bluuebunny/crossref_metadata_2025 huggingface dataset:
New information on the Cretaceous sauropod dinosaurs of Zhejiang Province, China: impact on Laurasian titanosauriform phylogeny and biogeography
Authors: Mannion Philip D. , Upchurch Paul , Jin Xingsheng , Zheng Wenjie
Published: August 2019

Titanosaurs were a globally distributed clade of Cretaceous sauropods. Historically regarded as a primarily Gondwanan radiation, there is a growing number of Eurasian taxa, with several putative titanosaurs contemporaneous with, or even pre-dating, the oldest known Southern Hemisphere remains. The early Late Cretaceous Jinhua Formation, in Zhejiang Province, China, has yielded two putative titanosaurs,Jiangshanosaurus lixianensisandDongyangosaurus sinensis. Here, we provide a detailed re-description and diagnosis ofJiangshanosaurus, as well as new anatomical information onDongyangosaurus. Previously, a ‘derived’ titanosaurian placement forJiangshanosauruswas primarily based on the presence of procoelous anterior caudal centra. We show that this taxon had amphicoelous anterior-middle caudal centra. Its only titanosaurian synapomorphy is that the dorsal margins of the scapula and coracoid are approximately level with one another.Dongyangosauruscan clearly be differentiated fromJiangshanosaurus, and displays features that indicate a closer relationship to the titanosaur radiation. Revised scores for both taxa are incorporated into an expanded phylogenetic data matrix, comprising 124 taxa scored for 548 characters. Under equal weights parsimony,Jiangshanosaurusis recovered as a member of the non-titanosaurian East Asian somphospondylan clade Euhelopodidae, andDongyangosauruslies just outside of Titanosauria. However, when extended implied weighting is applied, both taxa are placed within Titanosauria. Most other ‘middle’ Cretaceous East Asian sauropods are probably non-titanosaurian somphospondylans, but at leastXianshanosaurusappears to belong to the titanosaur radiation. Our analyses also recover the Early Cretaceous European sauropodNormanniasaurus genceyias a ‘derived’ titanosaur, clustering with Gondwanan taxa. These results provide further support for a widespread diversification of titanosaurs by at least the Early Cretaceous.
Persistent and substantial impacts of the Deepwater Horizon oil spill on deep-sea megafauna
Authors: McClain Craig R. , Nunnally Clifton , Benfield Mark C.
Published: August 2019

The Deepwater Horizon spill is one of the largest environmental disasters with extensive impacts on the economic and ecological health of the Gulf of Mexico. Surface oil and coastal impacts received considerable attention, but the far larger oil spill in the deep ocean and its effects received considerably less examination. Based on 2017 ROV surveys within 500 m of the wellhead, we provide evidence of continued impacts on diversity, abundance and health of deep-sea megafauna. At locations proximal to the wellhead, megafaunal communities are more homogeneous than in unimpacted areas, lacking many taxonomic groups, and driven by high densities of arthropods. Degraded hydrocarbons at the site may be attracting arthropods. The scope of impacts may extend beyond the impacted sites with the potential for impacts to pelagic food webs and commercially important species. Overall, deep-sea ecosystem health, 7 years post spill, is recovering slowly and lingering effects may be extreme.
Enumeration–screening method for the design of simple polygonal tensegrities
Authors: Zhang Li-Yuan , Li Yue , Xu Guang-Kui , Feng Xi-Qiao
Published: August 2019

Tensegrities, consisting of axially pre-compressed bars and pre-stretched strings, hold broad applications in the design of, for instance, architectures, soft robotics and metamaterials. In this paper, we propose an enumeration–screening method to design planar tensegrities of simple polygonal shapes. In such a polygonal tensegrity, the strings are joined pair-wise to form a simple polygon (a planar shape consisting of straight, non-intersecting line segments) and only one bar is added at each node. The total number of simple polygonal tensegrities designed by this scheme increases exponentially with the number of bars. Moreover, we demonstrate that each of these designed topologies can produce a self-equilibrated and stable tensegrity configuration. This work helps understand the topological features of simple polygonal tensegrities, which can be used as elementary cells to design some novel two- and three-dimensional tensegrity structures.
Hard-particle rotation enabled soft–hard integrated auxetic mechanical metamaterials
Authors: Yang Weizhu , Gao Zongzhan , Yue Zhufeng , Li Xiaodong , Xu Baoxing
Published: August 2019

An auxetic design is proposed by soft–hard material integration and demonstrate negative Poisson's ratio (NPR) can be achieved by leveraging unique rotation features of non-connected hard particles in a soft matrix. A theoretical mechanics framework that describes rotation of hard particles in a soft matrix under a mechanical loading is incorporated with overall Poisson's ratio of the soft–hard integrated metamaterials. The theoretical analysis shows that the auxetic behaviour of the soft–hard integrated structures not only relies critically on geometry of particles, but also depends on their periodic arrangements in the soft matrix. Extensive finite-element analyses (FEA) are performed and validate the theoretical predictions of hard-particle rotation and overall Poisson's ratio of soft–hard integrated structures. Furthermore, uniaxial tensile tests are carried out on three-dimensional printed soft–hard integrated structures and confirm auxetic behaviour of soft–hard integrated structures enabled by the rotation of hard particles. Besides, Poisson's ratio varies nonlinearly with the thickness of specimens and reaches a maximum NPR far out of the bounds of plane stress and plane strain situations, which agrees well with FEA. This work provides a theoretical foundation for the design of mechanical metamaterials enabled by soft–hard material integration with auxetic deformation behaviour.
Modelling transport and mean age of dense core vesicles in large axonal arbours
Authors: Kuznetsov I. A. , Kuznetsov A. V.
Published: August 2019

A model simulating the transport of dense core vesicles (DCVs) in type II axonal terminals of
Drosophila
motoneurons has been developed. The morphology of type II terminals is characterized by the large number of
en passant
boutons. The lack of both scaled-up DCV transport and scaled-down DCV capture in boutons results in a less efficient supply of DCVs to distal boutons. Furthermore, the large number of boutons that DCVs pass as they move anterogradely until they reach the most distal bouton may lead to the capture of a majority of DCVs before they turn around in the most distal bouton to move in the retrograde direction. This may lead to a reduced retrograde flux of DCVs and a lack of DCV circulation in type II terminals. The developed model simulates DCV concentrations in boutons, DCV fluxes between the boutons, age density distributions of DCVs and the mean age of DCVs in various boutons. Unlike published experimental observations, our model predicts DCV circulation in type II terminals after these terminals are filled to saturation. This disagreement is likely because experimentally observed terminals were not at steady state, but rather were accumulating DCVs for later release. Our estimates show that the number of DCVs in the transiting state is much smaller than that in the resident state. DCVs travelling in the axon, rather than DCVs transiting in the terminal, may provide a reserve of DCVs for replenishing boutons after a release. The techniques for modelling transport of DCVs developed in our paper can be used to model the transport of other organelles in axons.
The role of humidity and metabolic status on lean mass catabolism in migratory Swainson's thrushes (Catharus ustulatus)
Authors: Groom Derrick J. E. , Deakin Jessica E. , Lauzau M. Collette , Gerson Alexander R.
Published: August 2019

Migratory birds use protein as a fuel source during flight, but the mechanisms and benefits of protein catabolism during migration are poorly understood. The tissue-specific turnover rate hypothesis proposes that lean mass loss depends solely on the constitutive rate of protein degradation for a given tissue, and is therefore independent of metabolic rate or environmental stimuli. However, it has been demonstrated that environmental stressors such as humidity affect the rate of lean mass catabolism during flight, a finding that seemingly contradicts the tissue-specific turnover rate hypothesis. In order to resolve this, we placed migratory Swainson's thrushes in either high (HEWL) or low (LEWL) evaporative water loss conditions at rest and while undergoing simulated migratory flight at 8 m s−1in a wind tunnel to test the impact of both environmental stressors and metabolic rate on the rate of protein breakdown. The total quantity and rate of lean mass loss was not different between flight and rest birds, but was affected by humidity condition, with HEWL losing significantly more lean mass. These results show that the rate of protein breakdown in migratory birds is independent of metabolic rate, but it can be augmented in response to environmental stressors.
From synaptic input to muscle contraction: arm muscle cells of
Octopus vulgaris
show unique neuromuscular junction and excitation–contraction coupling properties
Authors: Nesher Nir , Maiole Federica , Shomrat Tal , Hochner Benyamin , Zullo Letizia
Published: August 2019

The muscular-hydrostat configuration of octopus arms allows high manoeuvrability together with the efficient motor performance necessary for its multitasking abilities. To control this flexible and hyper-redundant system the octopus has evolved unique strategies at the various levels of its brain-to-body organization. We focus here on the arm neuromuscular junction (NMJ) and excitation–contraction (E-C) properties of the arm muscle cells. We show that muscle cells are cholinergically innervated at single eye-shaped locations where acetylcholine receptors (AChR) are concentrated, resembling the vertebrate neuromuscular endplates. Na
+
and K
+
contribute nearly equally to the ACh-activated synaptic current mediating membrane depolarization, thereby activating voltage-dependent L-type Ca
2+
channels. We show that cell contraction can be mediated directly by the inward Ca
2+
current and also indirectly by calcium-induced calcium release (CICR) from internal stores. Indeed, caffeine-induced cell contraction and immunohistochemical staining revealed the presence and close association of dihydropyridine (DHPR) and ryanodine (RyR) receptor complexes, which probably mediate the CICR. We suggest that the dynamics of octopus arm contraction can be controlled in two ways; motoneurons with large synaptic inputs activate vigorous contraction via activation of the two routs of Ca
2+
induced contraction, while motoneurons with lower-amplitude inputs may regulate a graded contraction through frequency-dependent summation of EPSP trains that recruit the CICR. Our results thus suggest that these motoneuronal pools are likely to be involved in the activation of different E-C coupling modes, thus enabling a dynamics of muscles activation appropriate for various tasks such as stiffening versus motion generation.
Slow life-history strategies are associated with negligible actuarial senescence in western Palaearctic salamanders
Authors: Cayuela Hugo , Olgun Kurtuluş , Angelini Claudio , Üzüm Nazan , Peyronel Olivier , Miaud Claude , Avcı Aziz , Lemaitre Jean-François , Schmidt Benedikt R.
Published: August 2019

Actuarial senescence has been viewed for a long time as an inevitable and uniform process. However, the work on senescence has mainly focused on endotherms with deterministic growth and low regeneration capacity during the adult stage, leading to a strong taxonomic bias in the study of ageing. Recent studies have highlighted that senescence could indeed display highly variable trajectories that correlate with species life-history traits. Slow life histories and indeterminate growth seem to be associated with weak and late senescence. Furthermore, high regenerative abilities could lead to negligible senescence in ectotherms. However, demographic data for species that would allow testing of these hypotheses are scarce. Here, we investigated senescence patterns in ‘true salamanders’ from the western Palaearctic. Our results showed that salamanders have slow life histories and that they experience negligible senescence. This pattern was consistent at both intra- and interspecific levels, suggesting that the absence of senescence may be a phylogenetically conserved trait. The regenerative capacities of salamanders, in combination with other physiological and developmental features such as an indeterminate growth and a low metabolic rate, probably explain why these small ectotherms have lifespans similar to that of large endotherms and, in contrast with most amniotes, undergo negligible senescence. Our study seriously challenges the idea that senescence is a ubiquitous phenomenon in the tree of life.
Climate drives spatial variation in Zika epidemics in Latin America
Authors: Harris Mallory , Caldwell Jamie M. , Mordecai Erin A.
Published: August 2019

Between 2015 and 2017, Zika virus spread rapidly through populations in the Americas with no prior exposure to the disease. Although climate is a known determinant of many
Aedes
-transmitted diseases, it is currently unclear whether climate was a major driver of the Zika epidemic and how climate might have differentially impacted outbreak intensity across locations within Latin America. Here, we estimated force of infection for Zika over time and across provinces in Latin America using a time-varying susceptible–infectious–recovered model. Climate factors explained less than 5% of the variation in weekly transmission intensity in a spatio-temporal model of force of infection by province over time, suggesting that week to week transmission within provinces may be too stochastic to predict. By contrast, climate and population factors were highly predictive of spatial variation in the presence and intensity of Zika transmission among provinces, with pseudo-
R
2
values between 0.33 and 0.60. Temperature, temperature range, rainfall and population size were the most important predictors of where Zika transmission occurred, while rainfall, relative humidity and a nonlinear effect of temperature were the best predictors of Zika intensity and burden. Surprisingly, force of infection was greatest in locations with temperatures near 24°C, much lower than previous estimates from mechanistic models, potentially suggesting that existing vector control programmes and/or prior exposure to other mosquito-borne diseases may have limited transmission in locations most suitable for
Aedes aegypti
, the main vector of Zika, dengue and chikungunya viruses in Latin America.
The evolutionary dynamics of the early Palaeozoic marine biodiversity accumulation
Authors: Kröger Björn , Franeck Franziska , Rasmussen Christian M. Ø.
Published: August 2019

The early Palaeozoic Era records the initial biodiversification of the Phanerozoic. The increase in biodiversity involved drastic changes in taxon longevity, and in rates of origination and extinction. Here, we calculate these variables in unprecedented temporal resolution. We find that highly volatile origination and extinction rates are associated with short genus longevities during the Cambrian Period. During the Ordovician and Silurian periods, evolutionary rates were less volatile and genera persisted for increasingly longer intervals. The 90%-genus life expectancy doubled from 5 Myr in the late Cambrian to more than 10 Myr in the Ordovician–Silurian periods. Intervals with widespread ecosystem disruption are associated with short genus longevities during the Cambrian and with exceptionally high longevities during the Ordovician and Silurian periods. The post-Cambrian increase in persistence of genera, therefore, indicates an elevated ability of the changing early Palaeozoic marine ecosystems to sustainably maintain existing genera. This is evidence of a new level of ecosystem resilience which evolved during the Ordovician Period.
Deepprune: Learning efficient and interpretable convolutional networks through weight pruning for predicting DNA-protein binding
Authors: Luo Xiao , Chi Weilai , Deng Minghua
Published: August 2019

Convolutional neural network (CNN) based methods have outperformed conventional machine learning methods in predicting the binding preference of DNA-protein binding. Although studies in the past have shown that more convolutional kernels help to achieve better performance, visualization of the model can be obscured by the use of many kernels, resulting in overfitting and reduced interpretation because the number of motifs in true models is limited. Therefore, we aim to arrive at high performance, but with limited kernel numbers, in CNN-based models for motif inference.

We herein present Deepprune, a novel deep learning framework, which prunes the weights in the dense layer and fine-tunes iteratively. These two steps enable the training of CNN-based models with limited kernel numbers, allowing easy interpretation of the learned model. We demonstrate that Deepprune significantly improves motif inference performance for the simulated datasets. Furthermore, we show that Deepprune outperforms the baseline with limited kernel numbers when inferring DNA-binding sites from ChIP-seq data.
Dynamic turnover of centromeres drives karyotype evolution in Drosophila
Authors: Bracewell Ryan , Chatla Kamalakar , Nalley Matthew J. , Bachtrog Doris
Published: August 2019

Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes for multipleDrosophila obscuragroup species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and the creation of metacentric chromosomes in some species was driven byde novoseeding of new centromeres at ancestrally gene-rich regions, independently of chromosomal rearrangements. The emergence of centromeres resulted in a drastic size increase due to repeat accumulation, and dozens of genes previously located in euchromatin are now embedded in pericentromeric heterochromatin. Metacentric chromosomes secondarily became telocentric in thepseudoobscurasubgroup through centromere repositioning and a pericentric inversion. The former (peri)centric sequences left behind shrunk dramatically in size after their inactivation, yet contain remnants of their evolutionary past, including increased repeat-content and heterochromatic environment. Centromere movements are accompanied by rapid turnover of the major satellite DNA detected in (peri)centromeric regions.
Essentiality ofCREBBPinEP300truncated B-cell lymphoma revealed by genome-wide CRISPR-Cas9 screen
Authors: Nie Man , Du Likun , Zhang Bo , Ren Weicheng , Joung Julia , Ye Xiaofei , Fuenzalida Jonathan Arias , Shi Xi , Liu Dongbing , Wu Kui , Zhang Feng , Pan-Hammarström Qiang
Published: August 2019

Histone acetyltransferases (HATs), includingCREBBPandEP300, are frequently mutated in B-cell malignancies and usually play a tumor-suppressive role. In this study, we performed whole genome and transcriptome sequencing and a genome-wide CRISPR-Cas9 knockout screen to study a germinal center B-cell like diffuse large B-cell lymphoma (DLBCL) cell line (RC-K8). Using a summarizing method that is optimized to address the complexity introduced by the time-course design, we identified a distinct pattern of genetic essentialities in RC-K8, including a dependency onCREBBPandMDM2, shown already at early time points and a gradually increased dependency on oxidative phosphorylation related genes. The dependency onCREBBPis associated with the corresponding genetic alterations identified in this cell line, i.e. a balanced translocation involvesEP300, which resulted in a truncated form of protein that lacks the critical bromodomain and HAT domain. We further evaluated the previously published CRISPR-Cas9 screens and identified a genetic essentiality ofCREBBPorEP300gene in a small set of cancer cell lines, including several DLBCL cell lines that are highly sensitive forEP300knockout and withCREBBPmutations or copy number loss. The dependency of the remaining HAT function inCREBBPand/orEP300-deficient genotype was validated by testing the HAT-domain inhibitor A-485. Our study suggests that integration of the unbiased, time-course-based functional screen results with the genomic and transcriptomic data can identify druggable vulnerability in individual or subgroups of cell lines/patients, which may help to develop more effective therapeutic strategies for cancers that are genetically highly heterogeneous, like DLBCL.
Identifying a task-invariant cognitive reserve network using task potency
Authors: van Loenhoud A.C. , Habeck C. , van der Flier W.M. , Ossenkoppele R. , Stern Y.
Published: August 2019

Cognitive reserve (CR) is thought to protect against the consequence of age- or disease-related structural brain changes across multiple cognitive domains. The neural basis of CR may therefore comprise a functional network that is actively involved in many different cognitive processes. To investigate the existence of such a “task-invariant” CR network, we measured functional connectivity in a cognitively normal sample between 20-80 years old (N=265), both at rest and during the performance of 11 separate tasks that aim to capture four latent cognitive abilities (i.e. vocabulary, episodic memory, processing speed, and fluid reasoning). For each individual, we determined the change in functional connectivity from the resting state to each task state, which is referred to as “task potency” (Chauvin et al., 2017; Chauvin et al., 2018). Task potency was calculated for each pair among 264 nodes (Power et al., 2011) and then summarized across tasks reflecting the same cognitive ability. Subsequently, we established the correlation between task potency and premorbid IQ or education (i.e. CR factors). We identified a set of 57 pairs in which task potency showed significant correlations with IQ, but not education, across all four cognitive abilities. These pairs were included in a principal component analysis, from which we extracted the first component to obtain a latent variable reflecting task potency in this task-invariant CR network. This task potency variable moderated the relationship between cortical thickness and episodic memory performance (β=−.64, p=.01), and showed a direct effect on fluid reasoning (β=.08, p<.01) after adjusting for the effects of cortical thickness. Our identification of this task-invariant network contributes to a better understanding of the mechanism underlying CR, which may facilitate the development of CR-enhancing treatments. Our work also offers a useful alternative operational measure of CR future studies.
A mixture of three engineered phosphotriesterases enables rapid detoxification of the entire spectrum of known threat nerve agents
Authors: Despotovic Dragana , Aharon Einav , Dubovetskyi Artem , Leader Haim , Ashani Yacov , Tawfik Dan S.
Published: August 2019

Nerve agents are organophosphates that potently inhibit acetylcholinesterase and their enzymatic detoxification has been a long-standing goal. Nerve agents vary widely in size, charge, hydrophobicity, and the cleavable ester bond. A single enzyme is therefore unlikely to efficiently hydrolyze all agents. Here, we describe a mixture of three previously developed variants of the bacterial phosphotriesterase (Bd-PTE) that are highly stable and nearly sequence identical. This mixture enables effective detoxification of a broad spectrum of known threat agents – GA (tabun), GB (sarin), GD (soman), GF (cyclosarin), VX, and Russian-VX. The potential for dimer dissociation and exchange that could inactivateBd-PTE has minimal impact, and the three enzyme variants are as active in a mixture as they are individually. To our knowledge, this engineered enzyme ‘cocktail’ comprises the first solution for enzymatic detoxification of the entire range of threat nerve agents.
Origins and long-term patterns of copy-number variation in rhesus macaques
Authors: Thomas Gregg W.C , Wang Richard J. , Nguyen Jelena , Harris R. Alan , Raveendran Muthuswamy , Rogers Jeffrey , Hahn Matthew W.
Published: August 2019

Mutations play a key role in the development of disease in an individual and the evolution of traits within species. Recent work in humans and other primates has clarified the origins and patterns of single nucleotide variants, showing that most arise in the father’s germline during spermatogenesis. It remains unknown whether larger mutations, such as deletions and duplications of hundreds or thousands of nucleotides, follow similar patterns. Such mutations lead to copy-number variation (CNV) within and between species, and can have profound effects by deleting or duplicating genes. Here we analyze patterns of CNV mutations in 32 rhesus macaque individuals from 14 parent-offspring trios. We find the rate of CNV mutations per generation is low (less than one per genome) and we observe no correlation between parental age and the number of CNVs that are passed on to offspring. We also examine segregating CNVs within the rhesus macaque sample and compare them to a similar dataset from humans, finding that both species have far more segregating deletions than duplications. We contrast this with long-term patterns of gene copy-number evolution between 17 mammals, where the proportion of deletions that become fixed along the macaque lineage is much smaller than the proportion of segregating deletions. These results suggest purifying selection acting on deletions, such that the majority of them are removed from the population over time. Rhesus macaques are an important biomedical model organism, so these results will aid in our understanding of this species and the disease models it supports.
Systematic identification of factors bound to isolated metaphase ESC chromosomes reveals a role for chromatin repressors in compaction
Authors: Djeghloul Dounia , Kohler Anne-Céline , Patel Bhavik , Kramer Holger , Veland Nicolas , Whilding Chad , Dimond Andrew , Elliott James , Feytout Amelie , Bharat Tanmay A.M. , Tarafder Abul K. , Löwe Jan , Ng Bee L. , Guo Ya , Brown Karen , Guy Jacky , Merkenschlager Matthias , Fisher Amanda G.
Published: August 2019

Epigenetic information is transmitted from mother to daughter cells through mitosis. To identify trans-acting factors and cis-acting elements that might be important for conveying epigenetic memory through cell division, we isolated native (unfixed) chromosomes from metaphase-arrested cells using flow cytometry and performed LC-MS/MS to determine the repertoire of chromosome-bound proteins. Quantitative proteomic comparisons between metaphase-arrested cell lysates and chromosome-sorted samples revealed a cohort of proteins that were significantly enriched on mitotic ESC chromosomes. These include pluripotency-associated transcription factors, repressive chromatin-modifiers (such as PRC2 and DNA methyl-transferases) and proteins governing chromosome architecture. We showed that deletion of PRC2, DNMT1/3a/3b or Mecp2 provoked an increase in the size of individual mitotic chromosomes consistent with de-condensation, as did experimental cleavage of cohesin complexes. These data provide a comprehensive inventory of chromosome-bound factors in pluripotent stem cells at mitosis and reveal an unexpected role for chromatin repressor complexes in preserving mitotic chromosome compaction.
A versatile nanoreactor for complementary in situ X-ray and electron microscopy studies in catalysis and materials science
Authors: Fam Yakub , Sheppard Thomas L. , Becher Johannes , Scherhaufer Dennis , Lambach Heinz , Kulkarni Satishkumar , Keller Thomas F. , Wittstock Arne , Wittwer Felix , Seyrich Martin , Brueckner Dennis , Kahnt Maik , Yang Xiaogang , Schropp Andreas , Stierle Andreas , Schroer Christian G. , Grunwaldt Jan-Dierk
Published: August 2019

Two in situ `nanoreactors' for high-resolution imaging of catalysts have been designed and applied at the hard X-ray nanoprobe endstation at beamline P06 of the PETRA III synchrotron radiation source. The reactors house samples supported on commercial MEMS chips, and were applied for complementary hard X-ray ptychography (23 nm spatial resolution) and transmission electron microscopy, with additional X-ray fluorescence measurements. The reactors allow pressures of 100 kPa and temperatures of up to 1573 K, offering a wide range of conditions relevant for catalysis. Ptychographic tomography was demonstrated at limited tilting angles of at least ±35° within the reactors and ±65° on the naked sample holders. Two case studies were selected to demonstrate the functionality of the reactors: (i) annealing of hierarchical nanoporous gold up to 923 K under inert He environment and (ii) acquisition of a ptychographic projection series at ±35° of a hierarchically structured macroporous zeolite sample under ambient conditions. The reactors are shown to be a flexible and modular platform for in situ studies in catalysis and materials science which may be adapted for a range of sample and experiment types, opening new characterization pathways in correlative multimodal in situ analysis of functional materials at work. The cells will presently be made available for all interested users of beamline P06 at PETRA III.
Steric and electronic evaluations of P(o-tol)R
2, where R is phenyl or cyclohexyl: crystal structures of SeP(o-tol)R
2
Authors: Davis Wade L. , Muller Alfred
Published: August 2019

The crystal structures of SeP(o-tol)R
2, where o-tol is ortho-tolyl (2-methylphenyl) and R is Ph (phenyl), namely (2-methylphenyl)diphenylphosphane selenide, C19H17PSe, or Cy (cyclohexyl), namely dicyclohexyl(2-methylphenyl)phosphane selenide, C19H29PSe, were determined to aid in the evaluation of the steric and electronic behaviour of these analogous phosphane compounds. The compounds crystallized in similar monoclinic crystal systems, but are differentiated in their unit cells by a doubling of the number of independent molecules for R = Cy (Z′ = 2) and the choice of glide plane by convention. The preferred orientation for the o-tolyl substituent obtained from the X-ray structural analysis is gauche for R = Ph and anti for R = Cy (using the Se—P—C
ipso
—C
ortho
torsion angles as reference). Density functional theory (DFT) calculations showed both conformations to be equally probable and indicate that the preferred solid-state conformer is probably due to the minimization of repulsion energies, resulting in a packing arrangement primarily featuring weak C—H...Se interactions and additional C—H...π interactions in the R = Ph structure. A detailed electronic and steric analysis was conducted on both phosphanes using Se—P bond lengths, multinuclear NMR 1
J
Se–P coupling constants, theoretical topological evaluation and crystallographic and solid-angle calculations, and compared to selected literature examples. The results indicate that the use of the o-tolyl substituent increases both the electron-donating capability and the steric size, but is also dependent on whether the o-tolyl group adopts a gauche or anti conformation. The single-crystal geometrical data are unable to detect electronic differences between these two structures due to the somewhat large displacement parameters observed for the Se atom in the R = Cy structure.
Structural basis for the substrate recognition of aminoglycoside 7′′-phosphotransferase-Ia from Streptomyces hygroscopicus
Authors: Takenoya Mihoko , Shimamura Tatsuro , Yamanaka Ryuji , Adachi Yuya , Ito Shinsaku , Sasaki Yasuyuki , Nakamura Akira , Yajima Shunsuke
Published: August 2019

Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7′′-phosphotransferase-Ia [APH(7′′)-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7′′ and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7′′)-Ia and APH(4)-Ia, the crystal structure of APH(7′′)-Ia complexed with HygB is reported. The overall structure of APH(7′′)-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7′′)-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7′′)-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.
Supercell refinement: a cautionary tale
Authors: Lovelace Jeffrey , Petrícek Václav , Murshudov Garib , Borgstahl Gloria E. O.
Published: August 2019

Theoretically, crystals with supercells exist at a unique crossroads where they can be considered as either a large unit cell with closely spaced reflections in reciprocal space or a higher dimensional superspace with a modulation that is commensurate with the supercell. In the latter case, the structure would be defined as an average structure with functions representing a modulation to determine the atomic location in 3D space. Here, a model protein structure and simulated diffraction data were used to investigate the possibility of solving a real incommensurately modulated protein crystal using a supercell approximation. In this way, the answer was known and the refinement method could be tested. Firstly, an average structure was solved by using the `main' reflections, which represent the subset of the reflections that belong to the subcell and in general are more intense than the `satellite' reflections. The average structure was then expanded to create a supercell and refined using all of the reflections. Surprisingly, the refined solution did not match the expected solution, even though the statistics were excellent. Interestingly, the corresponding superspace group had multiple 3D daughter supercell space groups as possibilities, and it was one of the alternate daughter space groups that the refinement locked in on. The lessons learned here will be applied to a real incommensurately modulated profilin–actin crystal that has the same superspace group.
A crisis of consumers’ trust in scientists and its influence on consumer attitude toward genetically modified foods
Authors: Deng Haiyan , Hu Ruifa
Published: August 2019

Purpose

The purpose of this paper is to examine Chinese consumers’ attitudes toward genetically modified (GM) foods and the impact that consumers’ trust in different actors – GM scientists, non-GM scientists or individuals, the government and the media, has on their attitudes.

Design/methodology/approach

Consumers in Beijing were surveyed about their attitudes toward GM foods and their trust in different actors. The surveys were conducted from June to July of 2015. The sample size is 1,460 people. Given the potential endogeneity of trust variable, bivariate probit models are employed to estimate the impact of trust in different actors on consumers’ attitudes.

Findings

The results show that 55 percent of the Chinese consumers are opposed to GM foods and nearly 60 percent do not trust GM scientists. In total, 42 percent of Chinese consumers trust in the government and 39 percent trust the non-GM scientists or individuals. Around 35 percent of consumers believe the misinformation on GM technology that were provided by the media. Trust in the GM scientists and trust in the government have a significant positive impact on consumers’ acceptance of GM foods while trust in the non-GM scientists or individuals and believing the misinformation have a significant negative effect on the acceptance. Nearly 70 percent of Chinese consumers acquired information about GM food safety from the internet or via WeChat. Consumers who acquired GM technology information from the internet or via WeChat are less likely to embrace GM foods than those who obtain information from other sources.

Originality/value

Consumer trust plays a crucial role to accept biotech products in the market and it is crucial for producers, policy makers and consumers to have faith in new biotech products. The results of this study suggest that the government and GM scientists should make more effort to gain the trust and support of consumers, while the media should provide objective reports on GM products based on scientific evidence.
Are library electronic resources providing adequate support for research? A case study of a federal university in the United Arab Emirates
Authors: Ho Lilly Hoi Sze
Published: August 2019

Purpose

Middle Eastern universities have recently been included in international rankings, driving a shift in priorities from teaching to research. However, research-centric collection assessments are rarely applied in the region. The Library and Learning Commons of Zayed University has recently completed the first phase of collection assessment for this transition. This study aims to provide an overview of how electronic resources adequacy was measured, and correlations between utilization of resources and research output were determined. A systematic approach is presented to assess electronic resources impact and to investigate and demonstrate the Library’s support of research output in local research and the scholarly environment.

Design/methodology/approach

Journal article publications from 2009 to 2016 with at least one Zayed University affiliated author were collected from Scopus, the abstract and citation database operated by Elsevier BV. Sources used within these articles were analyzed. COUNTER usage statistics of three indicators (searches, sessions and full-text downloads) were collected from the most used electronic resources in the Library to define the correlation between usage and research activities in the university during the assessment period.

Findings

The change in university direction toward research is apparent in the data since Fall 2014. Since then, faculty publication output grew rapidly and was positively correlated with library resources use. Sessions and searches displayed a strong positive relationship with research output while the correlation with full-text downloads was moderate. This was true for individual colleges as well as for the university as a whole, supporting the assumption that library utilization is highly correlated with the growth of research productivity.

Practical implications

Results of this assessment were used to justify the budget allocation of Zayed University Library for supporting research and improve the focus of collection development to better meet researchers’ needs. The most important outcomes were to provide evidence-based information to Library management for strategic planning and evaluation of their changing role in the digital age.

Originality/value

The systematic approach described has enabled Zayed University library to assess the relevance of its resources to its changed focus toward research, both for the university as a whole and among the more research-productive colleges. This initial approach may be useful for other libraries going through a similar transition, particularly within the region.
Of locals and insiders
Authors: Kuipers Erin Hedwig Christina , Desportes Isabelle , Hordijk Michaela
Published: August 2019

Purpose

Through the case of the response to the 2017 Mocoa mudslide, the purpose of this paper is to contribute to a deeper understanding of why and how humanitarian response should be locally led, particularly in more complex contexts such as those affected by conflict.

Design/methodology/approach

The study draws on qualitative data collected during a four-month period in 2017, with a focus on the immediate April 2017 emergency phase which presented the largest diversity of local, national and international actors.

Findings

The study has found that competing legitimacy claims between the state and non-state response blocs led to tensions and confrontations between disaster response actors and consequently a problematic response process and outcome. The institutional map that was plotted based on locally perceived actor legitimacies indicates a local state-led response would have better served the broader goals of humanitarian support, development and peacebuilding.

Practical implications

These findings have significant implications for the understanding of how the locally led response should be understood. Better alignment with local needs and feasibilities requires a differential outlook on what is to be understood as “local.” This study puts forward the insider/outsider lens as a tool to identify the actors who possess local trust and legitimacy and are thus best suited to bridge the elements of the humanitarian-development-peacebuilding triple nexus.

Originality/value

This study gives a voice to state actors, which was largely absent in previous studies.
Practical evaluation of a reference architecture for the management of privacy level agreements
Authors: Diamantopoulou Vasiliki , Mouratidis Haralambos
Published: August 2019

Purpose

The enforcement of the General Data Protection Regulation imposes specific privacy- and -security related requirements that any organisation that processes European Union citizens’ personal data must comply with. The application of privacy- and security-by-design principles are assisting organisation in achieving compliance with the Regulation. The purpose of this study is to assist data controllers in their effort to achieve compliance with the new Regulation, by proposing the adoption of the privacy level agreement (PLA). A PLA is considered as a formal way for the data controllers and the data subjects to mutually agree the privacy settings of a service provisioned. A PLA supports privacy management, by analysing privacy threats, vulnerabilities and information systems’ trust relationships.

Design/methodology/approach

However, the concept of PLA has only been proposed on a theoretical level. To this aim, two different domains have been selected acting as real-life case studies, the public administration and the health care, where special categories of personal data are processed.

Findings

The results of the evaluation of the adoption of the PLA by the data controllers are positive. Furthermore, they indicate that the adoption of such an agreement facilitates data controllers in demonstrating transparency of their processes. Regarding data subjects, the evaluation process revealed that the use of the PLA increases trust levels on data controllers.

Originality/value

This paper proposes a novel reference architecture to enable PLA management in practice and reports on the application and evaluation of PLA management.
Searching for trustworthiness: culture, trust and negotiating new business relationships
Authors: Brett Jeanne M. , Mitchell Tyree
Published: August 2019

Purpose

This study aims to address three important but under-researched questions in the trust and negotiation literature: What do negotiators do to determine the trustworthiness of a potential business partner? What trust criteria motivate their search and help them interpret the information their search reveals? Whether there are systematic cultural differences in search and criteria, and if different, why?

Design/methodology/approach

This study used qualitative methodology. The data are from interviews with 82 managers from 33 different national cultures in four regions of the world identified by cultural levels of trust in negotiation and tightness-looseness. Interviews focused on how negotiators determined the trustworthiness of potential business partners in intracultural negotiations.

Findings

Analyses revealed four search activities negotiators use to gather information about a potential business partner: due diligence, brokerage, good will building and testing; and five criteria for determining the trustworthiness of a new business partner: respect, mutual values, competence, openness and professionalism. Quotes illustrate how these search activities and criteria manifest in different cultures.

Research limitations/implications

This study used multiple cases to build a longitudinal picture of the process. It did not follow a single case in depth. The study focused on identifying cultural central tendencies at the same time recognizing that there is always variability within a culture.

Practical implications

Knowing what is culturally normative allows negotiators to anticipate, interpret and respect their counterpart’s behavior. Such knowledge should facilitate trust development.

Originality/value

This study provides an in-depth understanding of cultural similarities and differences in the process of trust development in negotiating new business relationships.
Strength, fatigue and bagging properties of plated plain knitted fabrics containing different rates of elastane
Authors: Uyanik Seval , Kaynak Kubra Hatice
Published: August 2019

Purpose

Elastane yarns contribute significant elastic properties to all types of fabrics and these properties for very important for wears including tights, sportswear, under wear, casual wear, swimwear, corsetry, etc. in terms of appearance, comfort and duration of wear. The paper aims to discuss this issue.

Design/methodology/approach

It is investigated with this study strength, fatigue and bagging properties of plated plain knitted fabrics containing different rates of elastane.

Findings

The study showed that single jersey, not having elastane and having the lowest fabric tightness, has the lowest bursting strength, the highest fatigue loading values in high extensions, the lowest fatigue height values and the worst bagging behavior. On the contrary of single jersey, full elastane fabric has the exact opposite characteristics considering the fabric properties examined.

Originality/value

Fabric with 1×1 elastane and fabric with 2×1 elastane is similar, and these fabrics show bagging behavior better than single jersey and worse than full elastane fabric whereas the other properties of these fabrics are close to full elastane fabric.