprogramming of primary human skin fibroblasts into induced pluripotent stem cells (iPSC) using CRISPRa, targeting endogenous OCT4, SOX2, KLF4, MYC and LIN28A promoters. The basal reprogramming efficiency can be improved by an order of magnitude by additionally targeting a conserved Alu-motif, enriched near genes involved in embryo genome activation (EEA-motif). This effect is mediated in part by more efficient activation of NANOG and REX1. These data constitute a proof of principle that somatic cells can be reprogrammed into iPSC using only CRISPRa. Furthermore, the results unravel previously uncharacterized involvement of EEA-motif-associated mechanisms in cellular reprogramming.
Taxon disappearance from microbiome analysis indicates need for mock communities as a standard in every sequencing run
Authors: Yeh Yi-Chun , Needham David M. , Sieradzki Ella T. , Fuhrman Jed A.
Published: October 2017

Mock communities have been used in microbiome method development to help estimate biases introduced in PCR amplification, sequencing, and to optimize pipeline outputs. Nevertheless, the necessity of routine mock community analysis beyond initial method development is rarely, if ever, considered. Here we report that our routine use of mock communities as internal standards allowed us to discover highly aberrant and strong biases in the relative proportions of multiple taxa in a single Illumina HiSeqPE250 run. In this run, an important archaeal taxon virtually disappeared from all samples, and other mock community taxa showed >2-fold high or low abundance, whereas a rerun of those identical amplicons (from the same reaction tubes) on a different date yielded “normal” results. Although obvious from the strange mock community results, due to natural variation of microbiomes at our site, we easily could have missed the problem had we not used the mock communities. The “normal” results were validated over 4 MiSeqPE300 runs and 3 HiSeqPE250 runs, and run-to-run variation was usually low (Bray-Curtis distance was 0.12±0.04). While validating these “normal” results, we also discovered some mock microbial taxa had relatively modest, but consistent, differences between sequencing platforms. We suggest that using mock communities in every sequencing run is essential to distinguish potentially serious aberrations from natural variations. Such mock communities should have more than just a few members and ideally at least partly represent the samples being analyzed, to detect problems that show up only in some taxa, as we observed.

Importance

Despite the routine use of standards and blanks in virtually all chemical or physical assays and most biological studies (a kind of “control”), microbiome analysis has traditionally lacked such standards. Here we show that unexpected problems of unknown origin can occur in such sequencing runs, and yield completely incorrect results that would not necessarily be detected without the use of standards. Assuming that the microbiome sequencing analysis works properly every time risks serious errors that can be avoided by the use of suitable mock communities.
Phase retrieval of coherent diffractive images with global optimization algorithms
Authors: Truong Nguyen Xuan , Whittaker Eric , Denecke Melissa A.
Published: October 2017

Coherent diffractive imaging (CDI) or lensless microscopy has recently been of great interest as a promising alternative to electron microscopy in achieving atomic spatial resolution. Reconstruction of images in real space from a single experimental diffraction pattern in CDI is based on applying iterative phase-retrieval (IPR) algorithms, such as the hybrid input–output and the error reduction algorithms. For noisy data, these algorithms might suffer from stagnation or trapping in local minima. Generally, the different local minima have many common as well as complementary features and might provide useful information for an improved estimate of the object. Therefore, a linear combination of a number of chosen minima, termed a basis set, gives an educated initial estimate, which might accelerate the search for the global solution. In this study, a genetic algorithm (GA) is combined with an IPR algorithm to tackle the stagnation and trapping in phase-retrieval problems. The combined GA–IPR has been employed to reconstruct an irregularly shaped hole and has proven to be reliable and robust. With the concept of basis set, it is strongly believed that many effective local and global optimization frameworks can be combined in a similar manner to solve the phase problem.
Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements
Authors: Anada Masato , Nakanishi-Ohno Yoshinori , Okada Masato , Kimura Tsuyoshi , Wakabayashi Yusuke
Published: October 2017

Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites.
The electrostatic potential of dynamic charge densities
Authors: Hübschle Christian B. , van Smaalen Sander
Published: October 2017

A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of DL-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å−3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.
Variant selection in surface martensite
Authors: Baur Annick P. , Cayron Cyril , Logé Roland E.
Published: October 2017

A significant variant selection is reported in isothermal martensite formed on the surface of an Fe–30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic–body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing.
Analysis of XFEL serial diffraction data from individual crystalline fibrils
Authors: Wojtas David H. , Ayyer Kartik , Liang Mengning , Mossou Estelle , Romoli Filippo , Seuring Carolin , Beyerlein Kenneth R. , Bean Richard J. , Morgan Andrew J. , Oberthuer Dominik , Fleckenstein Holger , Heymann Michael , Gati Cornelius , Yefanov Oleksandr , Barthelmess Miriam , Ornithopoulou Eirini , Galli Lorenzo , Xavier P. Lourdu , Ling Wai Li , Frank Matthias , Yoon Chun Hong , White Thomas A. , Bajt Saša , Mitraki Anna , Boutet Sebastien , Aquila Andrew , Barty Anton , Forsyth V. Trevor , Chapman Henry N. , Millane Rick P.
Published: October 2017

Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.
The N253F mutant structure of trehalose synthase fromDeinococcus radioduransreveals an open active-site topology
Authors: Chow Sih-Yao , Wang Yung-Lin , Hsieh Yu-Chiao , Lee Guan-Chiun , Liaw Shwu-Huey
Published: October 2017

Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures ofDeinococcus radioduransTS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site. Analysis of these structures suggests that substrate binding induces a domain rotation to close the active site. Such a substrate-induced domain rotation has also been observed in some other GH13 enzymes.
Structure of the staphylococcal enterotoxin B vaccine candidate S19 showing eliminated superantigen activity
Authors: Jeong Woo Hyeon , Song Dong Hyun , Hur Gyeung Haeng , Jeong Seong Tae
Published: October 2017

Four mutations (N23A, Y90A, R110A and F177A) were introduced into S19, a vaccine candidate for staphylococcal enterotoxin B (SEB), resulting in a lower binding affinity towards the T-cell receptor beta chain (TCB) and reducing its superantigen activity. The structure of S19 was solved and was superposed on the native or complex structure of SEB. In the superposition model, mutations that were introduced seemed to reduce the number of hydrogen bonds at the SEB–TCB interface. S19 also displayed an unexpected structural change around the flexible-loop region owing to the Y90A mutation. This local structural change provided evidence that the mutated form of S19 could have a lower affinity for major histocompatibility complex (MHC) class II than wild-type SEB.
[μ2-Bis(diphenylphosphanyl)hexane]bis[undecacarbonyl-triangulo-triruthenium(3Ru—Ru)] hexane monosolvate: crystal structure and Hirshfeld surface analysis
Authors: Shawkataly Omar bin , Sirat Siti Syaida , Jotani Mukesh M. , Tiekink Edward R. T.
Published: October 2017

In the title cluster complex hexane solvate, [Ru6(C30H32P2)(CO)22]·C6H14, two Ru3(CO)11fragments are linked by a Ph2P(CH2)6PPh2bridge with the P atoms equatorially disposed with respect to the Ru3triangle in each case; the hexane solvent molecule is statistically disordered. The Ru...Ru distances span a relatively narrow range,i.e. 2.8378 (4) to 2.8644 (4) Å. The hexyl chain within the bridge has an all-transconformation. In the molecular packing, C—H...O interactions between cluster molecules, and between cluster and hexane solvent molecules lead to a three-dimensional architecture. In addition, there are a large number of C[triple-bond]O...π(arene) interactions in the crystal. The importance of the carbonyl groups in establishing the packing is emphasized by the contribution of 53.4% to the Hirshfeld surface by O...H/H...O contacts.
Zwitterionic 1-{(1E)-[(4-hydroxyphenyl)iminio]methyl}naphthalen-2-olate: crystal structure and Hirshfeld surface analysis
Authors: Devika Bhai R. , Girija C. R. , Shalini Suresh , Jotani Mukesh M. , Tiekink Edward R. T.
Published: October 2017

The title zwitterion, C17H13NO2(systematic name: 1-{(1E)-[(4-hydroxyphenyl)iminiumyl]methyl}naphthalen-2-olate), features an intramolecular charge-assisted N+—H...O−hydrogen bond. A twist in the molecule is evident around the N—C(hydroxybenzene) bond [C—N—C—C torsion angle = 39.42 (8)°] and is reflected in the dihedral angle of 39.42 (8)° formed between the aromatic regions of the molecule. In the crystal, zigzag supramolecular chains along theaaxis are formed by charge-assisted hydroxy-O—H...O(phenoxide) hydrogen bonding. These are connected into a layer in theabplane by charge-assisted hydroxybenzene-C—H...O(phenoxide) interactions and π–π contacts [inter-centroid distance between naphthyl-C6rings = 3.4905 (12) Å]. Layers stack along thecaxis with no specific interactions between them. The Hirshfeld surface analysis points to the significance C...H contacts between layers.
Crystal structure of (1R,5S)-endo-(8-methyl-8-azoniabicyclo[3.2.1]oct-3-yl)ammonium aquatrichloridonitratocopper(II)
Authors: Britvin Sergey N. , Rumyantsev Andrey M.
Published: October 2017

The structure of a salt of diprotonatedendo-3-aminotropane crystallized with a copper(II) anionic cluster is reported,viz.(C8H18N2)[CuCl3(NO3)(H2O)]. Neither ion in the salt has been structurally characterized previously. In the crystal, the ions pack together to form a three-dimensional structure held together by a network of intermolecular N—H...O, O—H...Cl and N—H...Cl hydrogen-bonding interactions. Selective crystallization of the title compound can be considered as a simple method for the separation of theexoandendoisomers of 3-aminotropane.
Crystal structure of (E)-4-methyl-N-{2-[2-(4-nitrobenzylidene)hydrazin-1-yl]-2-oxoethyl}benzenesulfonamideN,N-dimethylformamide monosolvate
Authors: Purandara H. , Foro Sabine , Thimme Gowda B.
Published: October 2017

The molecule of the title Schiff base compound, C16H16N4O5S·C3H7NO, displays atransconformation with respect to the C=N double bond. The C—N and N—N bonds are relatively short compared to their normal bond lengths, indicating some degree of delocalization in the molecule. The molecule is bent at the S atom, with an S—N—C—C torsion angle of 164.48 (11)°. The dihedral angle between the two aromatic rings is 84.594 (7)°. Intermolecular N—H...O and C —H...O hydrogen bonds connect centrosymmetrically related molecules into dimers forming rings ofR33(11) andR22(10) graph-set motif stacked along theaaxis into a columnar arrangement. The molecular columns are further linked into a three-dimensional network by C—H...π interactions.
Crystal structure of 2,4,6-trimethylbenzoic anhydride
Authors: Land Michael A. , Robertson Katherine N. , Clyburne Jason A. C.
Published: October 2017

The title compound, C20H22O3, was formed in the reaction between 2,4,6-trimethylbenzoic acid andN,N-diisopropylethylamine in the presence of 1,3-dichloro-1,3-bis(dimethylamino)propenium hydrogen dichloride, and was recrystallized from diethyl ether solution. It is the first exclusively alkyl-substituted benzoic anhydride to have been structurally characterized. The asymmetric unit consists of a half molecule, the other half of which is generated by twofold rotation symmetry; the dihedral angle between the symmetry-related aromatic rings is 54.97 (3)°. The geometric parameters of the aromatic ring are typical of those for 2,4,6-trimethylphenyl substituted groups. The C=O and C—O bond lengths are 1.1934 (12) and 1.3958 (11) Å, respectively, and the angle between these three atoms (O=C—O) is 121.24 (9)°. In the crystal, molecules are linked by weak C—H...O hydrogen bonds and C—H...π interactions. The packing features wavy chains that extend parallel to [001].
Synthesis and crystal structures of two purpurin derivatives: 1,4-dihydroxy-2-propoxyanthraquinone and 2-butoxy-1,4-dihydroxyanthraquinone
Authors: Bosch Eric , McClain Emily N.
Published: October 2017

The title compounds were obtained by deprotonation of 1,2,4-trihydroxyanthraquinone (purpurin) using sodium hydride followed by reaction with either 1-bromopropane or 1-bromobutane. 1,4-Dihydroxy-2-propoxyanthraquinone crystallizes as a 1:1 solvate from acetonitrile, C17H14O5·CH3CN. The anthraquinone core of the molecule is essentially planar and both hydroxy groups participate in intramolecular O—H...O (carbonyl) hydrogen bonds. The propyl chain is angled slightly above the plane of the anthraquinone moiety with a maximum deviation of 0.247 (2) Å above the plane for the terminal carbon atom. In contrast, 2-butoxy-1,4-dihydroxyanthraquinone, C18H16O5, crystallizes from nitromethane with two independent molecules in the asymmetric unit. The anthraquinone core of each independent molecule is essentially planar and both hydroxy groups on both molecules participate in intramolecular O—H...O(carbonyl) hydrogen bonds. The butyl chain in one molecule is also angled slightly above the plane of the anthraquinone moiety, with a maximum deviation of 0.833 (5) Å above the plane for the terminal carbon atom. In contrast, the butyl group on the second molecule is twisted out of the plane of the anthraquinone core with a torsion angle of 65.1 (3)°, resulting in a maximum deviation of 1.631 (5) Å above the plane for the terminal carbon atom.
Crystal structure of the co-crystalline adduct 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD)–4-iodophenol (1/2): supramolecular assembly mediated by halogen and hydrogen bonding
Authors: Rivera Augusto , Rojas Jicli José , Ríos-Motta Jaime , Bolte Michael
Published: October 2017

The asymmetric unit of the title co-crystalline adduct, 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD)–4-iodophenol (1/2), C8H16N4·2C6H5IO, comprises a half molecule of the aminal cage polyamine plus a 4-iodophenol molecule. A twofold rotation axis generates the other half of the adduct. The components are linked by two intermolecular O—H...N hydrogen bonds. The adducts are further linked into a three-dimensional framework structure by a combination of N...I halogen bonds and weak non-conventional C—H...O and C—H...I hydrogen bonds.
A new approach to alkaloid-like systems: synthesis and crystal structure of 1-(2-acetyl-11-methoxy-5,6-dihydro[1,3]dioxolo[4,5-g]pyrrolo[2,1-a]isoquinolin-1-yl)propan-2-one
Authors: Anh Le Tuan , Titov Alexander A. , Samavati Reza , Voskressensky Leonid G. , Varlamov Alexey V. , Khrustalev Victor N.
Published: October 2017

The title compound, C19H19NO5, (I), is the product of a domino reaction between cotarnine chloride and acetylacetylene catalysed by copper(I) iodide. The molecule of (I) comprises a fused tetracyclic system containing two terminal five-membered rings (pyrrole and 1,3-dioxole) and two central six-membered rings (dihydropyridine and benzene). The five-membered 1,3-dioxole ring has an envelope conformation and the central six-membered dihydropyridine ring adopts a twist-boat conformation. The acyl substituent is almost coplanar with the pyrrole ring, whereas the methoxy substituent is twisted by 27.93 (16)° relative to the benzene ring. The 2-oxopropan-1-yl substituent is roughly perpendicular to the pyrrole ring. In the crystal, molecules are stacked along thea-axis direction; the stacks are linked by weak C—H...O hydrogen bonds into puckered layers lying parallel to (001).
Crystal structure and Hirshfield analysis of the 4-(dimethylamino)pyridine adduct of 4-methoxyphenylborane
Authors: Shooter Jesse , Allen Caleb J. , Tinsley Colby W. K. , Zakharov Lev N. , Abbey Eric R.
Published: October 2017

The title compound [systematic name: 4-(dimethylamino)pyridine–4-methoxyphenylborane (1/1)], C14H19BN2O, contains two independent molecules in the asymmetric unit. Both molecules exhibit coplanar, mostlysp2-hybridized methoxy and dimethylamino substituents on their respective aromatic rings, consistent with π-donation into the aromatic systems. The B—H groups exhibit an intramolecular close contact with a C—H group of the pyridine ring, which may be evidence of electrostatic attraction between the hydridic B—H and the electropositive aromatic C—H. There appears to be weak C—H...π(arene) interactions between two of the H atoms of an aminomethyl group and the methoxy-substituted benzene ring of the other independent molecule, and another C—H...π (arene) interaction between one of the pyridine ring H atoms and the same benzene ring.
Structure and function of the thermostableL-asparaginase fromThermococcus kodakarensis
Authors: Guo Jingxu , Coker Alun R. , Wood Steve P. , Cooper Jonathan B. , Chohan Shahid Mahmood , Rashid Naeem , Akhtar Muhummad
Published: October 2017

L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia. The thermostable type I L-asparaginase fromThermococcus kodakarensis(TkA) is composed of 328 amino acids and forms homodimers in solution, with the highest catalytic activity being observed at pH 9.5 and 85°C. It has aKmvalue of 5.5 mMfor L-asparagine, with no glutaminase activity being observed. The crystal structure of TkA has been determined at 2.18 Å resolution, confirming the presence of two α/β domains connected by a short linker region. The N-terminal domain contains a highly flexible β-hairpin which adopts `open' and `closed' conformations in different subunits of the solved TkA structure. In previously solved L-asparaginase structures this β-hairpin was only visible when in the `closed' conformation, whilst it is characterized with good electron density in all of the subunits of the TkA structure. A phosphate anion resides at the active site, which is formed by residues from both of the neighbouring monomers in the dimer. The high thermostability of TkA is attributed to the high arginine and salt-bridge content when compared with related mesophilic enzymes.
The use of the performance measures in Thai public hospitals
Authors: Buathong Suwimon , Bangchokdee Sirilak
Published: October 2017

Purpose

The purpose of this paper is to examine the relationships between participation in performance measurement systems (PMS) and the use of performance measures; the use of performance measures and managerial performance; and participation in PMS and managerial performance in public hospitals in Thailand.

Design/methodology/approach

Data were collected using a mailed questionnaire. A total of 304 middle managers in public hospitals in Southern Thailand participated in the study. The data were analyzed using structural equation modeling.

Findings

The results reveal a positive relationship between participation in PMS and the use of performance measures, and a positive relationship between the use of performance measures and managerial performance. The results also indicate a positive relationship between participation in PMS and improved managerial performance.

Practical implications

Results indicate that top managers in hospitals should allow middle managers to have greater participation in their organization’s PMS. By sharing information between top and middle managers, a PMS can be developed that reflects the organization’s goals, as well as being suitable for departmental performance evaluation. This enhances PMS acceptance by middle managers, and reduces task ambiguity, leading to improved managerial performance.

Originality/value

As middle managers participate more in PMS, their acceptance of PMS increases. They then make greater use of both financial and non-financial performance measures to obtain comprehensive feedback about their department’s performance. This enhances their decision outcomes, resulting in improved managerial performance.
Homelessness among clients of Sydney’s supervised injecting facility
Authors: M. Salmon Allison , Belackova Vendula , Schwanz Ricardo Starling , Jauncey Marianne , Hiley Sarah , Demirkol Apo
Published: October 2017

Purpose

The Uniting Medically Supervised Injecting Centre (MSIC) opened in Sydney, Australia, in May 2001. Homelessness among people who inject drugs (PWID) in Australia has been increasing, and establishing how supervised injecting facilities (SIFs) might best support clients into housing is an important goal. The purpose of this paper is to update knowledge regarding the accommodation status of MSIC clients, thereby supporting a better understanding of the complex needs of these clients.

Design/methodology/approach

Client accommodation status at MSIC registration (first visit) and in a brief survey (conducted in May 2016) were compared; unstable accommodation was defined as rough sleeping, couch surfing, hostel, boarding house or crisis accommodation. The bivariate logistic regression analysis was used to explore the association between socio-demographics and accommodation status at both time points; a paired t-test was used to compare the visit records for those who reported stable and unstable accommodation in May 2016.

Findings

Of 232 clients who were present at MSIC during the week the Brief Survey was conducted, 107 participated. Most were male (79 per cent) with a mean age of 41.4 years. A total of 64 (60 per cent) identified as living in unstable accommodation; having increased from 40 per cent at the time of registration (first visit). There were significant positive associations between unstable accommodation status and unemployment, imprisonment and history of overdose, all measured at registration. In May 2016, unstable accommodation status was significantly associated with age of first injection and with unemployment status (as measured at registration); those living in unstable accommodation in May 2016 had a lower number of visits, a lower number of referrals to health and social services and a lower number of overdoses at MSIC than those living in a stable accommodation.

Originality/value

The rates of unstable accommodation among MSIC clients have been increasing. These findings highlight the importance of SIFs and drug consumption rooms as venue to address the essential needs of PWID, such as housing. The window of opportunity to support PWID who experience housing instability seems to be narrower than for those who live in stable accommodation.
Thailand’s national alcohol survey as a policy monitoring tool
Authors: Saengow Udomsak
Published: October 2017

Purpose

The purpose of this paper is to assess to what extent the Smoking and Alcohol Drinking Behavior Survey (SADBeS), the national alcohol survey, could be used in monitoring goals and cost-effective measures suggested by the National Alcohol Strategy (NAS) issued by public health authorities in 2010.

Design/methodology/approach

The NAS was reviewed. Strategies, measures, and corresponding indicators were extracted. Questionnaire items used in the 2014 SADBeS were assessed in comparison with those indicators.

Findings

Four primary indicators indicate overall success of the NAS. In all, 6 out of 15 measures were in accordance with best-buy or good-buy policies – cost-effective policies suggested by the World Health Organization. After excluding indicators unlikely to be obtained from population-based surveys, the SADBeS could be used in monitoring 5 out of 14 indicators corresponding to best-buy or good-buy measures. Of 103 questionnaire items, 26.2 percent of items could be used to monitor primary indicators of the NAS; 34.0 percent could be used to estimate indicators corresponding to best-buy or good-buy measures. Overall, only 35.0 percent of questionnaire items provided useful information for monitoring primary indicators and cost-effective measures suggested in the NAS.

Practical implications

The SADBeS questionnaire items should be added or replaced to cover feasibly obtained indicators corresponding to best-buy or good-buy policies in the next wave of the survey.

Originality/value

This is the first study addressing the compatibility between the national strategy and the national alcohol survey. It also includes the overview of Thailand’s alcohol strategy, which is, to the author’s knowledge, never presented in any English articles.
Exploring problem use, discrimination, ethnic identity and social networks
Authors: De Kock Charlotte , Decorte Tom
Published: October 2017

Purpose

Possessing a strong ethnic identity and ethnic network are described in some epidemiological literature as moderating factors in the relation between perceived discrimination and varying types of substance use in people with a migration background (PMB). The purpose of this paper is to qualitatively explore problem use, discrimination, ethnic identity and social networks in a small purposive sample of users with a Turkish and Eastern European migration background in Ghent, Belgium.

Design/methodology/approach

The authors present data retrieved within the framework of a qualitative community-based participatory research study that primarily aims to understand the nature of substance use in PMB. In the secondary analysis, the authors focus on a sub-study examining substance use by people with a Turkish (n=55) and Eastern European (n=62) migration background and explore how individuals perceive discrimination, ethnic identity and (ethnic) social networks in 117 qualitative interviews.

Findings

Almost all the respondents in this study reported perceived (inter-)ethnic discrimination. The authors establish that problem users in this study have a complex but albeit weak sense of ethnic identity nor do they have a strong ethnic network. This, in combination with perceived discrimination, is a risk factor for continued problem substance use and may hamper recovery related to problem use.

Originality/value

This article intends to lay the groundwork for future research that should focus more on longitudinally studying the intertwined relation between problem use, discrimination, ethnic identity and especially social instead of solely ethnic networks, their complex nature as well as their relation to recovery processes among persons with a migration background.
Culturally sustaining pedagogy in higher education: teaching so that Black Lives Matter
Authors: Cole Courtney E.
Published: October 2017

Purpose

The purpose of this paper is to show how the principles of Black Lives Matter can be used to enact a culturally sustaining pedagogy (CSP) in higher education settings, particularly in small colleges that serve significant populations of students who are underrepresented in higher education.

Design/methodology/approach

Drawing on examples from college courses in media and society, organizational communication, and interpersonal communication, the case study shows application of the principles of Black Lives Matter in the college classroom at two different institutions in the urban Northeast USA, where the majority of the students are young people of color and/or first-generation college students.

Findings

The paper shows how founding principles of Black Lives Matter, particularly diversity, intersectionality, loving engagement, and empathy, can be used to guide concrete pedagogical practices. It provides examples of how to use Black Lives Matter as a framework to enhance and improve college teaching to make it more diverse and inclusive.

Research limitations/implications

This case study is based on the author’s experiences teaching at two majority-minority colleges in Greater Boston, Massachusetts, USA. This paper is not the result of a systematic research study.

Practical implications

This paper has significant implications for how to enact CSP in higher education settings. This paper is valuable to those looking for specific strategies to include more diverse and inclusive teaching strategies. This research also shows both the utility and impact of Black Lives Matter when applied to higher education.

Social implications

This paper improves public understanding of Black Lives Matter as a social movement.

Originality/value

Since the Black Lives Matter movement is fairly new, there is limited academic research on it. Further, there has not been attention to how Black Lives Matter provides insight into pedagogy, particularly in higher education.
Libraries on the frontlines: neutrality and social justice
Authors: Gibson Amelia N. , Chancellor Renate L. , Cooke Nicole A. , Park Dahlen Sarah , Lee Shari A. , Shorish Yasmeen L.
Published: October 2017

Purpose

The purpose of this paper is to examine libraries’ responsibility to engage with and support communities of color as they challenge systemic racism, engage in the political process, and exercise their right to free speech. Many libraries have ignored the Black Lives Matter (BLM) movement, citing the need to maintain neutrality. Despite extensive scholarship questioning the validity of this concept, the framing of library neutrality as nonpartisanship continues. This paper examines librarianship’s engagement with, and disengagement from black communities through the lens of the BLM movement. It also explores the implications of education, engagement, and activism for people of color and libraries today.

Design/methodology/approach

The authors have engaged the topic from a critical race perspective as a practice in exercising voice – telling stories, presenting counterstories, and practicing advocacy (Ladson-Billings, 1998).

Findings

The assertion that libraries have been socially and politically neutral organizations is ahistorical. When libraries decide not to address issues relevant to people of color, they are not embodying neutrality; they are actively electing not to support the information and service needs of a service population. In order for libraries to live up to their core values, they must engage actively with communities, especially when those communities are in crisis.

Originality/value

As a service field, librarianship has an ethos, values, and history that parallel those of many other service fields. This paper has implications for developing understanding of questions about equitable service provision.