bluuebunny/crossref_metadata_2025 huggingface dataset:
A chimeric Japanese encephalitis vaccine protects against lethal yellow fever virus infection without inducing neutralizing antibodies
Authors: Mishra Niraj , Boudewijns Robbert , Schmid Michael A. , Marques Rafael Elias , Sharma Sapna , Neyts Johan , Dallmeier Kai
Published: July 2019

Recent massive outbreaks of yellow fever virus (YFV) in West Africa and Brazil resulted in rapid depletion of global vaccine emergency stockpiles and raised concerns about being not prepared against future YFV epidemics. Here we report that a live-attenuated virus similar to the Japanese encephalitis virus (JEV) vaccine JE-CVax/Imojev®that consists of YFV-17D vaccine from which the structural (prM/E) genes have been replaced with those of the JEV SA14-14-2 vaccine strain confers full protection in mice against lethal YFV challenge. In contrast to the YFV-17D mediated protection against YFV, this protection is not mediated by neutralizing antibodies but correlates with YFV-specific non-neutralizing antibodies and T cell responses against cell-associated YFV NS1 and other YFV non-structural (NS) proteins. Our findings reveal the importance of YFV NS proteins to mediate protection and demonstrate that chimeric flavivirus vaccines, such as Imojev®can confer protection against two flaviviruses. This dual protection has implications for the possible off-label use of JE-CVax in case of emergency and vaccine shortage during YFV outbreaks. In addition, populations in Asia that have been vaccinated with Imojev®may already be protected against YFV should outbreaks ever occur on that continent as feared by WHO.

IMPORTANCE

Efficient and safe vaccines exist against yellow fever (e.g. YFV-17D) that provide long-lasting protection by rapidly inducing neutralizing antibody responses. However, vaccine supply cannot cope with an increasing demand posed by massive urban outbreaks in recent years. Here we report that JE-CVax/Imojev®, a YFV-17D-based chimeric Japanese encephalitis vaccine also efficiently protects against YFV infection in mice. In case of shortage of the YFV vaccine during yellow fever outbreaks, (off-label) use of JE-CVax/Imojev®may be considered. Moreover, wider use of JE-CVax/Imojev®in Asia may lower the risk of the much-feared YFV spill over to the continent. More in general chimeric vaccines that combine surface antigens and replication machineries of two distinct flaviviruses can be considered dual vaccines, for the latter pathogen without induction of surface-specific antibodies. Following this rationale, novel flavivirus vaccines that do not hold a risk for antibody-dependent enhancement (ADE) of infection [inherent to current dengue vaccines and dengue vaccine candidates] could be designed.
A stochastic model of gene expression with polymerase recruitment and pause release
Authors: Cao Z. , Filatova T. , Oyarzún D. A. , Grima R.
Published: July 2019

Transcriptional bursting is a major source of noise in gene expression. The telegraph model of gene expression, whereby transcription switches between “on” and “off” states, is the dominant model for bursting. Recently it was shown that the telegraph model cannot explain a number of experimental observations from perturbation data. Here we study an alternative model that is consistent with the data and which explicitly describes RNA polymerase recruitment and polymerase pause release, two steps necessary for mRNA production. We derive the exact steady-state distribution of mRNA numbers and an approximate steady-state distribution of protein numbers which are given by generalized hypergeometric functions. The theory is used to calculate the relative sensitivity of the coefficient of variation of mRNA fluctuations for thousands of genes in mouse fibroblasts. This indicates that the size of fluctuations is mostly sensitive to the rate of burst initiation and the mRNA degradation rate. Furthermore we show that (i) the time-dependent distribution of mRNA numbers is accurately approximated by a modified telegraph model with a Michaelis-Menten like dependence of the effective transcription rate on RNA polymerase abundance. (ii) the model predicts that if the polymerase recruitment rate is comparable or less than the pause release rate, then upon gene replication the mean number of RNA per cell remains approximately constant. This gene dosage compensation property has been experimentally observed and cannot be explained by the telegraph model with constant rates.

Statement of Significance

The random nature of gene expression is well established experimentally. Mathematical modelling provides a means of understanding the factors leading to the observed stochasticity. There is evidence that the classical two-state model of stochastic mRNA dynamics (the telegraph model) cannot describe perturbation experiments and a new model that includes polymerase dynamics has been proposed. In this paper, we present the first detailed study of this model, deriving an exact solution for the mRNA distribution in steady-state conditions, an approximate time-dependent solution and showing the model can explain gene dosage compensation. As well, we use the theory together with transcriptomic data, to deduce which parameters when perturbed lead to a maximal change in the size of mRNA fluctuations.
Toxicity and bioaccumulation of Cadmium, Copper and Zinc in a direct comparison at equitoxic concentrations in common carp (Cyprinus carpio) juveniles
Authors: Delahaut Vyshal , Rašković Božidar , Salvado Marta Satorres , Bervoets Lieven , Blust Ronny , De Boeck Gudrun
Published: July 2019

The individual toxicity and bioaccumulation of cadmium (Cd), copper (Cu) and zinc (Zn) towards common carp juveniles was evaluated in a direct comparison in two experimental setups. First, the fish were exposed for 10 days to different metal concentrations. Accumulated metals were quantified and showed a positive dose dependent uptake for cadmium and copper, but not for zinc. Toxicity was in the order Cd>Cu>Zn with 96h LC50values (concentration where 50% of the animals dies within 96h) for Cd at 0.20±0.16 μM, Cu at 0.77±0.03 μM, and Zn at 29.89±9.03 μM respectively, and incipient lethal levels (concentration where 50% of the animals survives indefinitely) at 0.16 μM, 0.77 μM and 28.33 μM respectively. Subsequently, a subacute exposure experiment was conducted, where carp juveniles were exposed to 2 equitoxic concentrations (10% and 50% of LC5096 h) of the three metals. The gill metal content was quantified after 1, 3 and 7 days, and was correlated to electrolyte levels and structural damage of the gill tissue and associated pathological effects. Again a significant dose-dependent increase in gill cadmium and copper, but not in zinc, was observed during the 7-day exposure. Copper clearly affected the sodium levels in the gill tissue, while zinc and cadmium did not significantly alter any of the gill electrolytes. The overall histopathological effects (e.g. hyperemia and hypertrophy) of the metal exposures were mild for most of the alterations, and no metal specific pattern was elucidated for the tested metals except oedema of the primary epithelium which typically occurred in both levels of Zn exposure.
Titrating gene expression with series of systematically compromised CRISPR guide RNAs
Authors: Jost Marco , Santos Daniel A. , Saunders Reuben A. , Horlbeck Max A. , Hawkins John S. , Scaria Sonia M. , Norman Thomas M. , Hussmann Jeffrey A. , Liem Christina R. , Gross Carol A. , Weissman Jonathan S.
Published: July 2019

Biological phenotypes arise from the degrees to which genes are expressed, but the lack of tools to precisely control gene expression limits our ability to evaluate the underlying expression-phenotype relationships. Here, we describe a readily implementable approach to titrate expression of human genes using series of systematically compromised sgRNAs and CRISPR interference. We empirically characterize the activities of compromised sgRNAs using large-scale measurements across multiple cell models and derive the rules governing sgRNA activity using deep learning, enabling construction of a compact sgRNA library to titrate expression of ∼2,400 genes involved in central cell biology and a genome-widein silicolibrary. Staging cells along a continuum of gene expression levels combined with rich single-cell RNA-seq readout reveals gene-specific expression-phenotype relationships with expression level-specific responses. Our work provides a general tool to control gene expression, with applications ranging from tuning biochemical pathways to identifying suppressors for diseases of dysregulated gene expression.
FungalRoot: Global online database of plant mycorrhizal associations
Authors: Soudzilovskaia Nadejda A. , Vaessen Stijn , Barcelo Milargos , He Jinhong , Rahimlou Saleh , Abarenkov Kessy , Brundrett Mark C. , Gomes Sofia , Merckx Vincent , Tedersoo Leho
Published: July 2019

The urgent need to better understand profound impacts of mycorrhizas on functioning of terrestrial ecosystems, along with recent debates on resolving plant mycorrhizal associations, indicate that there is a great need for a comprehensive data of plant mycorrhizal associations able to support testing of ecological, biogeographic and phylogenetic hypotheses.

Here present a database, FungalRoot, which summarizes publicly available data on plant mycorrhizal type and intensity of root colonization by mycorrhizal fungi, accompanied by rich meta-data. We collected and digitized data on plant mycorrhizal colonization intensity published until April 2019 in 9 globally most important languages. The data were assessed for quality and updated for plant taxonomy.

The FungalRoot database contains 36,303 species by site observations for 14,870 plant species, tripling the previously available amount in any compilation. The great majority of ectomycorrhizal and ericod mycorrhizal plants are trees and shrubs, 92% and 85% respectively. The majority of arbuscular mycorrhizal and of non-mycorrhizal plant species are herbaceous (50% and 70%).

Besides acting as a compilation of referenced observations, our publicly available database provides a recommendation list of plant mycorrhizal status for ecological and evolutionary analyses to promote research on the links between above- and belowground biodiversity and functioning of terrestrial ecosystems.
Rational design of hepatitis C virus E2 core nanoparticle vaccines
Authors: He Linling , Tzarum Netanel , Lin Xiaohe , Shapero Benjamin , Sou Cindy , Mann Colin J. , Stano Armando , Zhang Lei , Nagy Kenna , Giang Erick , Law Mansun , Wilson Ian A. , Zhu Jiang
Published: July 2019

Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are critical for cell entry with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell-based HCV vaccine development through E2 optimization and nanoparticle display. We redesigned variable region 2 in a truncated form (tVR2) on E2 cores derived from genotypes 1a and 6a, resulting in improved stability and antigenicity. Crystal structures of three optimized E2 cores with human cross-genotype NAbs (AR3s) revealed how the modified tVR2 stabilizes E2 without altering key neutralizing epitopes. We then displayed these E2 cores on 24- and 60-meric nanoparticles and achieved high yield, high purity, and enhanced antigenicity. In mice, these nanoparticles elicited more effective NAb responses than soluble E2 cores. Next-generation sequencing (NGS) defined distinct B-cell patterns associated with nanoparticle-induced antibody responses, which cross-neutralized HCV by targeting the conserved neutralizing epitopes on E2.

One Sentence Summary

An HCV vaccine strategy is presented that displays redesigned E2 cores on nanoparticles as vaccine candidates for eliciting a broadly neutralizing B-cell response.
Dormancy dampens the microbial distance-decay relationship
Authors: Locey KJ , Muscarella ME , Larsen ML , Bray SR , Jones SE , Lennon JT
Published: July 2019

Much of Earth’s biodiversity has the capacity to engage in dormancy whereby individuals enter a reversible state of reduced metabolic activity. By increasing resilience to unfavorable conditions, dormancy leads to the accumulation of “seed banks” that should diminish the influence of environmental filtering, while allowing passive dispersers to colonize new habitats. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biodiversity and biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) using 16S rRNA sequencing to characterize the total (DNA) and the active (RNA) bacterial communities in a regional survey of 49 forested ponds. As expected, the total community harbored greater diversity and exhibited weaker DDRs than the active portion of the community. These empirical observations were robust to different measures of community similarity and random resampling tests. Furthermore, findings from the field survey were reproduced by models that included aspects of dormancy along with the geographical coordinates and environmental characteristics of our study system. In addition to maintaining local diversity, our results support recent theoretical predictions that dormancy shapes geographical patterns of biodiversity.
Termite mounds contain distinct methanotroph communities that are kinetically adapted to elevated methane concentrations
Authors: Chiri Eleonora , Greening Chris , Arndt Stefan K. , Nauer Philipp A.
Published: July 2019

Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH4) emissions, but the aerobic methane-oxidizing bacteria (methanotrophs) responsible for this consumption have not been resolved. Here we describe the abundance, composition, and kinetics of the methanotroph communities in the mounds of three distinct termite species. We show that methanotrophs are rare members of the termite mound biosphere and have a comparable abundance, but distinct composition, to those of adjoining soil samples. Across all mounds, the most abundant and prevalent particulate methane monooxygenase sequences detected were affiliated with Upland Soil Cluster α (USCα), with sequences homologous toMethylocystisand Tropical Upland Soil Cluster also detected. The Michaelis-Menten kinetics of CH4oxidation in mounds were estimated fromin situreaction rates. The apparent CH4affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH4source such as landfill-cover soils. The rate constant of CH4oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH4emissions have selected for unique methanotroph communities that are kinetically adapted to elevated CH4concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH4emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH4concentrations and suggest a higher functional diversity within this group than previously recognised.
Role for Merlin/NF2 in transcription elongation through interaction with the PAF complex
Authors: Roehrig Anne E. , Klupsch Kristina , Oses-Prieto Juan A. , Chaib Selim , Henderson Stephen , Emmett Warren , Young Lucy C. , Surinova Silvia , Blees Andreas , Pfeiffer Anett , Tijani Maha , Brunk Fabian , Hartig Nicole , Muñoz-Alegre Marta , Hergovich Alexander , Jennings Barbara H. , Burlingame Alma L. , Rodriguez-Viciana Pablo
Published: July 2019

The PAF complex (PAFC) coordinates transcription elongation and mRNA processing events and its CDC73/parafibromin subunit functions as a tumour suppressor. The NF2/Merlin tumour suppressor functions at the cell cortex and nucleus and is a key mediator of contact inhibition. Here we provide a direct link between nuclear Merlin and transcription elongation controlled by cell-cell adhesion. Merlin interacts with the PAFC in a cell density-dependent manner and tumour-derived inactivating mutations in both Merlin and CDC73 mutually disrupt their interaction. Growth suppression by Merlin requires CDC73 and Merlin regulates PAFC association with chromatin in a subset of genes. We also identify by CDC73 affinity-proteomics a role for FAT cadherins in regulating the Merlin-PAFC interaction. Our results suggest that in addition to its function within the Hippo pathway, nuclear Merlin is part of a tumour suppressor network which coordinates postinitiation steps of the transcription cycle of genes mediating in contact inhibition.
Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape
Authors: Thatte Prachi , Chandramouli Anuradha , Tyagi Abhinav , Patel Kaushal , Baro Phulmani , Chhattani Himanshu , Ramakrishnan Uma
Published: July 2019

Aim

Maintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on connectivity in four wide-spread species- jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris). Location Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land-use types.

Methods

Microsatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on gene flow was inferred using a multi-model landscape resistance optimization approach.

Results

All four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on geneflow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables- land-use, human population density, density of linear features and roads- impacted the study species differently. Although land-use was found to be an important variable explaining genetic connectivity for all four species, the amount of variation explained, the optimum spatial resolution and the resistance offered by different land-use classes varied.

Main conclusions

As expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.
Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes
Authors: Wikberg Eva , Christie Diana , Sicotte Pascale , Ting Nelson
Published: July 2019

The gut microbiome is structured by social groups in a variety of host taxa. Whether this pattern is driven by relatedness, similar diets, or shared social environments is under debate because few studies have had access to the data necessary to disentangle these factors in wild populations. We investigated whether diet, relatedness, or the 1-meter proximity network best explains differences in the gut microbiome among 45 female colobus monkeys in 8 social groups residing at Boabeng-Fiema, Ghana. We combined demographic and behavioural data collected May-August 2007 and October 2008-April 2009 with 16S rRNA sequencing of faecal samples collected during the latter part of each observation period. Social group identity explained a large percentage of the variation in gut microbiome beta-diversity. When comparing the predictive power of dietary dissimilarity, relatedness, and connectedness in the 1-meter proximity network, the models with social connectedness received the strongest support, even in our analyses that excluded within-group dyads. This novel finding indicates that microbes may be transmitted during intergroup encounters, which could occur either indirectly via shared environments or directly via social contact. Lastly, some of the gut microbial taxa that appear to be transmitted via 1-meter proximity are associated with digestion of plant material, but further research is needed to investigate whether this type of gut microbe transmission yields health benefits, which could provide an incentive for the formation and maintenance of social bonds within and between social groups.
Nicotianamine synthase 2 is required for symbiotic nitrogen fixation inMedicago truncatulanodules
Authors: Escudero Viviana , Abreu Isidro , del Sastre Eric , Tejada-Jiménez Manuel , Larue Camile , Novoa-Aponte Lorena , Wen Jiangqi , Mysore Kirankumar S. , Abadía Javier , Argüello José M. , Castillo-Michel Hiram , Álvarez-Fernández Ana , Imperial Juan , González-Guerrero Manuel
Published: July 2019

Symbiotic nitrogen fixation carried out by the interaction between legumes and diazotrophic bacteria known as rhizobia requires of relatively large levels of transition metals. These elements act as cofactors of many key enzymes involved in this process. Metallic micronutrients are obtained from soil by the roots and directed to sink organs by the vasculature, in a process participated by a number of metal transporters and small organic molecules that mediate metal delivery in the plant fluids. Among the later, nicotianamine is one of the most important. Synthesized by nicotianamine synthases (NAS), this non-proteinogenic amino acid forms metal complexes participating in intracellular metal homeostasis and long-distance metal trafficking. Here we characterized theNAS2gene from model legumeMedicago truncatula. MtNAS2 is located in the root vasculature and in all nodule tissues in the infection and fixation zones. Symbiotic nitrogen fixation requires ofMtNAS2function, as indicated by the loss of nitrogenase activity in the insertional mutantnas2-1, a phenotype reverted by reintroduction of a wild-type copy ofMtNAS2. This would be the result of the altered iron distribution innas2-1nodules, as indicated by X-ray fluorescence studies. Moreover, iron speciation is also affected in these nodules. These data suggest a role of nicotianamine in iron delivery for symbiotic nitrogen fixation.

Significance Statement

Nicotianamine synthesis mediated by MtNAS2 is important for iron allocation for symbiotic nitrogen fixation by rhizobia inMedicago truncatularoot nodules.
Neural signatures of model-free learning when avoiding harm to self and other
Authors: Lockwood Patricia L. , Klein-Flügge Miriam , Abdurahman Ayat , Crockett Molly J.
Published: July 2019

Moral behaviour requires learning how our actions help or harm others. Theoretical accounts of learning propose a key division between ‘model-free’ algorithms that efficiently cache outcome values in actions and ‘model-based’ algorithms that prospectively map actions to outcomes, a distinction that may be critical for moral learning. Here, we tested the engagement of these learning mechanisms and their neural basis as participants learned to avoid painful electric shocks for themselves and a stranger. We found that model-free learning was prioritized when avoiding harm to others compared to oneself. Model-free prediction errors for others relative to self were tracked in the thalamus/caudate at the time of the outcome. At the time of choice, a signature of model-free moral learning was associated with responses in subgenual anterior cingulate cortex (sgACC), and resisting this model-free influence was predicted by stronger connectivity between sgACC and dorsolateral prefrontal cortex. Finally, multiple behavioural and neural correlates of model-free moral learning varied with individual differences in moral judgment. Our findings suggest moral learning favours efficiency over flexibility and is underpinned by specific neural mechanisms.
Characterization of clostridium botulinum neurotoxin serotype A (BoNT/A) and fibroblast growth factor receptor interactions using a novel receptor dimerization assay
Authors: James Nicholas G. , Malik Shiazah , Sanstrum Bethany J. , Rheaume Catherine , Broide Ron S. , Jameson David M. , Brideau-Andersen Amy , Jacky Birgitte
Published: July 2019

Clostridium botulinum neurotoxin serotype A (BoNT/A) is a potent neurotoxin that also serves as an effective therapeutic for a variety of neuromuscular and glandular diseases and disorders. The observed pharmacological effect of BoNT/A is due to specific targeting and entry into motor nerve terminals within muscles followed by cleavage of the SNARE protein, SNAP-25, inducing a block in neurotransmission and temporary muscular paralysis. Specific binding and internalization of BoNT/A into neuronal cells are mediated by its binding domain (HC/A), which binds to GT1b ganglioside and protein cell surface receptors. Previously, fibroblast growth factor receptor 3 (FGFR3) was identified as a BoNT/A receptor, in addition to synaptic vesicle protein (SV2). To further study BoNT/A interactions with FGFRs, an FCS & TIRF receptor dimerization assay was developed to measure dimerization of FGFRs in live cells, as FGFR dimerization can be considered an indirect measure for receptor-ligand binding interaction and downstream signaling. The ability of HC/A to facilitate dimerization of three FGFR subtypes (FGFR1-3) was assessed. Recombinant HC/A (rHC/A) was shown to dimerize FGFR subtypes in the rank order FGFR3c > FGFR2b > FGFR1c. With potencies (EC50 values) defined as the concentration of ligand required to dimerize 50% of the receptors, wild type rHC/A dimerized FGFR3c with an EC50 of 24 nM, similar to FGF9, a native FGFR3c ligand, which had an EC50 of 15 nM, while FGFR1c and FGFR2b required higher rHC/A concentrations (≥100 nM and 68 nM, respectively). Furthermore, addition of the GT1b ganglioside to the culture media resulted in increased dimerization, whereas a ganglioside mutant variant of HC/A (rHC/A W1266L;Y1267S) showed decreased dimerization. Interestingly, reduced dimerization was also observed with an SV2 mutant variant of HC/A (rHC/A T1145A;T1146A). These results support a model wherein BoNT/A interacts with FGFRs, gangliosides, and SV2 on the cell surface to facilitate cell uptake.
Automated recognition of functional compound-protein relationships in literature
Authors: Döring Kersten , Qaseem Ammar , Telukunta Kiran K , Becer Michael , Thomas Philippe , Günther Stefan
Published: July 2019

Motivation

Much effort has been invested in the identification of protein-protein interactions using text mining and machine learning methods. The extraction of functional relationships between chemical compounds and proteins from literature has received much less attention, and no ready-to-use open-source software is so far available for this task.

Method

We created a new benchmark dataset of 2,753 sentences from abstracts containing annotations of proteins, small molecules, and their relationships. Two kernel methods were applied to classify these relationships as functional or non-functional, named shallow linguistic and all-paths graph kernel. Furthermore, the benefit of interaction verbs in sentences was evaluated.

Results

The cross-validation of the all-paths graph kernel (AUC value: 84.2%, F1 score: 81.8%) shows slightly better results than the shallow linguistic kernel (AUC value: 81.6%, F1 score: 79.7%) on our benchmark dataset. Both models achieve state-of-the-art performance in the research area of relation extraction. Furthermore, the combination of shallow linguistic and all-paths graph kernel could further increase the overall performance. We used each of the two kernels to identify functional relationships in all PubMed abstracts (28 million) and provide the results, including recorded processing time.

Availability

The software for the tested kernels, the benchmark, the processed 28 million PubMed abstracts, all evaluation scripts, as well as the scripts for processing the complete PubMed database are freely available at https://github.com/KerstenDoering/CPI-Pipeline.

Author summary

Text mining aims at organizing large sets of unstructured text data to provide efficient information extraction. Particularly in the area of drug discovery, the knowledge about small molecules and their interactions with proteins is of crucial importance to understand the drug effects on cells, tissues, and organisms. This data is normally hidden in written articles, which are published in journals with a focus on life sciences. In this publication, we show how text mining methods can be used to extract data about functional interactions between small molecules and proteins from texts. We created a new dataset with annotated sentences of scientific abstracts for the purpose of training two diverse machine learning methods (kernels), and successfully classified compound-protein pairs as functional and non-functional relations, i.e. no interactions. Our newly developed benchmark dataset and the pipeline for information extraction are freely available for download. Furthermore, we show that the software can be easily up-scaled to process large datasets by applying the approach to 28 million abstracts.
Myco- and photobiont associations in crustose lichens in the McMurdo Dry Valleys (Antarctica) reveal high differentiation along an elevational gradient
Authors: Wagner Monika , Bathke Arne C. , Cary Craig , Junker Robert R. , Trutschnig Wolfgang , Ruprecht Ulrike
Published: July 2019

The climate conditions of the McMurdo Dry Valleys (78° S) are characterized by low temperatures and low precipitation. The annual temperatures at the valley bottoms have a mean range from −30 °C to −15 °C and decrease with elevation. Precipitation occurs mostly in form of snow (3-50 mm a−1water equivalent) and, liquid water is rare across much of the landscape for most of the year and represents the primary limitation to biological activity. Snow delivered off the polar plateau by drainage winds, dew and humidity provided by clouds and fog are important water sources for rock inhibiting crustose lichens. In addition, the combination of the extremely low humidity and drying caused by foehn winds, confined to lower areas of the valleys, with colder and moister air at higher altitudes creates a strongly improving water availability gradient with elevation.

We investigated the diversity and interaction specificity of myco-/photobiont associations of a total of 232 crustose lichen specimens, collected along an elevational gradient (171-959 m a.s.l.) within the McMurdo Dry Valleys with regard to the spatial distribution caused by climatological and geographical factors. For the identification of the mycobiont and photobiont species three markers each were amplified (nrITS, mtSSU, RPB1 and nrITS, psbJ-L, COX2, respectivley). Elevation, associated with a water availability gradient, turned out to be the key factor explaining most of the distribution patterns of the mycobionts. Pairwise comparisons showedLecidea cancriformisandRhizoplaca macleaniito be significantly more common at higher, andCarbonea vorticosaandLecidea polypycnidophoraat lower, elevations. Lichen photobionts were dominated by the globally distributedTrebouxiaOTU,Tr_A02 which occurred at all habitats. Network specialization resulting from mycobiont-photobiont bipartite network structure varied with elevation and associated abiotic factors.

Along an elevational gradient, the spatial distribution, diversity and genetic variability of the lichen symbionts appear to be mainly influenced by improved water relations at higher altitudes.
A dynamic regression panel approach to the determinants of monetary policy and economic growth
Authors: Olamide Ebenezer Gbenga , Maredza Andrew
Published: July 2019

Purpose

Empirically, the purpose of this paper is to investigate policy variables that determine monetary policy and economic growth of some selected countries within the economic bloc of Southern Africa Development Community (SADC). The selected countries are Botswana, Democratic Republic of Congo, Lesotho, Madagascar, Malawi, Mozambique, Namibia, South Africa, Swaziland, Zambia and Zimbabwe.

Design/methodology/approach

Annual time series data for a panel of 11 Southern African countries spanning 1980–2015 were employed in the study. The major instrument of estimation is the dynamic regression panel model. In order to conform to econometric principles, robustness checks were carried out on the variables of interest so as to avoid spurious results. An estimation of impulse response and variance decomposition analyses were to complement the approach to the study.

Findings

The result of the long-run dynamic panel regression reveals that GDP growth rate, inflation rate, exchange rate, money supply and oil and commodity prices do have profound impact on monetary policy within SADC. It was further revealed from the study that commodity price shock is the major exogenous determinant of monetary policy dynamics and the effect is transmitted via exchange rate channel to macroeconomics of the region; with inflation rate and money supply playing a major role in the transmission mechanism as it affects the economies of the countries in this region.

Practical implications

The policy implication is that inflation is seen as a major challenge to the countries under review. Among other things, a hybrid of inflation and monetary targeting should be adopted to complement each other as policy combination within the region.

Originality/value

The study accounts for the determinants of monetary policyvis-à-visgrowth potentials of some selected countries in SADC, using a combination of dynamic regression panel approach and SVAR elements.
Occupational commitment from a life span perspective
Authors: Spurk Daniel , Hofer Annabelle , Burmeister Anne , Muehlhausen Julia , Volmer Judith
Published: July 2019

Purpose

The purpose of this review is to integrate and organize past research findings on affective, normative and continuance occupational commitment (OC) within an integrative framework based on central life span concepts.

Design/methodology/approach

The authors identified and systematically analyzed 125 empirical articles (including 138 cases) that examined OC with a content valid measure to the here applied definition of OC. These articles provided information on the relationship between OC and four distinct life span concepts: chronological age, career stages, occupational and other life events, and occupational and other life roles. Furthermore, developmental characteristics of OC in terms of construct stability and malleability were reviewed.

Findings

The reviewed literature allowed to draw conclusions about the mentioned life span concepts as antecedents and outcomes of OC. For example, age and tenure is more strongly positively related to continuance OC than to affective and normative OC, nonlinear and moderating influences seem to be relevant in the case of the latter OC types. The authors describe several other findings within the results sections.

Originality/value

OC represents a developmental construct that is influenced by employees’ work- and life-related progress, associated roles, as well as opportunities and demands over their career. Analyzing OC from such a life span perspective provides a new angle on the research topic, explaining inconsistencies in past research and giving recommendation for future studies in terms of dynamic career developmental thinking.
3D coupled conduction-convection problem using in-house heat transfer experiments in conjunction with hybrid inverse approach
Authors: P.S. Vishweshwara , M.K. Harsha Kumar , Gnanasekaran N. , M. Arun
Published: July 2019

Purpose

Many a times, the information about the boundary heat flux is obtained only through inverse approach by locating the thermocouple or temperature sensor in accessible boundary. Most of the work reported in literature for the estimation of unknown parameters is based on heat conduction model. Inverse approach using conjugate heat transfer is found inadequate in literature. Therefore, the purpose of the paper is to develop a 3D conjugate heat transfer model without model reduction for the estimation of heat flux and heat transfer coefficient from the measured temperatures.

Design/methodology/approach

A 3 D conjugate fin heat transfer model is solved using commercial software for the known boundary conditions. Navier–Stokes equation is solved to obtain the necessary temperature distribution of the fin. Later, the complete model is replaced with neural network to expedite the computations of the forward problem. For the inverse approach, genetic algorithm (GA) and particle swarm optimization (PSO) are applied to estimate the unknown parameters. Eventually, a hybrid algorithm is proposed by combining PSO with Broyden–Fletcher–Goldfarb–Shanno (BFGS) method that outperforms GA and PSO.

Findings

The authors demonstrate that the evolutionary algorithms can be used to obtain accurate results from simulated measurements. Efficacy of the hybrid algorithm is established using real time measurements. The hybrid algorithm (PSO-BFGS) is more efficient in the estimation of unknown parameters for experimentally measured temperature data compared to GA and PSO algorithms.

Originality/value

Surrogate model using ANN based on computational fluid dynamics simulations and in-house steady state fin experiments to estimate the heat flux and heat transfer coefficient separately using GA, PSO and PSO-BFGS.
Hospital safety index: assessing the readiness and resiliency of hospitals in Indonesia
Authors: Sunindijo Riza Yosia , Lestari Fatma , Wijaya Oktomi
Published: July 2019

Purpose

This study aims to assess the hospital readiness and resiliency in a disaster-prone Indonesia.

Design/methodology/approach

Hospital Safety Index (HSI), containing 151 items, was used to assess ten hospital in West Java and five hospitals in Yogyakarta.

Findings

The average level of HSI for the hospitals under investigation is B, indicating that their ability to function during and after emergencies and disasters are potentially at risk, thus, intervention measures are needed in the short term. Hospitals in Yogyakarta scored lowly in terms of their emergency and disaster management, even though they have previously experienced major disasters in 2006 and 2010.

Practical implications

The role of the government is crucial to improve hospital readiness and resiliency in Indonesia. It is recommended that they: identify disaster-prone areas so that their hospital readiness and resiliency can be assessed; assess the readiness and resiliency of hospitals the prioritized areas; implement intervention measures; re-assess the readiness and resiliency of hospitals in the prioritized areas after implementing intervention measures; and develop a framework to ensure that the hospitals can maintain their level of readiness and resiliency over time.

Originality/value

Research on hospital readiness and resiliency in Indonesia is still limited despite the size of the country and its proneness to disasters. This research has investigated the feasibility and value of using HSI to assess hospital readiness and resilience in Indonesia.
Forced convection in a double tube heat exchanger using nanofluids with constant and variable thermophysical properties
Authors: Bahmani Mohammad Hussein , Akbari Omid Ali , Zarringhalam Majid , Ahmadi Sheikh Shabani Gholamreza , Goodarzi Marjan
Published: July 2019

Purpose

This paper aims to study forced convection in a double tube heat exchanger using nanofluids with constant and variable thermophysical properties.

Design/methodology/approach

The cold fluid was distilled water flowing in the annulus and the hot fluid was aluminum oxide/water nanofluid which flows in the inner tube. Thermal conductivity and viscosity were taken as variable thermophysical properties, and the results were compared against runs with constant values. Finite volume method was used for solving the governing equations. For distilled water, Re = 500 was used, while for nanofluid, nanoparticles volume fraction equal to 2.5-10 per cent and Re = 100-1,500 were used.

Findings

Heat transfer rate can be enhanced by increasing the volume fraction of nanoparticles and Reynolds number. Thermal efficiency is better with constant thermophysical characteristics and the average Nusselt number is better for variable characteristics.

Originality/value

Heat exchanger efficiency is evaluated by using distilled water and nanofluid bulk temperature, thermal efficiency and average and local Nusselt numbers for both variable and constant thermophysical characteristics.
“Only English Counts”: the impact of English hegemony on South-Korean athletes
Authors: Brown Clara Lee , Ward Natalia , Nam Benjamin H.
Published: July 2019

Purpose

While conceived to examine key factors affecting post-retirement career advancement of retired elite athletes in South Korea, the purpose of this paper is to report how English, as a de facto global lingua franca, functions as a powerful gatekeeper in the sports administration field.

Design/methodology/approach

Interpreted through the lens of Bourdieu’s linguistic capital and Gramsci’s hegemony of language, the present study draws on content analysis of semi-structured individual interviews, as well as focus group interviews, conducted with thirty former South Korean elite athletes.

Findings

Based on the data analysis, systematic bias toward athletes was uncovered, privileging English as the single determining factor for employment. Furthermore, the educational implications for adult learners of English as a Foreign or English an Additional Language reveal unrealistic expectations of top–down language policies.

Originality/value

Perspectives of athlete participants, an underrepresented group in educational research, within the South Korean globalization context shed critical light on the pervasive aspects of English hegemony and its unexamined dimensions.
Accounting for heritage assets
Authors: Aversano Natalia , Christiaens Johan , Tartaglia Polcini Paolo , Sannino Giuseppe
Published: July 2019

Purpose

Taking into consideration the lively debate about recognition, measurement, and disclosure criteria for heritage assets (HA) in financial reporting, the purpose of this paper is to examine the comment letters submitted by governmental organizations regarding the consultation paper (CP) on HA in order to understand what is the position of the governmental organizations in relation to critical issues of the accounting and financial reporting of HA.

Design/methodology/approach

From a methodological point of view, a content analysis was performed. First, the responses were classified according to level of agreement with the 13 items included in the CP on HA; second, the arguments adduced by respondents in supporting or contradicting the proposed approaches and definitions have been investigated.

Findings

The majority of responses came from countries with relevant differences in culture, administrative traditions and accounting systems. Governmental organizations strongly agreed with the recognition of heritage items as “assets” in financial reporting, while conflicting positions on measuring bases were identified.

Originality/value

This study is one of the few studies based on the content of the comment letters received in response to the CP on HA. The present study can also give an idea of the content of the future IPSAS on HA. Moreover, it is the first study attempting to enrich the debate on governmental organizations’ participation to the IPSAS standard-setting process.
Context from the data reuser’s point of view
Authors: Faniel Ixchel M. , Frank Rebecca D. , Yakel Elizabeth
Published: July 2019

Purpose

Taking the researchers’ perspective, the purpose of this paper is to examine the types of context information needed to preserve data’s meaning in ways that support data reuse.

Design/methodology/approach

This paper is based on a qualitative study of 105 researchers from three disciplinary communities: quantitative social science, archaeology and zoology. The study focused on researchers’ most recent data reuse experience, particularly what they needed when deciding whether to reuse data.

Findings

Findings show that researchers mentioned 12 types of context information across three broad categories: data production information (data collection, specimen and artifact, data producer, data analysis, missing data, and research objectives); repository information (provenance, reputation and history, curation and digitization); and data reuse information (prior reuse, advice on reuse and terms of use).

Originality/value

This paper extends digital curation conversations to include the preservation of context as well as content to facilitate data reuse. When compared to prior research, findings show that there is some generalizability with respect to the types of context needed across different disciplines and data sharing and reuse environments. It also introduces several new context types. Relying on the perspective of researchers offers a more nuanced view that shows the importance of the different context types for each discipline and the ways disciplinary members thought about them. Both data producers and curators can benefit from knowing what to capture and manage during data collection and deposit into a repository.
A review exploring the facets of the value of public libraries
Authors: Stenstrom Cheryl , Cole Natalie , Hanson Rachel
Published: July 2019

Purpose

The purpose of this paper is to discuss a review of the literature on the value of public libraries and propose a preliminary value framework for the public library based on the results. The review was conducted and the framework was developed as part of a larger ongoing project exploring the value of California’s public libraries.

Design/methodology/approach

This paper is a literature review of approximately 130 international, national and local resources from 1998 to 2018. Findings were developed through an analysis and synthesis of the works as they relate to public libraries.

Findings

The themes that emerged from the exploration of studies fell into three intersecting categories: support for personal advancement; support for vulnerable populations; and support for community development. A wide variety of quantitative and qualitative methods have been employed in this area of research. Among the many ways to discuss value, the most appropriate for the user will always depend on the context for which the concept of value is being defined.

Practical implications

Practitioners may find the various definitions of value useful when sharing information about public libraries with decision makers and other stakeholder audiences and when designing service models and outcomes.

Originality/value

The authors believe this paper is the first to identify the emergence of a value framework for the public library based on a literature review exploring both the social and financial value of public libraries.