bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the genetic architecture underlying eye size variation withinDrosophila melanogasterandDrosophila simulans
Authors: Gaspar Pedro , Arif Saad , Sumner-Rooney Lauren , Kittelmann Maike , Bodey Andrew J. , Stern David L. , Nunes Maria D. S. , McGregor Alistair P.
Published: February 2019

The compound eyes of insects exhibit striking variation in size, reflecting adaptation to different lifestyles and habitats. However, the genetic and developmental bases of variation in insect eye size is poorly understood, which limits our understanding of how these important morphological differences evolve. To address this, we further explored natural variation in eye size within and between four species of theDrosophila melanogasterspecies subgroup. We found extensive variation in eye size among these species, and flies with larger eyes generally had a shorter inter-ocular distance andvice versa. We then carried out quantitative trait loci (QTL) mapping of intra-specific variation in eye size and inter-ocular distance in bothD. melanogasterandD. simulans.This revealed that different genomic regions underlie variation in eye size and inter-ocular distance in both species, which we corroborated by introgression mapping inD. simulans. This suggests that although there is a trade-off between eye size and inter-ocular distance, variation in these two traits is likely to be caused by different genes and so can be genetically decoupled. Finally, although we detected QTL for intra-specific variation in eye size at similar positions inD. melanogasterandD. simulans, we observed differences in eye fate commitment between strains of these two species. This indicates that different developmental mechanisms and therefore, most likely, different genes contribute to eye size variation in these species. Taken together with the results of previous studies, our findings suggest that the gene regulatory network that specifies eye size has evolved at multiple genetic nodes to give rise to natural variation in this trait within and among species.
Protection of phage applications in crop production: a patent landscape
Authors: Holtappels D. , Lavigne R. , Huys I. , Wagemans J.
Published: February 2019

In agriculture, the prevention and treatment of bacterial infections represents an increasing challenge. Traditional (chemical) methods have been restricted to ensure public health and limit the occurrence of resistant strains. Bacteriophages could be a sustainable alternative. A major hurdle towards the commercial implementation of phage-based biocontrol strategies concerns aspects of regulation and intellectual property protection. Within this study, two datasets have been composed to analyze both scientific publications and patent documents and to get an idea on the focus of R&D by means of an abstract and claim analysis. 137 papers and 49 patent families were found searching public databases, their numbers increasing over time. Within this dataset, the majority of the patent documents were filed by non-profit organizations in Asia. There seems to be a good correlation between the papers and patent documents in terms of targeted bacterial genera. Furthermore, granted patents seem to claim rather broad and cover methods of treatment. This review shows that there is indeed a growing publishing and patenting activity concerning phage biocontrol. Targeted research is needed to further stimulate the exploration of phages within integrated pest management strategies and to deal with bacterial infections in crop production.
HIV-1 Gag specifically restricts PI(4,5)P2 and cholesterol mobility in living cells creating a nanodomain platform for virus assembly
Authors: Favard C. , Chojnacki J. , Merida P. , Yandrapalli N. , Mak J. , Eggeling C. , Muriaux D.
Published: February 2019

HIV-1 Gag protein self-assembles at the plasma membrane of infected cells for viral particle formation. Gag targets lipids, mainly the phosphatidylinositol (4, 5) bisphosphate, at the inner leaflet of this membrane. Here, we address the question whether Gag is able to trap specifically PI(4,5)P2 or other lipids during HIV-1 assembly in the host CD4+ T lymphocytes. Lipid dynamics within and away from HIV-1 assembly sites was determined using super-resolution STED microscopy coupled with scanning Fluorescence Correlation Spectroscopy in living T cells. Analysis of HIV-1 infected cells revealed that, upon assembly, HIV-1 is able to specifically trap PI(4,5)P2, and cholesterol, but not phosphatidylethanolamine or sphingomyelin. Furthermore, our data show that Gag is the main driving force to restrict PI(4,5)P2 and cholesterol mobility at the cell plasma membrane. This is first direct evidence showing that HIV-1 creates its own specific lipid environment by selectively recruiting PI(4,5)P2 and cholesterol, as a membrane nano-platform for virus assembly.
Crowdfunded whole-genome sequencing of the celebrity cat Lil BUB identifies causal mutations for her osteopetrosis and polydactyly
Authors: Bridavsky Mike , Kuhl Heiner , Woodruff Arthur , Kornak Uwe , Timmermann Bernd , Mages Norbert ,   99 Lives Consortium, Lupiáñez Darío G. , Symmons Orsolya , Ibrahim Daniel M.
Published: February 2019

Rare diseases and their underlying molecular causes are often poorly studied, posing challenges for patient diagnosis and prognosis. The development of next-generation sequencing and its decreasing costs promises to alleviate such issues by supplying personal genomic information at a moderate price. Here, we used crowdfunding as an alternative funding source to sequence the genome of Lil BUB, a celebrity cat affected by rare disease phenotypes characterized by supernumerary digits, osteopetrosis and dwarfism, all phenotypic traits that also occur in human patients. We discovered that Lil BUB is affected by two distinct mutations: a heterozygous mutation in the limb enhancer of the Sonic hedgehog gene, previously associated with polydactyly in Hemingway cats; and a novel homozygous frameshift deletion affecting the TNFRSF11A (RANK) gene, which has been linked to osteopetrosis in humans. We communicated the progress of this project to a large online audience, detailing the ‘inner workings’ of personalized whole genome sequencing with the aim of improving genetic literacy. Our results highlight the importance of genomic analysis in the identification of disease-causing mutations and support crowdfunding as a means to fund low-budget projects and as a platform for scientific communication.
Centrosomes control kinetochore-fiber plus-end dynamics via HURP to ensure symmetric divisions
Authors: Dudka Damian , Liaudet Nicolas , Vassal Hélène , Meraldi Patrick
Published: February 2019

During mitosis centrosomes can affect the length of kinetochore-fibers (k-fibers) and the stability of kinetochore-microtubule attachments, implying that they regulate k-fiber dynamics. The exact cellular and molecular mechanisms by which centrosomes regulate k-fibers remain, however, unknown. Here, we created human non-cancerous cells with only one centrosome to investigate these mechanisms. Such cells formed highly asymmetric bipolar spindles that resulted in asymmetric cell divisions. K-fibers in acentrosomal spindles were shorter, more stable, had a reduced poleward microtubule flux at minus-ends, and more frequent pausing events at their plus-ends. This indicates that centrosomes regulate k-fiber dynamics both locally at minus-ends and far away at plus-ends. At the molecular level we find that the microtubule-stabilizing protein HURP is enriched on the k-fiber plus-ends in the acentrosomal spindles of cells with only one centrosome. HURP depletion rebalance k-fiber stability and dynamics in such cells, and improved spindle and cell division symmetry. Our data further indicate that HURP accumulates on k-fibers inversely proportionally to half-spindle length. We propose that centrosomes regulate k-fiber plus-ends indirectly via length-dependent accumulation of HURP. Thus by ensuring equal k-fiber length, centrosomes promote HURP symmetry, reinforcing the symmetry of the mitotic spindle and of cell division.
Identifying cortical substrates underlying the phenomenology of stereopsis and realness: A pilot fMRI study
Authors: Uji Makoto , Lingnau Angelika , Cavin Ian , Vishwanath Dhanraj
Published: February 2019

Viewing a real scene or a stereoscopic image (e.g., 3D movies) with both eyes yields a vivid subjective impression of object solidity, tangibility, immersive negative space and sense of realness; something that is not experienced when viewing single pictures of 3D scenes normally with both eyes. This phenomenology, sometimes referred to as stereopsis, is conventionally ascribed to the derivation of depth from the differences in the two eye’s images (binocular disparity). Here we report on a pilot study designed to explore if dissociable neural activity associated with the phenomenology of realness can be localised in the cortex. In order to dissociate subjective impression from disparity processing, we capitalised on the finding that the impression of realness associated with stereoscopic viewing can also be generated when viewing a single picture of a 3D scene with one eye through an aperture. Under a blocked fMRI design, subjects viewed intact and scrambled images of natural 3-D objects and scenes under three viewing conditions: (1) single pictures viewed normally with both eyes (binocular) (2) single pictures viewed with one eye through an aperture (monocular-aperture); (3) stereoscopic anaglyph images of the same scenes viewed with both eyes (binocular stereopsis). Fixed-effects GLM contrasts aimed at isolating the phenomenology of stereopsis demonstrated a selective recruitment of similar posterior parietal regions for both monocular and binocular stereopsis conditions. Our findings provide preliminary evidence that the cortical processing underlying the subjective impression of realness may be dissociable and distinct from the derivation of depth from disparity.
A voltage-based metaplasticity rule applied to the model hippocampal granule cell accounts for homeostatic heterosynaptic plasticity
Authors: Shirrafiardekani Azam , Benuskova Lubica , Frauendiener Jörg
Published: February 2019

Long-term potentiation (LTP) and long-term depression (LTD) of synaptic efficacies are involved in establishment of long-term memories. In this process, neurons need to adjust the overall efficacy of their synapses by using mechanisms of homeostatic plasticity to balance their activity and control their firing rate. For instance, in the dentate granule cell in vivo, induction of homosynaptic LTP in the tetanized medial perforant path is accompanied by heterosynaptic LTD in the non-tetanized lateral perforant path. We used the compartmental model of this cell to test the following hypotheses: 1. Using plasticity and metaplasticity rules both based on postsynaptic voltage we can reproduce homosynaptic LTP and concurrent heterosynaptic LTD, provided there is an ongoing noisy spontaneous activity; 2. Frequency of an ongoing noisy spontaneous activity along the lateral path determines the magnitude of heterosynaptic LTD. In experiments where procaine was used to block the lateral spontaneous activity, no heterosynaptic LTD occurred. However, when the procaine was washed out and a second tetanization was applied to the medial path, no heterosynaptic LTD could have been induced neither. Our simulations predict that the reduced frequency of spontaneous activity in the lateral perforant path can account for this lasting absence of heterosynaptic LTD.
Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor
Authors: Steele John FC , Hughes Richard K , Banfield Mark J
Published: February 2019

Plant NLRs are modular immune receptors that trigger rapid cell death in response to attempted infection by pathogens. A highly conservednucleotide-binding domain shared withAPAF-1, variousR-proteins andCED-4 (NB-ARC domain) is proposed to act as a molecular switch, cycling between ADP (repressed) and ATP (active) bound forms. Studies of plant NLR NB-ARC domains have revealed functional similarities to mammalian homologues, and provided insight into potential mechanisms of regulation. However, further advances have been limited by difficulties in obtaining sufficient yields of protein suitable for structural and biochemical techniques. From protein expression screens inEscherichia coliandSf9insect cells, we defined suitable conditions to produce the NB-ARC domain from the tomato NLR NRC1. Biophysical analyses of this domain showed it is a folded, soluble protein. Structural studies revealed the NRC1 NB-ARC domain had co-purified with ADP, and confirmed predicted structural similarities between plant NLR NB-ARC domains and their mammalian homologues.
Is testosterone responsible for athletic success in female athletes?
Authors: Ahmetov Ildus I. , Roos Thomas R. , Stepanova Albina A. , Biktagirova Elnara M. , Semenova Ekaterina A. , Shchuplova Irina S. , Bets Larisa V.
Published: February 2019

The aim of this study is to determine the interrelationship between the resting serum testosterone (T) levels (an inherited trait) of female athletes from different types of sporting events and their athletic success. The study involves 599 Russian international-level female athletes (95 highly elite, 190 elite, and 314 sub-elite) and 298 age-matched female controls. All subjects were age 16-35 years old and to the best of our knowledge have always tested negative for performance enhancing substances. The athlete cohort was stratified into four groups according to event duration, distance, and type of activity: 1) endurance athletes, 2) athletes with mixed activity, 3) speed/strength athletes, and 4) sprinters. Athletic success was measured by determining the level of achievement of each athlete. The mean (SD) T levels of athletes and controls were 1.65 (0.87) and 1.76 (0.6) nmol/L (P=0.057) with ranges of 0.08-5.80 and 0.38-2.83 nmol/L in athletes and controls, respectively. No significant differences in T levels were found between different groups of athletes. T levels were positively correlated (r=0.62, P<0.0001) with athletic success in sprinters (runners, cyclists, kayakers, speed skaters, swimmers). Moreover, none of the sub-elite sprinters had T > 1.9 nmol/L, while 50% of elite and highly elite sprinters had T > 1.9 nmol/L (95% CI: 2.562-862.34; OR=47.0; P<0.0001). We do not observe the benefits of having high T levels for success in other groups of athletes. Conversely, highly elite middle-distance (P=0.235) and mixed activity athletes (P=0.096) tended to have lower T levels than less successful athletes. Our data suggest that the measurement of the serum T levels significantly correlates with athletic success in sprinters but not other types of athletes and in the future may be useful in the prediction of sprinting ability.
Developmental changes in the processing of faces as revealed by EEG decoding
Authors: Mares Inês , Ewing Louise , Farran Emily K. , Smith Fraser W , Smith Marie L
Published: February 2019

Rapidly and accurately processing information from faces is a critical human function that is known to improve with developmental age. Understanding the underlying drivers of this improvement remains a contentious question, with debate continuing as to the presence of early vs. late maturation of face-processing mechanisms. Recent behavioural evidence suggests an important ‘hallmark’ of expert face processing – the face inversion effect – is present in very young children, yet neural support for this remains unclear. To address this, we conducted a detailed investigation of the neural dynamics of face-selective processing in children spanning a range of ages (6 – 11 years) and adults. Uniquely, we applied multivariate pattern analysis (MVPA) to the electroencephalogram signal (EEG) to test for the presence of a distinct neural profile associated with canonical upright faces when compared both to other objects (houses) and to inverted faces. Results revealed robust discrimination profiles, at the individual level, of differentiated neural activity associated with broad face categorization and further with its expert processing, as indexed by the face inversion effect, from the youngest ages tested. This result is consistent with an early functional maturation of broad face processing mechanisms. Yet, clear quantitative differences between the response profile of children and adults is suggestive of age-related refinement of this system with developing face and general expertise. Standard ERP analysis also provides some support for qualitative differences in the neural response to inverted faces in children in contrast to adults. This neural profile is in line with recent behavioural studies that have reported impressively expert early face abilities during childhood, while also providing novel evidence of the ongoing neural specialisation between child and adulthood.
Deciphering the structural intricacy in virulence effectors for proton-motive force mediated unfolding and type-III protein secretion
Authors: Khanppnavar Basavraj , Roy Anupam , Chandra Kousik , Maiti Nakul Chandra , Datta Saumen
Published: February 2019

Many gram-negative pathogenic bacteria use type III secretion system (T3SS) to inject virulence effectors directly into the cytosol of targeted host cells. Given that the protein unfolding requisite for secretion via nano-size pore of T3SS injectisome is an energetically unfavorable process, “How do pathogenic bacteria unfold and secrete hundreds of toxic proteins in seconds” remain largely unknown. In this study, first, from an in-depth analysis of folding and stability of T3SS effector ExoY, we show that the proton-concentration gradient (∼pH 5.8-6.0) generated by proton-motive force (PMF) can significantly amortize tertiary structural folding and stability of effectors without significant entropic cost. Strikingly, it was found that the lower energetic cost associated with the global unfolding of ExoY is mainly due to its weakly folded geometry and abundance of geometrical frustrations stemming from buried water molecules and native-like folded intermediates in the folded cores. From in-silico structural analysis of 371 T3SS effectors, it can be curtained that T3SS effectors belong to typical class (disorder globules) of IDPs and have evolved similar conserved intrinsic structural archetypes to mediate early-stage unfolding. The slower folding kinetics in effector proteins requisite for efficient T3SS-mediated secretion mostly stems from reduced hydrophobic density and enhanced polar-polar repulsive interactions in their sequence landscapes. Lastly, the positively evolved histidine-mediated stabilizing interactions and gate-keeper residues in effector proteins shed light on collaborative role of evolved structural chemistry in T3SS effectors and PMF in the spatial-temporal regulation of effector folding and stability essential for maintaining balance in secretion and function trade-off.
Ion beam subcellular tomography
Authors: Coskun Ahmet F. , Han Guojun , Chen Shih-Yu , Clavé Xavier Rovira , Jiang Sizun , Schürch Christian M. , Bai Yunhao , Hitzman Chuck , Nolan Garry P.
Published: February 2019

Multiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions in single cells within tissue slices. Here, a mathematical and technical framework for three-dimensional subcellular MIBI is presented. We term the approach ion beam tomography (IBT) wherein ion beam images are acquired iteratively across successive, multiple scans and later compiled into a 3D format. For IBT, cells were imaged at 0.2-4 pA ion current across 1,000 axial scans. Consecutive subsets of ion beam images were binned over 3 to 20 slices (above and below) to create a resolved image, wherein binning was incremented one slice at a time to yield an enhanced multi-depth data without loss of depth resolution. Algorithmic deconvolution, tailored for ion beams, was then applied to the transformed ion image series using a hybrid deblurring algorithm and an ion beam current-dependent point-spread function. Three-dimensional processing was implemented by segmentation, mesh, molecular neighborhoods, and association maps. In cultured cancer cells and tissues, IBT enabled accessible visualization of three-dimensional volumetric distributions of genomic regions, RNA transcripts, and protein factors with 65-nm lateral and 5-nm axial resolution. IBT also enabled label-free elemental mapping of cells, allowing “point of source” cellular component measurements not possible for most optical microscopy targets. Detailed multiparameter imaging of subcellular features at near macromolecular resolution should now be made possible by the IBT tools and reagents provided here to open novel venues for interrogating subcellular biology.
Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Dynamics Simulations
Authors: Wilson Blake A. , Ramanathan Arvind , Lopez Carlos F.
Published: February 2019

Cardiolipin is a unique anionic lipid found in mitochondrial membranes where it contributes to various mitochondrial functions, including metabolism, mitochondrial membrane fusion/fission dynamics, and apoptosis. Dysregulation of cardiolipin synthesis and remodeling have also been implicated in several diseases, such as diabetes, heart disease and Barth Syndrome. Although cardiolipin’s structural and dynamic roles have been extensively studied in binary mixtures with other phospholipids, the biophysical properties of cardiolipin in ternary lipid mixtures are still not well resolved. Here, we used molecular dynamics simulations to investigate the cardiolipin-dependent properties of ternary lipid bilayer systems that mimic the major components of mitochondrial membranes. We found that changes to cardiolipin concentration only resulted in minor changes to bilayer structural features, but that the lipid diffusion was significantly affected by those alterations. We also found that cardiolipin position along the bilayer surfaces correlated to negative curvature deflections, consistent with the induction of negative curvature stress in the membrane monolayers. This work contributes to a foundational understanding of the role of CL in altering the properties in ternary lipid mixtures composed of the major mitochondrial phospholipids, providing much needed insights to help understand how cardiolipin concentration modulates the biophysical properties of mitochondrial membranes.
High-resolution cryo-EM structures of the E. coli hemolysin ClyA oligomers
Authors: Peng Wei , Souza Santos Marcela de , Li Yang , Tomchick Diana R. , Orth Kim
Published: February 2019

Pore-forming proteins (PFPs) represent a functionally important protein family, that are found in organisms from viruses to humans. As a major branch of PFPs, bacteria pore-forming toxins (PFTs) permeabilize membranes and usually cause the death of target cells. E. coli hemolysin ClyA is the first member with the pore complex structure solved among α-PFTs, employing α-helices as transmembrane elements. ClyA is proposed to form pores composed of various numbers of protomers. With high-resolution cryo-EM structures, we observe that ClyA pore complexes can exist as newly confirmed oligomers of a tridecamer and a tetradecamer, at estimated resolutions of 3.2 Å and 4.3 Å, respectively. The 2.8 Å cryo-EM structure of a dodecamer dramatically improves the existing structural model. Structural analysis indicates that protomers from distinct oligomers resemble each other and neighboring protomers adopt a conserved interaction mode. We also show a stabilized intermediate state of ClyA during the transition process from soluble monomers to pore complexes. Unexpectedly, even without the formation of mature pore complexes, ClyA can permeabilize membranes and allow leakage of particles less than ∼400 Daltons. In addition, we are the first to show that ClyA forms pore complexes in the presence of cholesterol within artificial liposomes. These findings provide new mechanistic insights into the dynamic process of pore assembly for the prototypical α-PFT ClyA.
Forest change within and outside protected areas in the Dominican Republic, 2000-2016
Authors: Lloyd John D. , León Yolanda M.
Published: February 2019

We used Landsat-based estimates of tree cover change to document the loss and gain of forest in the Dominican Republic between 2000 and 2016. Overall, 2,795 km2 of forest were lost, with forest gain occurring on only 393 km2, yielding a net loss of 2,402 km2 of forest, a decline of 11.1% or 0.7% per year. Deforestation occurred in all of the major forest types in the country, and ranged from a 13% decline in the area of semi-moist broadleaf forest to a 5.9% loss of cloud forest, mostly attributed to agriculture. Fire was a significant driver of forest loss only in Hispaniolan pine (Pinus occidentalis) forests and, to a lesser extent, in adjacent cloud forest. Deforestation rates were lower within protected areas, especially in dry and semi-moist broadleaf forests at lower elevations. Protected areas had a smaller, and generally negligible, effect on rates of forest loss in pine forest and cloud forest, largely due to the effects of several large wildfires. Overall, rates of deforestation in the Dominican Republic were higher than regional averages from across the Neotropics and appeared to have accelerated during the later years of our study period. Stemming deforestation will likely require enforcement of prohibitions on large-scale agricultural production within protected areas and development of alternatives to short-cycle, shifting agriculture.
TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
Authors: Rasmussen Kasper D. , Berest Ivan , Keβler Sandra , Nishimura Koutarou , Simón-Carrasco Lucía , Vassiliou George S. , Pedersen Marianne T. , Christensen Jesper , Zaugg Judith B. , Helin Kristian
Published: February 2019

The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development and lead to altered DNA methylation landscapes and an increased risk of hematopoietic malignancy. Here, we show by genome-wide mapping of TET2 binding sites in different cell types that TET2 localizes to regions of open chromatin and cell-type–specific enhancers. We find that deletion of Tet2 in native hematopoiesis as well as fully transformed acute myeloid leukemia (AML) results in changes in transcription factor (TF) activity within these regions, and we provide evidence that loss of TET2 leads to attenuation of chromatin binding of members of the basic helix–loop–helix (bHLH) TF family. Together, these findings demonstrate that TET2 activity shapes the local chromatin environment at enhancers to facilitate TF binding and provides an example of how epigenetic dysregulation can affect gene expression patterns and drive disease development.
X-ray optics for advanced ultrafast pump–probe X-ray experiments at SACLA
Authors: Katayama Tetsuo , Hirano Takashi , Morioka Yuki , Sano Yasuhisa , Osaka Taito , Owada Shigeki , Togashi Tadashi , Yabashi Makina
Published: February 2019

X-ray optics were implemented for advanced ultrafast X-ray experiments with different techniques at the hard X-ray beamline BL3 of SPring-8 Ångstrom Compact free-electron LAser. A double channel-cut crystal monochromator (DCCM) and compound refractive lenses (CRLs) were installed to tailor the beam conditions. These X-ray optics can work simultaneously with an arrival-timing monitor that compensates for timing jitter and drift. Inner-walls of channel-cut crystals (CCs) in the DCCM were processed by plasma chemical vaporization machining to remove crystallographic damage. Four-bounced reflection profiles of the CCs were investigated and excellent diffraction qualities were achieved. The use of CRLs enabled two-dimensional X-ray focusing with a spot size of ∼1.5 µm × 1.5 µm full width at half-maximum, while keeping reasonable throughputs for a wide photon energy range of 5−15 keV.
An experimental platform using high-power, high-intensity optical lasers with the hard X-ray free-electron laser at SACLA
Authors: Yabuuchi Toshinori , Kon Akira , Inubushi Yuichi , Togahi Tadashi , Sueda Keiichi , Itoga Toshiro , Nakajima Kyo , Habara Hideaki , Kodama Ryosuke , Tomizawa Hiromitsu , Yabashi Makina
Published: February 2019

An experimental platform using X-ray free-electron laser (XFEL) pulses with high-intensity optical laser pulses is open for early users' experiments at the SACLA XFEL facility after completion of the commissioning. The combination of the hard XFEL and the high-intensity laser provides capabilities to open new frontiers of laser-based high-energy-density science. During the commissioning phase, characterization of the XFEL and the laser at the platform has been carried out for the combinative utilization as well as the development of instruments and basic diagnostics for user experiments. An overview of the commissioning and the current capabilities of the experimental platform is presented.
MXCuBE2: the dawn of MXCuBE Collaboration
Authors: Oscarsson Marcus , Beteva Antonia , Flot David , Gordon Elspeth , Guijarro Matias , Leonard Gordon , McSweeney Sean , Monaco Stephanie , Mueller-Dieckmann Christoph , Nanao Max , Nurizzo Didier , Popov Alexander N. , von Stetten David , Svensson Olof , Rey-Bakaikoa Vicente , Chado Idrissou , Chavas Leonard M. G. , Gadea Laurent , Gourhant Patrick , Isabet Tatiana , Legrand Pierre , Savko Martin , Sirigu Serena , Shepard William , Thompson Andrew , Mueller Uwe , Nan Jie , Eguiraun Mikel , Bolmsten Fredrick , Nardella Alberto , Milàn-Otero Antonio , Thunnissen Marjolein , Hellmig Michael , Kastner Alexandra , Schmuckermaier Lukas , Gerlach Martin , Feiler Christian , Weiss Manfred S. , Bowler Matthew W. , Gobbo Alexandre , Papp Gergely , Sinoir Jeremy , McCarthy Andrew A. , Karpics Ivars , Nikolova Marina , Bourenkov Gleb , Schneider Thomas , Andreu Jordi , Cuní Guifré , Juanhuix Judith , Boer Roeland , Fogh Rasmus , Keller Peter , Flensburg Claus , Paciorek Wlodek , Vonrhein Clemens , Bricogne Gerard , de Sanctis Daniele
Published: February 2019

MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF – the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.
Synthesis and crystal structure of a new coordination polymer based on lanthanum and 1,4-phenylenediacetate ligands
Authors: Camara Magatte , Badiane Insa , Diallo Mamoudou , Daiguebonne Carole , Guillou Olivier
Published: February 2019

Reaction in gel between the sodium salt of 1,4-phenylenediacetic acid (Na2C10O4H8–Na2p-pda) and lanthanum chloride yields single crystals of the three-dimensional coordination polymer poly[[tetraaquatris(μ-1,4-phenylenediacetato)dilanthanum(III)] octahydrate], {[La2(C10H8O4)3(H2O)4]·8H2O}∞. The LaIIIcoordination polyhedron can be described as a slightly distorted monocapped square antiprism. One of the twop-pda2−ligands is bound to four LaIIIions and the other to two LaIIIions. Each LaIIIatom is coordinated by five ligands, thereby generating a metal–organic framework with potential porosity properties.
Synthesis and crystal structure of 2,4,6,8-tetrakis(3,5-di-tert-butylphenoxy)pyrimido[5,4-d]pyrimidine: expansion of the Piedfort concept
Authors: Gall James H. , MacNicol David D. , MacSween Ross , Frampton Christopher S.
Published: February 2019

The title host compound, C62H84N4O4, designed to self-assemble to form a new type of extended core Piedfort unit reminiscent of an eight-legged spider host, forms a number of crystalline inclusion compounds favouring oxygen-containing guest molecules. We have established the presence of this unit in the unsolvated molecular crystal at 100 K, which is monoclinic, space group P21/n, with Z = 8. The new Piedfort unit is chiral and its core structure closely approximates to D
2 symmetry, with both enantiomers present in the crystal. Rather than being superposed with a staggered arrangement of nitrogen atoms, the rings are rotated by an angle of approximately 45° with respect to each other, and the shortest contact between them is 3.181 (2) Å. The compound's significant inclusion properties may be taken to suggest the participation of an extended Piedfort unit in the microcrystalline adducts formed. The presence of such a dimeric host unit in the clathrates has, however, not yet been established because of the current lack of suitable single crystals for X-ray analysis.
Crystal structure of Ba2Co(BO3)2
Authors: N'Faoui Fatima-Ezahra , Aride Jilali , Boukhari Ali , Taibi M'Hamed , Saadi Mohamed , El Ammari Lahcen
Published: February 2019

Single crystals of dibarium cobalt(II) bis(orthoborate), Ba2Co(BO3)2, have been obtained from the melt. The crystal structure is composed of two isolated (BO3)3− triangles linked to Co2+ cations. The resulting [CoO5] square pyramids and the borate anions make up branched rows extending parallel to [010]. The barium cations occupy two sites in the voids of this arrangement and exhibit coordination numbers of nine each. A comparison with the structures of other A
2
M(BO3)2 compounds reveals a unique five-coordination of the small metal M in the title compound instead of four- or six-coordination for the other A
2
M(BO3)2 compounds with M = Cu, Zn, Mg, Ca, or Cd.
The sodium chloride complex catena-poly[[{μ3-2-[bis(2-hydroxyethyl)amino]ethan-1-ol}sodium] chloride], N(CH2CH2OH)3·NaCl
Authors: Krabbe Christina , Gock Vinusuya , Lutter Michael , Jurkschat Klaus
Published: February 2019

The reaction of sodium chloride with 2-[bis(2-hydroxyethyl)amino]ethan-1-ol results in the formation of the title salt {[Na{N(CH2CH2OH)3}]Cl}
n
. The polymeric structure is characterized by a sodium cation coordinated by one nitrogen and five oxygen atoms in a distorted octahedral environment. The resulting one-dimensional {—O—Na—O—Na—O}— coordination polymer extends parallel to [010] and is connected through the chloride counter-anion via O—H...Cl hydrogen bonding, giving rise to a two-dimensional supramolecular structure parallel to (001).
1-(4-Fluorophenyl)-5-methyl-N′-{1-[5-methyl-1-(4-methylphenyl)-1H-1,2,3-triazol-4-yl]ethylidene}-1H-1,2,3-triazole-4-carbohydrazide
Authors: El-Hiti Gamal A. , Abdel-Wahab Bakr F. , Yousif Emad , Alotaibi Mohammad Hayal , Hegazy Amany S. , Kariuki Benson M.
Published: February 2019

The title molecule, C22H21FN8O, comprises fluorophenyl (A), methyltriazolyl (B), methyltriazolyl (C) and tolyl (D) rings. The twist angles between the planes through neighbouring ring pairs A/B, B/C and C/D are 45.0 (1), 9.4 (1) and 43.2 (1)°, respectively. Intermolecular π–π interactions between rings A and C and between B and D propagate the structure in the [010] direction and weak C—H...O interactions also occur.
Students’ commuting pattern from the viewpoint of environmentalism: comparing Australia with China
Authors: Soltani Ali , Allan Andrew , Nguyen Ha Anh , Berry Stephen
Published: February 2019

Purpose

This paper aims to clarify the differences between students’ travel behaviours in Australia and China and the association between students’ environmental attitudes and their travel behaviours in both countries.

Design/methodology/approach

The paper extensively reviewed most of existing literature work on commuting patterns of higher education students with referring to different studies around the world and then used it to build a theoretical framework and conceptual model to relate the travel patterns of students to built environment, personal demographics and environmental knowledge/consideration. An online survey was used with 230 students at Mawson Lakes campus of University of South Australia and Beiyangyuan campus of Tianjin University (China). Statistical tests (i.e. mean test, one-way analysis of variance, factor analysis) were used to analyse the data.

Findings

The study reveals that a high dependence on private vehicles amongst students at the Mawson Lakes campus, whilst a more environmentally sustainable modal choice dominated at the Beiyangyuan campus. Those who studied at Mawson Lakes campus tended to have stronger involvement in environmental activities than their counterparts at Beiyangyuan campus, which presented a clear association between environmental awareness and the travel behaviours of the sampled students.

Research limitations/implications

The study focussed on two respective campuses of both universities in Australia and China. Future work could be expanded with students at all campuses of two universities.

Practical implications

The study affirmed the value of nurturing environmental awareness for students in both universities to encourage more environmentally sustainable travel behaviours amongst students. The paper provides policy recommendations such as establishing infrastructure, and facilities for new stream of mobility included sharing bike schemes, which would be very practical due to flexibility and cost effectiveness within University campuses. The paper attempted to transfer lessons from Chinese bike friendly society to Adelaide’s car dominated campus.

Originality/value

This study brings remarkable contributions as comparing university students’ travel behaviours in two different nations. It is the first one in Australia, which links the environmental concerns among university students with their travel behaviours. The paper was successful in getting the gap between theory and practice filled to some extent. The paper has a capability to be used as an evidence-base work in the area of sustainability education.
Personality, belief in a just world, and attitudes toward criminal responsibility defenses: a preliminary study
Authors: Mooney Robyn
Published: February 2019

Purpose

In Canada, if it can be proven that a defendant was suffering from a mental disorder at the time they committed an offense, they can be found Not Criminally Responsible on Account of Mental Disorder (NCRMD). These cases are often decided by jury. The purpose of this paper is to examine the influence of the dark triad (DT), social dominance orientation (SDO) and belief in a just world (BJW) on undergraduate students’ attitudes toward the NCRMD defense.

Design/methodology/approach

A total of 421 undergraduate students completed questionnaires measuring SDO and the DT. After being primed for high, low or neutral BJW, they indicated their attitudes toward NCRMD.

Findings

The BJW manipulation had no effect on attitudes. High-SDO/DT participants held less favorable attitudes toward NCRMD than participants who scored low on these variables, F(1, 420)=20.65, p<0.01,

η

p

2

=
0.05

. Psychology and criminology students had significantly more favorable attitudes toward NCRMD than business students.

Practical implications

This study can be helpful in improving jury impartiality in trials involving mental illness and criminal responsibility; assessment of SDO and the DT; awareness of career roles relating to insanity defense bias; and improving the voir dire process.

Originality/value

The results of this study may be used to improve the voir dire process in trials involving the issue of mental illness and criminal responsibility and to preserve the impartiality of the jurors selected for these trials.
Information Intermediary or De Facto Standard Setter? Field Evidence on the Indirect and Direct Influence of Proxy Advisors
Authors: HAYNE CHRISTIE , VANCE MARSHALL
Published: February 2019

We examine whether proxy advisory firms (PAs) serve primarily an information intermediary role by providing research and voting recommendations to shareholders, or directly influence executive compensation by exerting pressure on firms to adopt preferred pay practices. Through a field study, we find that PAs are perceived as both information intermediaries and agenda setters and that these roles provide leverage to enable PAs to exercise significant influence over executive pay practices. Boards feel, and sometimes yield to, pressure to conform to PA “best” practices despite their own preferred compensation philosophies, even in the absence of overt PA scrutiny or negative shareholder votes. We also find that PAs are susceptible to conflicts of interest and generally use a “one‐size‐fits‐all” approach to voting recommendations. Overall, however, PAs are viewed as improving compensation practices by increasing transparency and accountability and fostering dialogue between firms and their shareholders.
Larger tumors are associated with inferior progression‐free survival of first‐line EGFR‐tyrosine kinase inhibitors and a lower abundance of EGFR mutation in patients with advanced non‐small cell lung cancer
Authors: Pan Yingying , Gao Guanghui , Chen Xiaoxia , Tian Qinrui , Wu Fengying , Liu Qian , Wang Yan , Jiang Tao , Liu Yiwei , Li Xuefei , Yang Shuo , Xu Chuan , Su Chunxia , Zhou Fei , Ren Shengxiang , Zhou Caicun
Published: February 2019

Background

The impact of primary tumor size on the therapeutic outcomes of EGFR‐tyrosine kinase inhibitors (TKIs) in advanced non‐small cell lung cancer (NSCLC) with EGFR mutation remains unclear.

Methods

A total of 291 consecutive patients with advanced EGFR‐mutant NSCLC administered first‐line EGFR‐TKIs were enrolled. Computed tomography was used to assess primary tumor diameter. The amplification refractory mutation system plus was used to quantitatively evaluate the abundance of EGFR mutations. Associations between depth of response, abundance of EGFR mutations, and tumor size was investigated.

Results

Patients were divided into three groups according to T classification: ≤ 3 cm (n = 109), 3–5 cm (n = 121), and > 5 cm (n = 61). Median progression‐free survival (PFS) was significantly longer in the ≤ 3 cm and 3–5 cm groups compared to the > 5 cm group (10.8 vs. 10.5 vs. 7.1 months; P < 0.001). Subgroup analysis revealed a consistent result in patients with exon 19 deletion and 21 L858R mutation. Multivariate analysis revealed that tumor size was an independent predictive factor for PFS (hazard ratio 1.528, 95% confidence interval 1.104–2.115; P = 0.010). Larger tumors (> 5 cm) were marginally significantly less EGFR‐mutant abundant than smaller tumors (≤ 5 cm) (mean ± standard deviation 30.5 ± 29.5% vs. 45.8 ± 43.1%; P = 0.08).

Conclusion

Larger tumors (> 5 cm) were associated with inferior PFS of first‐line EGFR‐TKI therapy in advanced NSCLC patients with activating EGFR mutations. A potential explaination might be that EGFR mutations are less abundant in larger tumors.
The financial distress pricing puzzle in banking firms
Authors: Kim Dongcheol , Lee Inro
Published: February 2019

This paper examines whether the financial distress pricing puzzle observed for non‐financial firms is also observed for financial firms and how this puzzle differs according to the extent of short‐sale constraints. By using the eight distress measures developed for financial firms, we find that there is a strong negative relation in the cross‐section between financial distress and subsequent bank stock returns, regardless of adjustment for risk. However, this distress pricing puzzle is statistically significant only for high short‐sale constrained banks, but not for low short‐sale constrained banks. Thus, short‐sale constraints are at least one non‐risk attribute that causes the distress pricing puzzle for financial firms. We also find that despite its simple form, compared to the other complex distress measures, non‐performing loans (NPLs) are the most informative in predicting future bank stock returns as well as bankruptcy and failure.
Factors affecting species richness and distribution spatially and temporally within a protected area using multi‐season occupancy models
Authors: Moore J. F. , Hines J. E. , Mulindahabi F. , Masozera M. K.
Published: February 2019

Exploring trends in species richness and the distribution of individual species over time as well as the factors affecting these trends informs conservation priorities in protecting species and ecosystems as a whole. We used data from 41 park‐wide line transect surveys in 2009 and 2014 and multi‐season occupancy models with multi‐species data to explore trends in species richness and distribution of individual species and factors affecting these trends in Nyungwe National Park (NNP), Rwanda. Mammalian species richness and the distributional range of 5 of the 7 species increased between 2009 and 2014 in NNP. The probability of colonization of a species into a new area in 2014, where it was not present in 2009, was highest in sites with a lower probability of poaching activity, close to tourist trails, and at lower elevations. The probability of colonization with no poaching activity was about 50% but dropped to about 10% with a 100% chance of poaching activity. Duiker species had the largest increase in distribution during the study, while there was a decrease in the distribution of the eastern chimpanzee and blue monkey. Our results suggest that increased patrols could be implemented in areas of the park with low species richness and areas with a low probability of occurrence for species of conservation concern to combat poaching activity and thus increase the probability of a species moving into a new area. Our use of a single multi‐season model for multiple species explicitly accounts for imperfect detection and species‐specific identities, while allowing for inferences to be made about rarely detected species by sharing covariates with common species. These results can be used to improve conservation planning in NNP for species management and ranger patrol protocols, and our modelling framework is broadly applicable to any protected area with presence/absence species field data.
A stereological analysis on the calculation of the volume values of thoracic segments in ducks
Authors: Cakmak Gamze , Cetin Ragbetli Murat
Published: February 2019

Stereology is a method for examining two‐dimensional objects as three‐dimensional objects. The aim of this study was to offer volume values for thoracic segments in ducks by means of stereological methods. This study examined the data obtained from stereological analysis of the total volume and grey and white matter volume values of the thoracic segment, a part of the adult duck spinal cord with a weight of 3–4 kg. In the study, study samples consisted of 10 adult ducks (Anas) used without gender discrimination. To perfuse all of the animals, 10% formaldehyde was utilised. The perfused animals were kept in 10% formaldehyde for one week. The spinal cord was uncovered following the removal of arcus vertebrae parts of thoracic vertebrae in the thoracic part of dissected ducks. Tissue samples of thoracic segments were taken; 5‐µm‐thick cross sections from these tissue samples were taken via microtome. Attention was paid to obtaining samples at the ratio of 1/250 by taking 12 cross sections from each segment. The cross sections were subjected to haematoxylin‐eosin staining. Photographs of all cross sections were taken using a microscope. The volume values of all tissue and grey and white matter structures in each thoracic segment of the spinal cord were calculated. The total volume, grey and white matter volume densities in thoracic segments of ducks, as well as the data obtained as a result of proportioning volume values of one another are represented in the conclusion section of this study.