bluuebunny/crossref_metadata_2025 huggingface dataset:
Host carbon dioxide concentration is an independent stress for Cryptococcus neoformans that affects virulence and antifungal susceptibility
Authors: Krysan Damian J. , Zhai Bing , Beattie Sarah R. , Misel Kara M. , Wellington Melanie , Lin Xiaorong
Published: June 2019

The ability of Cryptococcus neoformans to cause disease in humans varies significantly among strains with highly related genotypes. In general, environmental isolates of pathogenic species such as C. neoformans var. grubii have reduced virulence relative to clinical isolates, despite having no differences in the expression of the canonical virulence traits (high temperature growth, melanization and capsule formation). In this observation, we report that environmental isolates of C. neoformans tolerate host CO2 concentrations poorly compared to clinical isolates and that CO2 tolerance correlates well with the ability of the isolates to cause disease in mammals. Initial experiments also suggest that CO2 tolerance is particularly important for dissemination of C. neoformans from the lung to the brain. Furthermore, CO2 concentrations affect the susceptibility of both clinical and environmental C. neoformans isolates to the azole class of antifungal drugs, suggesting that antifungal testing in the presence of CO2 may improve the correlation between in vitro azole activity and patient outcome.

Importance

A number of studies comparing either patient outcomes or model system virulence across large collections of Cryptococcus isolates have found significant heterogeneity in virulence even among strains with highly related genotypes. Because this heterogeneity cannot be explained by variations in the three well-characterized virulence traits (growth at host body temperature; melanization; and polysaccharide capsule formation), it has been widely proposed that additional C. neoformans virulence traits must exist. C. neoformans natural niche is in the environment where the carbon dioxide concentration is very low (∼0.04%); in contrast, mammalian host tissue carbon dioxide concentrations are 125-fold higher (5%). We have found that the ability to grow in the presence of 5% carbon dioxide distinguishes low virulence strains from high virulence strains, even those with a similar genotype. Our findings suggest that carbon dioxide tolerance is a previously un-recognized virulence trait for C. neoformans.
TaAPO-A1, an ortholog of riceABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite hexaploid winter wheat varieties (Triticum aestivumL.)
Authors: Muqaddasi Quddoos H. , Brassac Jonathan , Koppolu Ravi , Plieske Jörg , Ganal Martin W. , Röder Marion S.
Published: June 2019

We dissected the genetic basis of total spikelet number (TSN) along with other traits, namely spike length (SL) and flowering time (FT) in a panel of 518 elite European winter wheat varieties. Genome-wide association studies based on 39,908 SNP markers revealed highly significant quantitative trait loci (QTL) for TSN on chromosomes 2D, 7A, and 7B, for SL on 5A, and FT on 2D, with 2D-QTL being the functional marker for the genePpd-D1. The physical region of the 7A-QTL for TSN revealed the presence of an ortholog toAPO1– a rice gene that positively controls spikelet number on panicles. Interspecific analyses ofTaAPO-A1orthologs showed that it is a highly conserved gene important for floral development, and present in a wide range of terrestrial plants. Intraspecific studies of the wheat orthologTaAPO-A1across wheat genotypes revealed a polymorphism in the highly conserved F-box domain, defining two haplotypes. A KASP maker developed on the polymorphic site showed a highly significant association ofTaAPO-A1with TSN, explaining 23.2% of the genotypic variance. Also, theTaAPO-A1alleles showed weak but significant differences for SL and grain yield. Our results demonstrate the importance of wheat sequence resources to identify candidate genes for important traits based on genetic analyses.
GSEA-InContext Explorer: An interactive visualization tool for putting gene set enrichment analysis results into biological context
Authors: Powers Rani K. , Sun Anthony , Costello James C.
Published: June 2019

GSEA-InContext Explorer is a Shiny app that allows users to perform two methods of gene set enrichment analysis (GSEA). The first, GSEAPreranked, applies the GSEA algorithm in which statistical significance is estimated from a null distribution of enrichment scores generated for randomly permuted gene sets. The second, GSEA-InContext, incorporates a user-defined set of background experiments to define the null distribution and calculate statistical significance. GSEA-InContext Explorer allows the user to build custom background sets from a compendium of over 5,700 curated experiments, run both GSEAPreranked and GSEA-InContext on their own uploaded experiment, and explore the results using an interactive interface. This tool will allow researchers to visualize gene sets that are commonly enriched across experiments and identify gene sets that are uniquely significant in their experiment, thus complementing current methods for interpreting gene set enrichment results.

Availability and implementation

The code for GSEA-InContext Explorer is available at: https://github.com/CostelloLab/GSEA-InContext_Explorer and the interactive tool is at: http://gsea-incontext_explorer.ngrok.io
Gravity highlights a dual role of the insula in internal models
Authors: Rousseau Célia , Barbiero Marie , Pozzo Thierry , Papaxanthis Charalambos , White Olivier
Published: June 2019

Movements rely on a mixture of predictive and reactive mechanisms. With experience, the brain builds internal representations of actions in different contexts. Many factors are taken into account in this process among which the immutable presence of gravity. Any displacement of a massive body in the gravitational field generates forces and torques that must be predicted and compensated by appropriate motor commands. Studies have shown that the insular cortex is a key brain area for graviception. However, none attempted to address whether the same internal representation of gravity is shared between reactive and predictive mechanisms. Here, participants either mentally simulated (only predictive) or performed (predictive and reactive) vertical movements of the hand. We found that the posterior part of the insular cortex was engaged when feedback was processed. The anterior insula, however, was activated only in mental simulation of the action. A psychophysical experiment shows participants’ ability to integrate the effects of gravity. Our results demonstrate a dual internal representation of gravity within the insula and discuss how they can conceptually be linked.
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
Authors: Devika N. T. , Raman Karthik
Published: June 2019

Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.
Gene-set Enrichment with Regularized Regression
Authors: Fang Tao , Davydov Iakov , Marbach Daniel , Zhang Jitao David
Published: June 2019

Motivation

Canonical methods for gene-set enrichment analysis assume independence between gene-sets. In practice, heterogeneous gene-sets from diverse sources are frequently combined and used, resulting in gene-sets with overlapping genes. They compromise statistical modelling and complicate interpretation of results.

Results

We rephrase gene-set enrichment as a regression problem. Given some genes of interest (e.g.a list of hits from an experiment) and gene-sets (e.g.functional annotations or pathways), we aim to identify a sparse list of gene-sets for the genes of interest. In a regression framework, this amounts to identifying a minimum set of gene-sets that optimally predicts whether any gene belongs to the given genes of interest. To accommodate redundancy between gene-sets, we propose regularized regression techniques such as theelastic net.We report that regression-based results are consistent with established gene-set enrichment methods but more parsimonious and interpretable.

Availability

We implement the model ingerr(gene-set enrichment with regularized regression), an R package freely available athttps://github.com/TaoDFang/gerrand submitted toBioconductor.Code and data required to reproduce the results of this study are available athttps://github.com/TaoDFang/GeneModuleAnnotationPaper.

Contact

Jitao David Zhang (jitao_david.zhang@roche.com), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124, 4070 Basel, Switzerland.
Computational design and interpretation of single-RNA translation experiments
Authors: Aguilera Luis U. , Raymond William , Fox Zachary R. , May Michael , Djokic Elliot , Morisaki Tatsuya , Stasevich Timothy J. , Munsky Brian
Published: June 2019

Advances in fluorescence microscopy have introduced new assays to quantify live-cell translation dynamics at single-RNA resolution. We introduce a detailed, yet efficient sequence-based stochastic model that generates realistic synthetic data for several such assays, including Fluorescence Correlation Spectroscopy (FCS), ribosome Run-Off Assays (ROA) after Harringtonine application, and Fluorescence Recovery After Photobleaching (FRAP). We simulate these experiments under multiple imaging conditions and for thousands of human genes, and we evaluate through simulations which experiments are most likely to provide accurate estimates of elongation kinetics. Finding that FCS analyses are optimal for both short and long length genes, we integrate our model with experimental FCS data to capture the nascent protein statistics and temporal dynamics for three human genes: KDM5B, β-actin, and H2B. Finally, we introduce a new open-source software package, RNA Sequence to NAscent Protein Simulator (RSNAPSIM), to easily simulate the single-molecule translation dynamics of any gene sequence for any of these assays and for different assumptions regarding synonymous codon usage, tRNA level modifications, or ribosome pauses. RSNAPSIM is implemented in Python and is available at: https://github.com/MunskyGroup/rSNAPsim.git.

Author summary

Translation is an essential step in which ribosomes decipher mRNA sequences to manufacture proteins. Recent advances in time-lapse fluorescence microscopy allow live-cell quantification of translation dynamics at the resolution of single mRNA molecules. Here, we develop a flexible computational framework to reproduce and interpret such experiments. We use this framework to explore how well different single-mRNA translation experiment designs would perform to estimate key translation parameters. We then integrate experimental data from the most flexible design with our stochastic model framework to reproduce the statistics and temporal dynamics of nascent protein elongation for three different human genes. Our validated computational method is packaged with a simple graphical user interface that (1) starts with mRNA sequences, (2) generates discrete, codon-dependent translation models, (3) provides visualization of ribosome movement as trajectories or kymographs, and (4) allows the user to estimate how optical single-mRNA translation experiments would be affected by different genetic alterations (e.g., codon substitutions) or environmental perturbations (e.g., tRNA titrations or drug treatments).
Chd1 regulates repair of promoter-proximal DNA breaks to sustain hypertranscription in embryonic stem cells
Authors: Bulut-Karslioglu Aydan , Jin Hu , Guzman-Ayala Marcela , Williamson Andrew JK , Hejna Miroslav , Whetton Anthony D , Song Jun S. , Ramalho-Santos Miguel
Published: June 2019

Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. The chromatin remodeler Chd1 binds to genes transcribed by RNA Polymerase (Pol) I and II and is required for hypertranscription in embryonic stem (ES) cellsin vitroand the early post-implantation epiblastin vivo. Biochemically, Chd1 has been shown to facilitate transcription at least in part by removing nucleosomal barriers to elongation, but its mechanism of action in stem cells remains poorly understood. Here we report a novel role for Chd1 in the repair of promoter-proximal endogenous double-stranded DNA breaks (DSBs) in ES cells. An unbiased proteomics approach revealed that Chd1 interacts with several DNA repair factors including Atm, Parp1, Kap1 and Topoisomerase 2β. We show that wild-type ES cells display high levels of phosphorylated H2A.X and Kap1 at chromatin, notably at rDNA in the nucleolus, in a Chd1-dependent manner. Loss of Chd1 leads to an extensive accumulation of DSBs at Chd1-bound Pol II-transcribed genes and rDNA. Genes prone to DNA breaks in Chd1 KO ES cells tend to be longer genes with GC-rich promoters, a more labile nucleosomal structure and roles in chromatin regulation, transcription and signaling. These results reveal a vulnerability of hypertranscribing stem cells to endogenous DNA breaks, with important implications for developmental and cancer biology.
Non-invasive recording from the human olfactory bulb
Authors: Iravani Behzad , Arshamian Artin , Ohla Kathrin , Wilson Donald A. , Lundström Johan N.
Published: June 2019

Current methods can, in a non-invasive manner, assess neural activity in all areas of the human brain but the olfactory bulb (OB). The OB is intimately involved in a long list of olfactory tasks, has been suggested to fulfill a role comparable to that of V1 and the thalamus in the visual system, and have been closely linked to a wide range of neuropathologies. Here we present a method for non-invasive recording of signals from the human OB with millisecond precision. We demonstrate that signals obtained via recordings from EEG electrodes at the nasal bridge represent responses from the olfactory bulb - recordings we term Electrobulbogram (EBG). The EBG is localized to the OB, is reliable, and follows response patterns demonstrated in non-human animal models. The EBG will aid future olfactory-related translational work but can also easily be implemented as an everyday clinical tool to detect pathology-related changes in human central olfactory processing in neurodegenerative diseases.
GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis throughmiR-126
Authors: Mahamud Md. Riaj , Geng Xin , Ho Yen-Chun , Cha Boksik , Kim Yuenhee , Ma Jing , Chen Lijuan , Myers Greggory , Camper Sally , Mustacich Debbie , Witte Marlys , Choi Dongwon , Hong Young-Kwon , Chen Hong , Varshney Gaurav , Engel James Douglas , Wang Shusheng , Kim Tae-Hoon , Lim Kim-Chew , Srinivasan R. Sathish
Published: June 2019

Mutations in the transcription factor GATA2 cause lymphedema. GATA2 is necessary for the development of lymphatic valves (LVs) and lymphovenous valves (LVVs), and for the patterning of lymphatic vessels. Here, we report that GATA2 is not necessary for valvular endothelial cell (VEC) differentiation. Instead, GATA2 is required for VEC maintenance and morphogenesis. GATA2 is also necessary for the expression of cell junction molecules VE-Cadherin and Claudin5 in lymphatic vessels. We identifiedmiR-126as a target of GATA2, andmiR-126−/−embryos recapitulate the phenotypes of mice lacking GATA2. Primary human lymphatic endothelial cells (HLECs) lacking GATA2 (GATA2ΔHLEC) have altered expression of Claudin5 and VE-Cadherin, and blockingmiR-126activity in HLECs phenocopies these changes in expression. Importantly, overexpression ofmiR-126in GATA2ΔHLECsignificantly rescues the cell junction defects. Thus, our work defines a new mechanism of GATA2 and uncoversmiR-126as a novel regulator of mammalian lymphatic vascular development.

Non-standard abbreviations

LECs, lymphatic endothelial cells;LVs, lymphatic valves;LV-ECs, lymphatic valve-forming endothelial cells;LVVs, lymphovenous valves;LVV-ECs, lymphovenous valve-forming endothelial cells;HLEC, primary human LECs;OSS, Oscillatory shear stress;IHC, immunohistochemistry.
Importance of the Landlocked Pond SmeltHypomesus nipponensisas a food resource of the Little TernSternula albifronson inland Andong Lake of Korea: A video image analysis
Authors: Shin Dong-Man , Han Jeong-Ho
Published: June 2019

We carried out the diet study of the little tern on the sandy islet in inland Andong Lake, Korea, during the beeding season (April to July 2018). To identify its diet and examine the importance of the main prey species as a food resource, we set two remote-control video cameras with 4K-resolution on the islet. One thousand two hundred seventy-five still images that the tern had prey in its bill were identified at the species level and measured on a monitor. Then, they were classified to five length-categories and compared among months and breeding stages. Freshwater fishes dominated the diet (100%; eleven species overall), where the landlocked pond smeltHypomesus nipponensis(80.8%) and largemouth bassMicropterus salmoides(13.7%) were the primary and next essential prey species, respectively. The average prey item length was 51.04 ± 20.89 mm and significantly differed among months and breeding stages (P< 0.001, respectively). 50–75 mm prey length category was the most frequent in the diet (42.2%). In April and May, larger fish >50 mm constituted the greater part of their diet (93.1%, 66.3%, respectively), whereas the diet in June and July consisted of smaller fishes <50 mm (56.2%, 68.8% respectively). The occurrence frequency of prey length categories also varied significantly among the breeding stages (P< 0.001): 1–25 mm and 50–75 mm were overrepresented and underrepresented, respectively, at the chicks in the nest stage. On the other hand, 50–75 mm was preferred for the pre-laying and incubation stages. In terms of the survival condition of pond smelts, the before- and after water surface temperatures of the day when terns flew away showed a significant difference (P= 0.004), where a threshold looks like between 29.11°C and 30.04°C. These results support the prey abundance hypothesis that, when cold-water pond smelts might wholly swim down into the deeper lake in the hot summer, the terns might also leave their colony for another foraging place with higher prey availability.
Recombinant rotaviruses rescued by reverse genetics reveal the role of NSP5 hyperphosphorylation in the assembly of viral factories
Authors: Papa Guido , Venditti Luca , Arnoldi Francesca , Schraner Elisabeth M. , Potgieter Christiaan , Borodavka Alexander , Eichwald Catherine , Burrone Oscar R.
Published: June 2019

Rotavirus (RV) replicates in round-shaped cytoplasmic viral factories although how they assemble remains unknown.

During RV infection, NSP5 undergoes hyperphosphorylation, which is primed by the phosphorylation of a single serine residue. The role of this post-translational modification in the formation of viroplasms and its impact on the virus replication remains obscure. Here we investigated the role of NSP5 during RV infection by taking advantage of a modified fully tractable reverse genetics system. An NSP5 trans-complementing cell line was used to generate and characterise several recombinant rotaviruses (rRVs) with mutations in NSP5. We demonstrate that a rRV lacking NSP5, was completely unable to assemble viroplasms and to replicate, confirming its pivotal role in rotavirus replication.

A number of mutants with impaired NSP5 phosphorylation were generated to further interrogate the function of this post-translational modification in the assembly of replication-competent viroplasms. We showed that the rRV mutant strains exhibit impaired viral replication and the ability to assemble round-shaped viroplasms in MA104 cells. Furthermore, we have investigated the mechanism of NSP5 hyper-phosphorylation during RV infection using NSP5 phosphorylation-negative rRV strains, as well as MA104-derived stable transfectant cell lines expressing either wt NSP5 or selected NSP5 deletion mutants. Our results indicate that NSP5 hyper-phosphorylation is a crucial step for the assembly of round-shaped viroplasms, highlighting the key role of the C-terminal tail of NSP5 in the formation of replication-competent viral factories. Such a complex NSP5 phosphorylation cascade may serve as a paradigm for the assembly of functional viral factories in other RNA viruses.

IMPORTANCE

Rotavirus (RV) double-stranded RNA genome is replicated and packaged into virus progeny in cytoplasmic structures termed viroplasms. The non-structural protein NSP5, which undergoes a complex hyperphosphorylation process during RV infection, is required for the formation of these virus-induced organelles. However, its roles in viroplasm formation and RV replication have never been directly assessed due to the lack of a fully tractable reverse genetics (RG) system for rotaviruses. Here we show a novel application of a recently developed RG system by establishing a stable trans-complementing NSP5-producing cell line required to rescue rotaviruses with mutations in NSP5. This approach allowed us to provide the first direct evidence of the pivotal role of this protein during RV replication. Furthermore, using recombinant RV mutants we shed light on the molecular mechanism of NSP5 hyperphosphorylation during infection and its involvement in the assembly and maturation of replication-competent viroplasms.
SweHLA: the high confidence HLA typing bio-resource drawn from 1 000 Swedish genomes
Authors: Nordin Jessika , Ameur Adam , Lindblad-Toh Kerstin , Gyllensten Ulf , Meadows Jennifer R.S.
Published: June 2019

There is a need to accurately call human leukocyte antigen (HLA) genes from existing short-read sequencing data, however there is no single solution that matches the gold standard of lab typing. Here we aimed to combine results from available software, minimising the biases of applied algorithm and HLA reference. The result is a robust HLA population resource for the published 1 000 Swedish genomes, and a framework for future HLA interrogation. HLA 2-field alleles were called using four imputation and inference methods for the classical eight genes (class I: HLA-A, -B, -C; class II: HLA-DPA1, -DPB1, -DQA1, -DQB1, -DRB1). A high confidence population set (SweHLA) was determined using an n-1 concordance rule for class I (four software) and class II (three software) alleles. Results were compared across populations and individual programs benchmarked to SweHLA. Per allele, 875 to 988 of the 1 000 samples were genotyped in SweHLA; 920 samples had at least seven loci. While a small fraction of reference alleles were common to all software (class I=1.9% and class II=4.1%), this did not affect the overall call rate. Gene-level concordance was high compared to European populations (>0.83%), with COX and PGF the dominant SweHLA haplotypes. We noted that 15/18 discordant alleles (delta allele frequency > 2) were previously reported as disease-associated. These differences could in part explain across-study genetic replication failures, reinforcing the need to use multiple software. SweHLA demonstrates a way to use existing NGS data to generate a population resource agnostic to individual HLA software biases.
Eco-evolutionary spatial dynamics of non-linear social dilemmas
Authors: Gokhale Chaitanya S. , Park Hye Jin
Published: June 2019

Spatial dynamics can promote the evolution of cooperation. While dispersal processes have been studied in simple evolutionary games, real-world social dilemmas are much more complicated. The public good, in many cases, does not increase linearly as per the investment in it. When the investment is low, for example, every additional unit of the investment may help a lot to increase the public good, but the effect vanishes as the number of investments increase. Such non-linear behaviour is the norm rather than an exception in a variety of social as well as biological systems. We take into account the non-linearity in the payoffs of the public goods game as well as the natural demographic effects of population densities. Population density has also been shown to impact the evolution of co-operation. Coupling these non-linear games and population size effect together with an explicitly defined spatial structure brings us one step closer to the complexity of real eco-evolutionary spatial systems. We show how the non-linearity in payoffs, resulting in synergy or discounting of public goods can alter the effective rate of return on the cooperative investment. Synergy or discounting in public goods accumulation affects the resulting spatial structure, not just quantitatively but in some cases, drastically changing the outcomes. In cases where a linear payoff structure would lead to extinction, synergy can support the coexistence of cooperators and defectors. The combined eco-evolutionary trajectory can thus be qualitatively different in cases on non-linear social dilemmas.
Operation of X-ray gas monitors at the European XFEL
Authors: Maltezopoulos Theophilos , Dietrich Florian , Freund Wolfgang , Jastrow Ulf Fini , Koch Andreas , Laksman Joakim , Liu Jia , Planas Marc , Sorokin Andrey A. , Tiedtke Kai , Grünert Jan
Published: June 2019

X-ray gas monitors (XGMs) are operated at the European XFEL for non-invasive single-shot pulse energy measurements and average beam position monitoring. They are used for tuning and maintaining the self-amplified spontaneous emission (SASE) operation and for sorting single-shot experimental data according to the pulse-resolved energy monitor data. The XGMs were developed at DESY based on the specific requirements for the European XFEL. In total, six XGM units are continuously in operation. Here, the main principle and experimental setup of an XGM are summarized, and the locations of the six XGMs at the facility are shown. Pulse energy measurements at 0.134 nm wavelength are presented, exceeding 1 mJ obtained with an absolute measurement uncertainty of 7–10%; correlations between different XGMs are shown, from which a SASE1 beamline transmission of 97% is deduced. Additionally, simultaneous position measurements close to the undulator and at the end of the tunnel are shown, along with the correlation of beam position data simultaneously acquired by an XGM and an imager.
On smart optimization of blazed soft X-ray gratings
Authors: Jark Werner
Published: June 2019

The first attempts to calculate the diffraction efficiencies of gratings in the soft X-ray range were made on a scalar model. The results were simple analytical equations, that always severely overestimated the performance of real objects. In this respect, computer programs were found to be more successful, which rigorously consider all diffracted and refracted waves. Consequently soft X-ray gratings are presently optimized using these tools, which requires rather extensive calculations for any instrument optimization as general trends are not immediately obvious. Here it will be shown that the results of the rigorous calculations for gratings with blaze or sawtooth profile can be approximated rather well with a simple analytical equation. This equation contains three multiplicative factors, which deal independently with the effect of the reflectivity, the blaze angle and the groove density. This opens the possibility to initially ignore the effects of the blaze angle and thus to start an optimization in a very general way. Such optimization can be based on isoreflectivity curves and it can then provide `blaze maximum efficiency maps', i.e. simple images. In these latter images, one can identify directly the optimum parameters for a grating, i.e. the groove density providing best efficiency for a requested spectral resolving power. Only successively will the blaze angle have to be fixed. Its choice is then not the result of an extensive optimization process but of a simple calculation applied for the photon energy at which maximum efficiency performance is requested. The maps presented here are used for the optimization of a medium-resolving-power soft X-ray monochromator, which can scan the photon energy range 300–2000 eV.
Compact hard X-ray split-and-delay line for studying ultrafast dynamics at free-electron laser sources
Authors: Rysov Rustam , Roseker Wojciech , Walther Michael , Grübel Gerhard
Published: June 2019

A compact hard X-ray split-and-delay line for studying ultrafast dynamics at free-electron laser sources is presented. The device is capable of splitting a single X-ray pulse into two fractions to introduce time delays from −5 to 815 ps with femtosecond resolution. The split-and-delay line can operate in a wide and continuous energy range between 7 and 16 keV. Compact dimensions of 60 × 60 × 30 cm with a total weight of about 60 kg make it portable and suitable for direct installation in an experimental hutch. The concept of the device is based on crystal diffraction. The piezo-driven stages utilized in the device give nanometre positioning accuracy. On-line monitoring systems based on X-ray cameras and intensity monitors are implemented to provide active alignment feedback. Performance estimates of the system are also presented.
High-pressure and -temperature spinning capillary cell for in situ synchrotron X-ray powder diffraction
Authors: Fraga Edmundo , Zea-Garcia Jesus D. , Yáñez Armando , De la Torre Angeles G. , Cuesta Ana , Valcárcel-Fernández Ricardo , Farré-París Francesc , Malfois Marc , Aranda Miguel A. G.
Published: June 2019

In situ research of materials under moderate pressures (hundreds of bar) is essential in many scientific fields. These range from gas sorption to chemical and biological processes. One industrially important discipline is the hydration of oil well cements. Existing capillary cells in this pressure range are static as they are easy to design and operate. This is convenient for the study of single-phase materials; however, powder diffraction quantitative analyses for multiphase systems cannot be performed accurately as a good powder average cannot be attained. Here, the design, construction and commissioning of a cost-effective spinning capillary cell for in situ powder X-ray diffraction is reported, for pressures currently up to 200 bar. The design addresses the importance of reducing the stress on the capillary by mechanically synchronizing the applied rotation power and alignment on both sides of the capillary while allowing the displacement of the supports needed to accommodate different capillaries sizes and to insert the sample within the tube. This cell can be utilized for multiple purposes allowing the introduction of gas or liquid from both ends of the capillary. The commissioning is reported for the hydration of a commercial oil well cement at 150 bar and 150°C. The quality of the resulting powder diffraction data has allowed in situ Rietveld quantitative phase analyses for a hydrating cement containing seven crystalline phases.
First measurements with the K-monochromator at the European XFEL
Authors: Freund Wolfgang , Fröhlich Lars , Karabekyan Suren , Koch Andreas , Liu Jia , Nölle Dirk , Wilgen Josef , Grünert Jan
Published: June 2019

Hard X-ray free-electron lasers (XFELs) generate intense coherent X-ray beams by passing electrons through undulators, i.e. very long periodic magnet structures, which extend over hundreds of meters. The SASE1 and SASE2 undulator systems of the European XFEL consist of 35 segments with variable-gap planar undulators which are initially tuned to precise on-axis magnetic field strengths in a magnetic measurement laboratory to keep an important quality parameter – the K-value variation from segment to segment – below a certain limit (3 × 10−4 for 12 keV photon energy). After tunnel installation only photon-based methods can determine the K-values of undulator segments with a similar accuracy. The synchrotron radiation from a single or a few segments can be spectrally filtered by a dedicated crystal monochromator (K-monochromator) and recorded with a photodiode or with an imager that provides 2D information, tuned for high sensitivity to detect low photon densities from distant single undulator segments. This instrumentation is applied for electron orbit analysis and optimization, and adjustment of individual undulators in terms of their central magnetic axis with respect to the electron beam. Single undulator segments were analysed by scanning the monochromator crystal angle and detecting the steepest slope of a photodiode signal. Alternatively, in the imaging method, an imager recorded the radiation cone of electrons passing through the undulator segment. From the spatial distribution of the radiation, the K-parameter was determined with a sufficiently high relative accuracy.
Structure and Hirshfeld surface analysis of the salt N,N,N-trimethyl-1-(4-vinylphenyl)methanaminium 4-vinylbenzenesulfonate
Authors: McAdam C. John , Hanton Lyall R. , Moratti Stephen C. , Simpson Jim , Wickramasinhage Ravindra N.
Published: June 2019

In the title compound, the asymmetric unit comprises an N,N,N-trimethyl-1-(4-vinylphenyl)methanaminium cation and a 4-vinylbenzenesulfonate anion, C12H18N+·C8H7O3S−. The salt has a polymerizable vinyl group attached to both the cation and the anion. The methanaminium and vinyl substituents on the benzene ring of the cation subtend angles of 86.6 (3) and 10.5 (9)° to the ring plane, while the anion is planar excluding the sulfonate O atoms. The vinyl substituent on the benzene ring of the cation is disordered over two sites with a refined occupancy ratio of 0.542 (11):0.458 (11). In the crystal, C—H...O hydrogen bonds dominate the packing and combine with a C—H...π(ring) contact to stack the cations and anions along the a-axis direction. Hirshfeld surface analysis of the salt and of the individual cation and anion components is also reported.
Crystal structure and Hirshfeld surface analysis of (2E)-3-(4-chloro-3-fluorophenyl)-1-(3,4-dimethoxyphenyl)prop-2-en-1-one
Authors: Çelikesir Sevim Türktekin , Sheshadri S. N. , Akkurt Mehmet , Chidan Kumar C. S. , Veeraiah M. K.
Published: June 2019

The molecular structure of the title compound, C17H14ClFO3, consists of a 4-chloro-3-fluorophenyl ring and a 3,4-dimethoxyphenyl ring linked via a prop-2-en-1-one spacer. The molecule has an E configuration about the C=C bond and the carbonyl group is syn with respect to the C=C bond. The F and H atoms at the meta positions of the 4-chloro-3-fluorophenyl ring are disordered over two orientations, with an occupancy ratio of 0.785 (3):0.215 (3). In the crystal, molecules are linked via pairs of C—H...O interactions with an R
2
2(14) ring motif, forming inversion dimers. The dimers are linked into a tape structure running along [10\overline{1}] by a C—H...π interaction. The intermolecular contacts in the crystal were further analysed using Hirshfield surface analysis, which indicates that the most significant contacts are H...H (25.0%), followed by C...H/H...C (20.6%), O...H/H...O (15.6%), Cl...H/H...Cl (10.7%), F...H/H...F (10.4%), F...C/C...F (7.2%) and C...C (3.0%).
Public–private equity joint ventures and risk transfers in motorways of the sea
Authors: Juan Carmen , Olmos Fernando
Published: June 2019

Purpose

The purpose of this paper is to present a new scheme of public–private partnership (PPP) within the framework of motorways of the sea (MoS) similar to that of an equity joint venture along with a methodology for valuing risk transfers arising from options embedded in the clauses included in such agreement.

Design/methodology/approach

The architecture of the proposed PPP is an adaptation to the scope of a MoS of collaborative schemes commonly used in industry such as equity joint ventures. The methodology for valuing options involved making use of a valuation tree of optimal cashflows along with algorithm designs from the field of financial and real options.

Findings

The proposed structure of public–private equity joint venture (PPEJV) increases the stability of private–public collaboration as compared with standard PPPs, so as to achieve the desired modal shift. The analyzed case study shows how the methodology provides valuable numerical information for both negotiating partners and policy makers.

Practical implications

This study provides a quantitative tool for policy makers to redefine the role that public agents and public funds should play in a future sustainable mobility model.

Originality/value

The originality of the authors’ contribution to the field of PPPs in transport is triple. First, there is no precedent in the literature on PPPs of an architecture similar to that of the proposed PPEJV. Second, unlike the usual practice in the valuation of financial or real options, no prior structure is assumed for modelling the behaviour of cashflows. Third, the type of options addressed is not usual neither in the real options literature in general nor in the valuation of guarantee mechanisms included in PPPs in particular.
Comparisons of students’ perceptions on BIM practice among Australia, China and UK
Authors: Jin Ruoyu , Zou Patrick Xiaowei , Li Bo , Piroozfar Poorang , Painting Noel
Published: June 2019

Purpose

University students are the future driving forces in and leaders of the architectural, engineering and construction (AEC) industry advancement. Although BIM pedagogical studies have been performed in different institutions, there has not been sufficient research providing a global perspective of BIM education and students’ perceptions toward BIM practice and application following their learning progress. The purpose of this paper is to adopt student samples from Swinburne University of Technology (SUT, Australia), Wenzhou University (WZU, China) and University of Brighton (UK) as three case studies to investigate the BIM practice and application-related perceptions and motivations.

Design/methodology/approach

Based on the thorough understanding of the BIM pedagogical delivery including teaching contents and assessment methods among the three institutions, a questionnaire survey approach was adopted to collect AEC students’ perceptions of BIM. Within each selected case, statistical analysis was conducted to investigate both the overall sample and subgroup differences regarding students’ opinions on BIM’s functions (e.g. as a 3D visualization tool) and BIM usefulness in various industry professions, their motivation in BIM-related jobs and their perceptions of challenges encountered in BIM practice and application. Multiple factors influencing BIM learners’ perceptions were discussed, such as pedagogical assessment approach, and individual factors (e.g. disciplines).

Findings

The results showed that students were able to discern the latest industry practices and critical thinking in BIM movements. For example, SUT students perceived more challenges from the government legislation or incentive policies, which was consistent with Australia’s BIM policy movement. WZU students tended to have less positive views on BIM usefulness. The results also indicated fewer differences regarding perceived challenges among students from these three institutions.

Originality/value

This study contributed to the body of knowledge in managerial BIM by focusing on learners’ perceptions from the perspective of students’ understanding, motivation and individual views of BIM, which were insightful to both BIM educators and employers. By initiating the framework of BIM learning process and its influence factors, the current study serves as a point of reference to continue the future work in strengthening the connection between institutional BIM education and industry practical needs worldwide.
Infrastructure procurement capacity gaps in Nigeria public sector institutions
Authors: Manu Patrick , Mahamadu Abdul-Majeed , Booth Colin , Olomolaiye Paul Olaniyi , Coker Akinwale , Ibrahim Ahmed , Lamond Jessica
Published: June 2019

Purpose

The achievement of sustainable development goals is linked to the procurement of public infrastructure in a manner that meets key procurement objectives, such as sustainability, value-for-money, transparency and accountability. At the heart of achieving these procurement objectives and others is the capacity of public procurement institutions. Whereas previous reports have hinted that there are deficiencies in procurement capacity in Nigeria, insights regarding critical aspects of organisational capacity deficiencies among different tiers of government agencies is limited. The purpose of this paper is to investigate the critical gaps in the procurement capacity of state and local government agencies involved in the procurement of public infrastructure in Nigeria.

Design/methodology/approach

The study employed a survey of public infrastructure procurement personnel which yielded 288 responses.

Findings

Among 23 operationalised items that are related to organisational procurement capacity, none is perceived to be adequate by the procurement personnel. Additionally, among 14 procurement objectives only 1 is perceived as being attained to at least a high extent.

Originality/value

The findings underscore the acuteness of organisational procurement capacity weaknesses among public procurement institutions within Nigeria’s governance structure. It is, thus, imperative for policy makers within state and local government to formulate, resource and implement procurement capacity building initiatives/programmes to address these deficiencies. Additionally, the organisational procurement capacity items operationalised in this study could serve as a useful blueprint for studying capacity deficiencies among public infrastructure procurement agencies in other developing countries, especially within sub-Saharan Africa where several countries have been implementing public procurement reforms.
Green maintainability assessment of high-rise vertical greenery systems
Authors: Conejos Sheila , Chew Michael Yit Lin , Azril Fikril Hakim Bin
Published: June 2019

Purpose

Vertical greenery systems (VGS) have been a widely accepted design strategy that contributes to creating sustainable built environments. However, green building technologies (e.g. VGS) have grown in complexity which poses maintainability challenges. Designing with maintainability in mind is crucial in delivering efficient and sustainable buildings. This paper aims to assist designers and allied professionals in terms of integrating maintainability and sustainable design in developing high-rise VGS directly from its design inception.

Design/methodology/approach

The study is grounded on the “Green Maintainability” concept which link maintainability, sustainability and facility management right at the outset. The Green Maintainability factors are translated into critical design criteria which are used to analyze the selected instrumental case studies to evaluate the high-rise VGS performance and maintainability potential. A qualitative approach via the triangulation of data collected from relevant literatures, field surveys and walkthrough interviews is undertaken.

Findings

Findings have shown that the major VGS defects which are mostly occurring in the case studies are issues concerning fallen leaves and dirt accumulation; safety issues during cleaning and repairs; insufficient maintenance access; algae/ mould growth; withering plants; water stagnation/ ponding; poor/faulty irrigation and water dripping and unavailability of natural elements. Best practices and lessons learned revealed few design oversight and technical issues concerning high-rise VGS façade implementation. While maintenance cost, biodiversity and lack of coordination among involved professionals are the additional issues which emerged during the stakeholders’ walkthrough interviews.

Originality/value

Current researches conducted on the maintainability of green building technologies (e.g. high-rise VGS) are still few. This research study is the first comprehensive assessment to determine the green maintainability potential and performance of high-rise VGS in tropical conditions.
Optimization of the heat flow by solving inverse problem in the protective layer of the TPS panel
Authors: Brodzik Łukasz , Frąckowiak Andrzej
Published: June 2019

Purpose

This paper aims to present the problem of heating the damaged insulation of an orbiter.

Design/methodology/approach

Changes of the insulation’s thermal properties, made by adding conductive material of high value of specific heat in a form of a dope to the protective layer, were examined. An iterative algorithm determining a variable of dope concentration in the material was developed.

Findings

Determination of distribution of conductive material concentration was made for materials which, after verification, demonstrated the most beneficial effect on protective properties of the modified insulation layer. The problem of determining the distribution of metal filings concentration in the insulation layer of the coating belongs to inverse heat conduction problems.

Originality/value

Change of properties was to enable time extension of the LI900 insulation tile heating up to the maximal temperature and, additionally, to lowering this temperature.