bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal analysis of land use dynamics and its potential indications on land surface temperature in Sokoto Metropolis, Nigeria
Authors: Ogunjobi K. O. , Adamu Y. , Akinsanola A. A. , Orimoloye I. R.
Published: January 2019

Land use change is the main driving force of global environmental change and is considered as most central to various debates on sustainable development. Even though a large volume of literature materials is available on land use/land cover change for many areas, very little work has been done on land use and its implications on land surface thermal characteristics over the Sokoto area of Nigeria, despite the strategic importance of the zone, including urbanization, increased population as well as the climate in the area, which is dominated by warm harmattan wind blowing Sahara dust inland. Thus, this study aimed at investigating the implications of urban growth on temporal variations of land surface temperature (LST) using remote sensing and geographic information system (GIS) techniques over Sokoto Metropolis, Nigeria between 1986 and 2016. The change detection of each land use class was carried out for each period using Landsat images obtained from the archives of the United States Geological Survey (USGS). The results revealed that the area has undergone a drastic transformation where built-up area witnessed changes at 10.77%, farmland and vegetation increased at the rate of 0.72% and 2.15%, respectively, for the period of study (1986–2016). While bare soil and water body decreased at the rate of 0.56% and 1.11%, respectively, during the study period. This shows that there exists a transformation from bare surface (desert) to vegetated surface especially between years 2009 and 2016. The LST of Sokoto Metropolis was calculated from the satellite data, and the land surface temperature of each land use class was assessed for the study period. The maximum LST of Sokoto was 30.6°C, 32.8°C and 34.6°C for 1986, 1999 and 2016, respectively. This study has revealed the existence of a positive relationship between built-up area and LST over the area. This development might be as a result of anthropogenic activities through urban growth coupled with its potential impacts on urban climate. These are intensified by constant changes of the space, causing imbalance in the interactions between surface and atmosphere which may be extensively influenced or modified by various forms of land use.
Improving anti-infrared radiation and heat insulation by potassium hexatitanate whisker-doped Al
2
O
3
–SiO
2
composite xerogel
Authors: Furong Liang , Weijun Liu , Xiuxiu Han , Boru Zhang , Shuhua Zhang
Published: January 2019

Taking potassium hexatitanate whisker (PTW) modified by silane coupling agent KH550, aluminium nitrate inorganic salt and tetraethyl orthosilicate and deionized water, respectively, as infrared sunscreen, aluminium source and raw materials forming the network structure of a composite xerogel, a series of structurally intact PTW-doped Al
2
O
3
–SiO
2
composite xerogel thermal-insulating materials were prepared by the sol–gel method and dried under atmospheric pressure. The infrared spectral characteristics, infrared radiation transmittance, microstructures, morphology and thermal conductivity of different composite materials prepared have been determined by a Fourier transform infrared spectrometer, UV–visible–near-infrared spectrophotometer, X-ray diffractometer, scanning electron microscope and thermal conductivity tester. The results exhibit that when the Al to Si molar ratio is 1 : 9, the composite material with 5 wt% modified PTW shows the best infrared radiation blocking performance and the lowest thermal conductivity (0.0604 W m
−1
K
−1
).
Identification of cordycepin biosynthesis-related genes through de novo transcriptome assembly and analysis in
Cordyceps cicadae
Authors: Liu Tengfei , Liu Ziyao , Yao Xueyan , Huang Ying , Qu Qingsong , Shi Xiaosa , Zhang Hongmei , Shi Xinyuan
Published: January 2019

Cordyceps cicadae
(Chanhua) is a parasitic fungus that grows on
Cicada flammata
larvae and is used to relieve exhaustion and treat numerous diseases, in part through its active constituent, cordycepin. We used de novo Illumina HiSeq 4000 sequencing to obtain transcriptomes of
C. cicadae
mycelium, fruiting body, and sclerotium, and identify differentially expressed genes. In the mycelium versus sclerotium libraries, 1576 upregulated and 2300 downregulated genes were identified. In the mycelium versus fruiting body and fruiting body versus sclerotium body libraries, 1604 and 1474 upregulated and 1365 and 1320 downregulated genes, respectively, were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified 19 genes differentially expressed in mycelium versus fruiting body as related to the purine pathway, along with 28 and 16 genes differentially expressed in the mycelium versus sclerotium and fruiting body versus sclerotium groups, respectively. Gene expression of six key enzymes was validated by quantitative polymerase chain reaction. Specifically, 5′-nucleotidase (c62060g1) and adenosine deaminase (c35629g1) in purine nucleotide metabolism, which are involved in cordycepin biosynthesis, were significantly upregulated in the sclerotium group. These findings improved our understanding of genes involved in the biosynthesis of cordycepin and other characteristic secondary metabolites in
C. cicadae
.
Chromatic transitions in the emergence of syntax networks
Authors: Corominas-Murtra Bernat , Sànchez Fibla Martí , Valverde Sergi , Solé Ricard
Published: January 2019

The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the
chromatic number
, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.
Captive jays exhibit reduced problem-solving performance compared to wild conspecifics
Authors: McCune Kelsey B. , Jablonski Piotr , Lee Sang-im , Ha Renee R.
Published: January 2019

Animal cognitive abilities are frequently quantified in strictly controlled settings, with laboratory-reared subjects. Results from these studies have merit for clarifying proximate mechanisms of performance and the potential upper limits of certain cognitive abilities. Researchers often assume that performance on laboratory-based assessments accurately represents the abilities of wild conspecifics, but this is infrequently tested. In this experiment, we quantified the performance of wild and captive corvid subjects on an extractive foraging task. We found that performance was not equivalent, and wild subjects were faster at problem-solving to extract the food reward. By contrast, there was no difference in the time it took for captive and wild solvers to repeat the behaviour to get additional food rewards (learning speed). Our findings differ from the few other studies that have statistically compared wild and captive performance on assessments of problem-solving and learning. This indicates that without explicitly testing it, we cannot assume that captive animal performance on experimental tasks can be generalized to the species as a whole. To better understand the causes and consequences of a variety of animal cognitive abilities, we should measure performance in the social and physical environment in which the ability in question evolved.
Striped bodypainting protects against horseflies
Authors: Horváth Gábor , Pereszlényi Ádám , Åkesson Susanne , Kriska György
Published: January 2019

Bodypainting is widespread in African, Australian and Papua New Guinean indigenous communities. Many bodypaintings use white or bright yellow/grey/beige stripes on brown skin. Where the majority of people using bodypainting presently live, blood-sucking horseflies are abundant, and they frequently attack the naked brown regions of the human body surface with the risk of transmitting the pathogens of dangerous diseases. Since horseflies are deterred by the black and white stripes of zebras, we hypothesized that white-striped paintings on dark brown human bodies have a similar effect. In a field experiment in Hungary, we tested this hypothesis. We show that the attractiveness to horseflies of a dark brown human body model significantly decreases, if it is painted with the white stripes that are used in bodypaintings. Our brown human model was 10 times more attractive to horseflies than the white-striped brown model, and a beige model, which was used as a control, attracted two times more horseflies than the striped brown model. Thus, white-striped bodypaintings, such as those used by African and Australian people, may serve to deter horseflies, which is an advantageous byproduct of these bodypaintings that could lead to reduced irritation and disease transmission by these blood-sucking insects.
Structure and vibrational spectroscopy of methanesulfonic acid
Authors: Zhong Lisha , Parker Stewart F.
Published: January 2019

In this work, we have used a combination of vibrational spectroscopy (infrared, Raman and inelastic neutron scattering) and periodic density functional theory to investigate the structure of methanesulfonic acid (MSA) in the liquid and solid states. The spectra clearly show that the hydrogen bonding is much stronger in the solid than the liquid state. The structure of MSA is not known; however, mineral acids typically adopt a chain structure in condensed phases. A periodic density functional theory (CASTEP) calculation based on the linear chain structure found in the closely related molecule trifluoromethanesulfonic acid gave good agreement between the observed and calculated spectra, particularly with regard to the methyl and sulfonate groups. The model accounts for the large widths of the asymmetric S-O stretch modes; however, the external mode region is not well described. Together, these observations suggest that the basic model of four molecules in the primitive unit cell, linked by hydrogen bonding into chains, is correct, but that MSA crystallizes in a different space group than that of trifluoromethanesulfonic acid.
Detection of ethyl carbamate in liquors using surface-enhanced Raman spectroscopy
Authors: Qi Haiyan , Chen Huacai , Wang Yan , Jiang Li
Published: January 2019

Ethyl carbamate (EC), a potential carcinogen, can be formed during the fermentation and storage of alcoholic beverages. In this work, quantitative detection of EC in alcoholic beverages by using surface-enhanced Raman spectroscopy (SERS) is reported. Flower-shaped silver nanostructure substrates and silver nanocube substrates were prepared and employed as SERS platform. Flower-like silver substrates had better Raman enhancement effect on EC and were selected for further EC detection. In EC SERS spectra based on flower-shaped silver substrates, the strongest and reproducible characteristic band at 857 cm
−1
was chosen for establishing a linear regression model in the concentrations ranging from 10
−5
to 10
−9
M, which effectively extended the application scope of the quantitative model for determination EC. Furthermore, a real alcoholic beverage was tested to verify the feasibility and reliability of the method.
Synthesis of an excellent MTP catalyst: hierarchical ZSM-5 zeolites with great mesoporosity
Authors: Song Guoqiang , Chen Wenting , Dang Peipei , Wang Yuanyi , Li Fuxiang
Published: January 2019

A unique organosiloxane-polyether amine (OPA) was produced and used as mesoporogen to efficiently synthesize hierarchical ZSM-5 zeolites with great mesoporosity. We have employed silica sol and tetraethylorthosilicate, respectively, to investigate the influence of different silicon sources on hierarchical zeolites in the presence of OPA. The mesopores of synthesized samples focused on 6–15 nm, and the external surface area varied from 185 to 463 m
2
g
−1
where the micropore surface area was maintained at 245–334 m
2
g
−1
. Benefiting from the superior structure properties, these samples were used as catalysts in the reaction of methanol to propylene, and the optimal one catalysed for 180 h with methanol conversion above 95%. The as-produced OPA could connect steadily with zeolite frameworks through covalent bonds (–Si–O–Si–) during the hydrothermal crystallization process. This type of connection mode could effectively avoid the formation of amorphous phase and the special molecular structure of OPA could efficiently introduce abundant mesopores with few micropores being consumed. The samples synthesized with silicon sol were made up of quasi-circular particles of about 800 nm in size and further consisted of nanocrystals of 40 nm, and the samples produced with TEOS have a particle size of about 1–2 µm aggregated with nanocrystals of 300 nm.
Critical autoignition conditions for arbitrary reaction order
Authors: Yu Filimonov V. , Koshelev K. B.
Published: January 2019

In this paper, the theoretical analysis of the critical autoignition conditions for exothermically reacting systems at any value of the reaction order was conducted. The calculated and approximate analytical dependencies for the relationship between the parameters at the ignition limit were obtained. On the basis of the obtained diagrams of critical parameters, the conditions of thermal explosion (TE) degeneration for reactions of arbitrary order were determined. It was established that the existing theory of TE gives the correct estimates of ignition temperatures for a given condition of exothermic reaction realization (heat transfer coefficient, specific surface area, initial concentration). However, the theory gives unsatisfactory predictions for the mentioned critical TE conditions at a given ambient temperature. Moreover, the classical theory cannot be applied in the intermediate case when the effect of reactant consumption is already significant but the reaction still proceeds with all the signs of a TE.
Predictive analysis across spatial scales links zoonotic malaria to deforestation
Authors: Brock Patrick M. , Fornace Kimberly M. , Grigg Matthew J. , Anstey Nicholas M. , William Timothy , Cox Jon , Drakeley Chris J. , Ferguson Heather M. , Kao Rowland R.
Published: January 2019

The complex transmission ecologies of vector-borne and zoonotic diseases pose challenges to their control, especially in changing landscapes. Human incidence of zoonotic malaria (
Plasmodium knowlesi
) is associated with deforestation although mechanisms are unknown. Here, a novel application of a method for predicting disease occurrence that combines machine learning and statistics is used to identify the key spatial scales that define the relationship between zoonotic malaria cases and environmental change. Using data from satellite imagery, a case–control study, and a cross-sectional survey, predictive models of household-level occurrence of
P. knowlesi
were fitted with 16 variables summarized at 11 spatial scales simultaneously. The method identified a strong and well-defined peak of predictive influence of the proportion of cleared land within 1 km of households on
P. knowlesi
occurrence. Aspect (1 and 2 km), slope (0.5 km) and canopy regrowth (0.5 km) were important at small scales. By contrast, fragmentation of deforested areas influenced
P. knowlesi
occurrence probability most strongly at large scales (4 and 5 km). The identification of these spatial scales narrows the field of plausible mechanisms that connect land use change and
P. knowlesi
, allowing for the refinement of disease occurrence predictions and the design of spatially-targeted interventions.
Fishing pressure impacts the abundance gradient of European lobsters across the borders of a newly established marine protected area
Authors: Nillos Kleiven Portia Joy , Espeland Sigurd Heiberg , Olsen Esben Moland , Abesamis Rene A. , Moland Even , Kleiven Alf Ring
Published: January 2019

Marine protected areas (MPAs) are considered viable fisheries management tools due to their potential benefits of adult spillover and recruitment subsidy to nearby fisheries. However, before–after control–impact studies that explore the biological and fishery effects of MPAs to surrounding fisheries are scarce. We present results from a fine-scale spatial gradient study conducted before and after the implementation of a 5 km
2
lobster MPA in southern Norway. A significant nonlinear response in lobster abundance, estimated as catch-per-unit-effort (CPUE) from experimental fishing, was detected within 2 years of protection. After 4 years, CPUE values inside the MPA had increased by a magnitude of 2.6 compared to before-protection values. CPUE showed a significant nonlinear decline from the centre of the MPA, with a depression immediately outside the border and a plateau in fished areas. Overall fishing pressure almost doubled over the course of the study. The highest increase in fishing pressure (by a magnitude of 3) was recorded within 1 km of the MPA border, providing a plausible cause for the depression in CPUE. Taken together, these results demonstrate the need to regulate fishing pressure in surrounding areas when MPAs are implemented as fishery management tools.
Symbiont evolution during the free-living phase can improve host colonization
Authors: Soto William , Travisano Michael , Tolleson Alexandra Rose , Nishiguchi Michele Kiyoko
Published: January 2019

For micro-organisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether evolution during the free-living stage can be positively pleiotropic to microbial fitness in a host environment. To address this topic, the squid host Euprymna tasmanica and the marine bioluminescent bacterium

Vibrio fischeri

were utilized. Microbial ecological diversification in static liquid microcosms was used to simulate symbiont evolution during the free-living stage. Thirteen genetically distinct

V. fischeri

strains from a broad diversity of ecological sources (e.g. squid light organs, fish light organs and seawater) were examined to see if the results were reproducible in many different genetic settings. Genetic backgrounds that are closely related can be predisposed to considerable differences in how they respond to similar selection pressures. For all strains examined, new mutations with striking and facilitating effects on host colonization arose quickly during microbial evolution in the free-living stage, regardless of the ecological context under consideration for a strain’s genetic background. Microbial evolution outside a host environment promoted host range expansion, improved host colonization for a micro-organism, and diminished the negative correlation between biofilm formation and motility.
SGK1.1 activation causes early seizure termination via effects on M-current
Authors: Armas-Capote Natalia , Maglio Laura E. , Pérez-Atencio Leonel , Martin-Batista Elva , Reboreda Antonio , Barios Juan A. , Hernandez Guadalberto , la Rosa Diego Alvarez de , Lamas José Antonio , Barrio Luis C. , Giraldez Teresa
Published: January 2019

Early termination of status epilepticus affords protection against brain damage and associated pathologies. Regulation of Kv7.2/7.3 potassium channels, underlying the neuronal M-current, is key for seizure control. This conductance is maintained during initiation of action potentials, affecting neuronal excitability and thus inhibiting epileptic discharges. The M-current is upregulated by the neuronal isoform of the serum and glucocorticoid-regulated kinase SGK1 (SGK1.1). We tested whether SGK1.1 is an anticonvulsant factor using the kainic acid (KA) model of acute seizures in a transgenic mouse model with expression of a constitutively active form of the kinase. Our results demonstrate that SGK1.1 confers robust protection against seizures associated to lower mortality levels, independently of sex or genetic background. SGK1.1-dependent protection results in reduced number, shorter duration, and early termination of EEG seizures. At the cellular level, it is associated to increased M-current amplitude mediated by Nedd4-2 phosphorylation, leading to decreased excitability of hippocampal CA1 neurons without alteration of basal synaptic transmission. Altogether, our results reveal that SGK1.1-mediated M-current upregulation in the hippocampus is a key component of seizure resistance in the KA epileptic paradigm, suggesting that regulation of this anticonvulsant pathway may improve adverse outcomes to status epilepticus, constituting a potential target for antiepileptic drugs.
Draft Genome Sequence and intraspecific diversification of the wild crop relativeBrassica creticaLam. using demographic model selection
Authors: Kioukis Antonis , Michalopoulou Vassiliki A. , Briers Laura , Pirintsos Stergios , Studholme David J. , Pavlidis Pavlos , Sarris Panagiotis F.
Published: January 2019

Crop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.

The genusBrassicais listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture.Brassica oleracea(or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.

Brassica creticaLam. is a wild relative crop in the brassica group andB. creticasubsp.niveahas been suggested as a separate subspecies. The speciesB. creticahas been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.

Here, we present the draftde novogenome assemblies of fourB. creticaindividuals, including twoB. creticasubsp.niveaand twoB. cretica.

De novoassembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size ofB. cretica(339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes,B. creticagenome based on our sequence data reveals approximately 30.360 proteins.

Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations ofB. creticaare not isolated. Our findings suggest that the classification of theB. creticain distinct subspecies is not supported from the genome sequence data we analyzed.
Mesenchymal stem cells (MSCs) offer a drug tolerant and immune- privileged niche to Mycobacterium tuberculosis
Authors: Jain Neharika , Kalam Haroon , Singh Lakshyaveer , Sharma Vartika , Kedia Saurabh , Das Prasenjit , Ahuja Vineet , Kumar Dhiraj
Published: January 2019

Anti-tuberculosis (TB) drugs while being highly potent in vitro require prolonged treatment to control Mycobacterium tuberculosis (Mtb) infections in vivo. We report here, mesenchymal stem cells (MSCs) shelter Mtb to help tolerate anti-TB drugs. MSCs uptake Mtb readily and allow them grow unabated despite having functional innate pathway of phagosome maturation. Unlike macrophage-resident ones, MSC-resident Mtb tolerates anti-TB drugs remarkably well, a phenomenon requiring proteins ABCC1, ABCG2 and vacuolar-type H+ATPases. Additionally, contrary to what is classically known, IFNγ and TNFα aid mycobacterial growth within MSCs. Mechanistically, evading drugs and inflammatory cytokines by MSC-resident Mtb is dependent on elevated PGE2 signaling, which we subsequently verified in vivo analyzing sorted CD45-CD73+SCA1+-MSCs from the lungs of infected mice. Moreover granulomas from human pulmonary and extra-pulmonary TB show presence of MSCs co-inhabiting with Mtb. Together the results show targeting the immune-privileged niche, provided by MSCs to Mtb, can revolutionize tuberculosis prevention and cure.
Autophagy regulates the localization and degradation of p16INK4a
Authors: Coryell Philip R. , Goraya Supreet K. , Griffin Katherine A. , Redick Margaret A. , Sisk Samuel R. , Purvis Jeremy E.
Published: January 2019

The tumor suppressor protein p16INK4a (p16) is a well-established hallmark of aging that induces cellular senescence in response to stress. Previous studies have focused primarily on p16 regulation at the transcriptional level; comparatively little is known about the protein’s intracellular localization and degradation. The autophagy-lysosomal pathway has been implicated in the subcellular trafficking and turnover of various stress-response proteins, but it is unclear whether p16 is involved in these pathways. Here, we investigate the role of autophagy, vesicular trafficking, and lysosomal degradation on p16 expression and localization in human epithelial cells. Time-lapse fluorescence microscopy using an endogenous p16-mCherry reporter revealed that autophagy induced by genotoxic stress stimulates rapid p16 recruitment to acidic cytoplasmic vesicles. When vesicular acidification was inhibited by NH4Cl, nuclear p16 levels increased. Single-cell imaging revealed that p16 localizes to lysosomes upon stress, implicating the autophagy pathway as a regulator of p16 localization. Blocking autophagy with bafilomycin, chloroquine, or NH4Cl resulted in elevated p16 protein levels without increased transcription. Increased p16 coincided with accumulation of autophagosome chaperone p62/SQSTM1 (p62) and decreased levels of phosphorylated-Rb. Furthermore, chloroquine caused p16 aggregation within stalled vesicles containing autophagosome marker LC3, demonstrating that p16 is transported and degraded by the autophagy-lysosomal pathway. Knockdown of p62 resulted in delocalization of p16 aggregates to autophagosomes, suggesting that p16 is targeted to these vesicles by p62. Taken together, these results implicate the autophagy pathway as a novel regulator of p16 degradation and localization, which could play a role in the etiology of cancer and age-related diseases.
Cardiac interstitial tetraploid cells that escape replicative senescence are found in rodents but not large mammals
Authors: Broughton Kathleen , Khieu Tiffany , Nguyen Nicky , Rosa Michael , Mohsin Sadia , Quijada Pearl , Wang Bingyan , Echeagaray Oscar , Kubli Dieter , Kim Taeyong , Firouzi Fareheh , Monsanto Megan , Gude Natalie , Adamson Robert M. , Dembitsky Walter P. , Davis Michael , Sussman Mark A.
Published: January 2019

Ploidy for cardiomyocytes is well described but remains obscure in cardiac interstitial cells (CICs). Ploidy of c-kit+CICs (cCICs) were assessed using a combination of confocal, karyotypic, and flow cytometric assessments coupled with molecular and bioinformatic analyses. Fundamental differences were found between cultured rodent (rat, mouse) cCICs possessing mononuclear tetraploid (4n) content versus large mammal (human, swine) with mononuclear diploid (2n) content. In-situ analysis, confirmed with fresh isolates, revealed diploid content in cCICs from human and a mixture of diploid and tetraploid nuclei in mouse. Molecular assessment of the p53 signaling pathway provides a plausible explanation for escape from replicative senescence in rodent but not human cCICs. Single cell transcriptional profiling reveals distinctions between diploid versus tetraploid populations in mouse cCICs, alluding to functional divergences. Collectively, these data reveal fundamental species-specific biological differences in cCICs that could account for challenges in extrapolation of myocardial preclinical studies from rodent to large animal models.
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
Authors: Behsaz Bahar , Mohimani Hosein , Gurevich Alexey , Prjibelski Andrey , Fisher Mark F. , Smarr Larry , Dorrestein Pieter C. , Mylne Joshua S. , Pevzner Pavel A.
Published: January 2019

Cyclic and branch cyclic peptides (cyclopeptides) represent an important class of bioactive natural products that include many antibiotics and anti-tumor compounds. However, little is known about cyclopeptides in the human gut, despite the fact that humans are constantly exposed to them. To address this bottleneck, we developed the CycloNovo algorithm for de novo cyclopeptide sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms. CycloNovo reconstructed many new cyclopeptides that we validated with transcriptome, metagenome, and genome mining analyses. Our benchmarking revealed a vast hidden cyclopeptidome in the human gut and other environments and suggested that CycloNovo offers a much-needed step-change for cyclopeptide discovery. Furthermore, CycloNovo revealed a wealth of anti-microbial cyclopeptides from food that survive the complete human gastrointestinal tract, raising the question of how these cyclopeptides might affect the human microbiome.

SIGNIFICANCE

The golden age of antibiotics was followed by a decline in the pace of antibiotics discovery in the 1990s. The key prerequisite for the resurgence of antibiotics research is the development of a computational discovery pipeline for antibiotics sequencing. We describe such pipeline for cyclic and branch cyclic peptides (cyclopeptides) that represent an important class of bioactive natural products such as antibiotics and anti-tumor compounds. Our CycloNovo algorithm for cyclopeptide sequencing reconstructed many new cyclopeptides that we validated with transcriptome, metagenome, and genome mining analyses. CycloNovo revealed a wealth of anti-microbial cyclopeptides from food that survive the complete human gastrointestinal tract, raising the question of how these cyclopeptides might affect the human microbiome.
Molecular mechanism of TRPV2 channel modulation by cannabidiol
Authors: Pumroy Ruth A. , Samanta Amrita , Liu Yuhang , Hughes Taylor E.T. , Zhao Siyuan , Yudin Yevgen , Huynh Kevin W. , Zhou Z. Hong , Rohacs Tibor , Han Seungil , Moiseenkova-Bell Vera Y.
Published: January 2019

Transient receptor potential vanilloid 2 (TRPV2) plays a critical role in neuronal development, cardiac function, immunity, and cancer. Cannabidiol (CBD), the non-psychotropic therapeutically active ingredient of Cannabis sativa, is a potent activator of TRPV2 and also modulates other transient receptor potential (TRP) channels. Here, we determined structures of the full-length TRPV2 channel in a CBD-bound state in detergent and in PI(4,5)P2 enriched nanodiscs by cryo-electron microscopy. CBD interacts with TRPV2 through a hydrophobic pocket located between S5 and S6 helices of adjacent subunits, which differs from known ligand and lipid binding sites in other TRP channels. Comparison between apo- and two CBD-bound TRPV2 structures reveals that the S4-S5 linker plays a critical role in channel gating upon CBD binding. The TRPV2 “vanilloid” pocket, which is critical for ligand-dependent gating in other TRPV channels, stays unoccupied by annular lipids, PI(4,5)P2, or CBD. Together these results provide a foundation to further understand TRPV channel gating properties and their divergent physiological functions and to accelerate structure-based drug design.
Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes
Authors: Tamames Javier , Cobo-Simón Marta , Puente-Sánchez Fernando
Published: January 2019

Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the usage of assemblies or the direct analysis of raw sequence reads instead. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable. We have studied this point by analysing several real and mock metagenomes using different methodologies and tools, and comparing the resulting taxonomic and functional profiles. Our results show that database completeness is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by sequencing depth, that in turn determines the completeness of the assembly. Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a significant number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.
A widespread Xrn1-resistant RNA motif composed of two short hairpins
Authors: Dilweg Ivar W. , Gultyaev Alexander P. , Olsthoorn René C.
Published: January 2019

Xrn1 is a major 5′-3′ exoribonuclease involved in the RNA metabolism of many eukaryotic species. RNA viruses have evolved ways to thwart Xrn1 in order to produce subgenomic non-coding RNA that affects the hosts RNA metabolism. The 3’ untranslated region of several beny-and cucumovirus RNAs harbors a so-called ‘coremin’ motif that is required for Xrn1 stalling. The structural features of this motif have not been studied in detail yet. Here, by using in vitro Xrn1 degradation assays, we tested over 50 different RNA constructs based on the Beet necrotic yellow vein virus sequence, to deduce putative structural features responsible for Xrn1-stalling. We demonstrated that the minimal benyvirus stalling site consists of two hairpins of 3 and 4 base pairs respectively. The 5’ proximal hairpin requires a YGAD (Y = U/C, D = G/A/U) consensus loop sequence, whereas the 3′ proximal hairpin loop sequence is variable. The sequence of the 9-nucleotide spacer that separates the hairpins is highly conserved and potentially involved in tertiary interactions. Similar coremin motifs were identified in plant virus isolates from other families including Betaflexiviridae, Virgaviridae and Secoviridae (order of the Picornavirales). We conclude that Xrn-stalling motifs are more widespread among RNA viruses than previously realized.
Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima
Authors: Li Gang , Rabe Kersten S. , Nielsen Jens , Engqvist Martin K. M.
Published: January 2019

Enzymes that catalyze chemical reactions at high temperatures are used for industrial biocatalysis, applications in molecular biology, and as highly evolvable starting points for protein engineering. The optimal growth temperature (OGT) of organisms is commonly used to estimate the stability of enzymes encoded in their genomes, but the number of experimentally determined OGT values are limited, particularly for ther-mophilic organisms. Here, we report on the development of a machine learning model that can accurately predict OGT for bacteria, archaea and microbial eukaryotes directly from their proteome-wide 2-mer amino acid composition. The trained model is made freely available for re-use. In a subsequent step we OGT data in combination with amino acid composition of individual enzymes to develop a second machine learning model – for prediction of enzyme catalytic temperature optima (Topt). The resulting model generates enzymeToptestimates that are far superior to using OGT alone. Finally, we predictToptfor 6.5 million enzymes, covering 4,447 enzyme classes, and make the resulting dataset available for researchers. This work enables simple and rapid identification of enzymes that are potentially functional at extreme temperatures.
Youth unemployment, NEETs and structural inequality in Spain
Authors: Rodriguez-Modroño Paula
Published: January 2019

Purpose

The purpose of this paper is to apply an intersectional analysis to assess the impact of structural factors on the risk of being a NEET for youth in Spain. The author study if inequalities have changed after the economic crisis, once youth policies designed to improve the Spanish school-to-work transition (SWT) system were implemented.

Design/methodology/approach

Drawing on microdata from the Spanish Survey on Income and Living Conditions, the paper compares the probability of becoming not in employment, education or training (NEET) of young men and women born inside or outside Spain and living in different types of households.

Findings

Although unemployment rates have improved since the end of the crisis, the situation regarding youth employment, poverty and inequalities remains challenging. Gender and other structural differences are usually ignored in policy debates and in the measures adopted to fight youth unemployment, leading to the persistance of inequalities.

Research limitations/implications

The analysis illustrates new lines and trajectories in the segmentation of youth labor markets along the lines of gender, household and country of origin.

Practical implications

The findings highlight the need for introducing an analysis of the different sources of vulnerability in policy designs in order to promote a real and sustainable change in SWTs.

Originality/value

The contribution of this research to the literature on NEET and SWT is to introduce a framework that allows for the intersectional analysis of gender and other structural inequalities.
The role of local labour market conditions and pupil attainment on post-compulsory schooling decisions
Authors: Meschi Elena , Swaffield Joanna , Vignoles Anna
Published: January 2019

Purpose

The purpose of this paper is to assess the role of local labour market conditions and pupil educational attainment as primary determinants of the post-compulsory schooling decision.

Design/methodology/approach

Through the specification of a nested logit model, the restrictive independence of irrelevant alternatives (IIA) assumption inherent in the multinomial logit (MNL) model is relaxed across multiple unordered outcomes.

Findings

The analysis shows that the factors influencing schooling decisions differ for males and females. For females, on average, the key drivers of the schooling decision are expected wage returns based on youth educational attainment, attitudes to school and parental aspirations, rather than local labour market conditions. For males, higher local unemployment rates encourage greater investment in education.

Originality/value

The contribution of this paper to the existing literature is threefold. First, a nested logit model is proposed as an alternative to a MNL. The former can formally incorporate the structured and sequential decision-making process that youths may engage with in relation to the post-compulsory schooling decision, as well as relaxing the restrictive IIA assumption inherent in the MNL across multiple unordered outcomes, an issue the authors discuss in more detail in the Methodology section below. Second, the analysis is based on extremely rich socio-economic data from the Longitudinal Study of Young People in England, matched to local labour market data and administrative data from the National Pupil Database and Pupil Level Annual School Census, which provide a broad set of unusually high-quality measures of prior attainment. The authors argue that such high-quality data and an appropriate model specification allows identification of the determinants of the post-compulsory decision in a more detailed manner than many previous analyses. Third, the data have the scale necessary to consider whether the determinants of post-compulsory schooling decisions vary by gender, a particularly important issue given the differential education participation rates of males and females (e.g. in this cohort, females are about 10 percentage points more likely to go on to higher education in the UK than males), and the gendered choices of occupation (see, e.g. Bertrand, 2011). The work will, therefore, provide recent empirical evidence from England on gender differences in the determinants of education choices.
Foreign direct investment and institutional stability: who drives whom?
Authors: Mahmood Nihal , Shakil Mohammad Hassan , Akinlaso Ishaq Mustapha , Tasnia Mashiyat
Published: January 2019

Purpose

The purpose of this paper is to examine the relationship between foreign direct investment (FDI) flows and institutional stability. The focus country is Canada. It is one of the few countries where the economy remained relatively stable compared to other economies during the Global Financial Crisis. It is crucial for Canada to determine the optimal level of institutional development to attract more FDI and sustain the sound financial stability in future.

Design/methodology/approach

This study uses the auto-regressive distributive lag (ARDL) approach to understand the relationship between FDI and institutional stability along with other controlled variables, for instance, gross national product, inflation and exports.

Findings

The key finding of this work is that FDI and institutional stability are cointegrated in the long run. The error correction model of ARDL shed light on institutional stability being an exogenous variable, and FDI is an endogenous variable. Institutional stability affects FDI, as it is exogenous. The findings will help policymakers to implement policies to strengthen the institution’s settings, and this, in turn, will attract more investment.

Originality/value

Based on previous theoretical and empirical literature, most of the research points to FDI positively affect institutional stability. In some cases, the relationship does not always hold true. This study will fix the gap in the literature by investigating the relationship between FDI and institutional stability of Canada.
Internet of Things-based intelligent evacuation protocol in libraries
Authors: Xie Kefan , Liu Zimei , Fu Liuliu , Liang Benbu
Published: January 2019

Purpose

The purpose of this paper is to propose a theoretical framework of applying the Internet of Things (IoT) technologies to the intelligent evacuation protocol in libraries at emergency situations.

Design/methodology/approach

The authors conducted field investigations on eight libraries in Wuhan, China, analyzed the characteristics of crowd gathering in libraries and the problems of the libraries’ existing evacuation plans. Therefore, an IoT-based intelligent evacuation protocol in libraries was proposed. Its basic structure consisted of five components: the information base, the protocol base, the IoT sensors, the information fusion system and the intelligent evacuation protocol generation system. In the information fusion system, Dempster–Shafer (D-S) evidence theory was employed as the information fusion algorithm to fuse the multi-sensor information at multiple time points, so as to reduce the uncertainty of disaster prediction. The authors also conducted a case study on the Library L in Wuhan, China. A specific evacuation route was generated for a fire and the crowd evacuation was simulated by the software Patherfind.

Findings

The proposed IoT-based evacuation protocol has four distinguishing features: scenario corresponding, precise evacuation, dynamic correction and intelligent decision-making. The case study shows that the proposed protocol is feasible in practice, indicating that the IoT technologies have great potential to be successfully applied to the safety management in libraries.

Research limitations/implications

The software and hardware requirements as well as the Internet network requirements of IoT technologies need to be further discussed.

Practical implications

The proposed IoT-based intelligent evacuation protocol can be widely used in libraries, which is one of the inspirations for the use of IoT technologies in modern constructers.

Originality/value

The application of IoT technologies in libraries is a brand-new topic that has drawn much attention in academia recently. The crowd safety management in libraries is of great significance, and there is little professional literature on it. This paper proposes an IoT-based intelligent evacuation protocol, aiming at improving the safety management in libraries at emergency situations.
Acceptance of remanufactured products in the circular economy: an empirical study in India
Authors: Singhal Deepak , Tripathy Sushant , Jena Sarat Kumar
Published: January 2019

Purpose

Acceptance of remanufactured products by the consumers is highly essential for the success of closed loop supply chain and for achieving the goal of circular economy. However, the literature shows that consumers are reluctant to purchase remanufactured products. Therefore, the study of attitude and purchase intention (PI) of the consumers toward remanufactured products becomes inevitable for popularizing these products. The paper aims to discuss this issue.

Design/methodology/approach

This research proposes a conceptual model to examine the critical factors influencing the PI of Indian consumers toward remanufactured products. Further, this model is empirically tested, using structural equation modeling technique, based on the data obtained from 1,534 respondents.

Findings

The findings of this research suggest that PI of consumers is influenced by attitude, personal benefits, remanufactured product knowledge, risk perception, subjective norm and market strategy. However, perceived behavior control and green awareness have a non-significant impact on the PI of Indian consumers.

Research limitations/implications

The proposed conceptual model is tested only against the data received from the students of Indian universities who possess electronic gadgets.

Practical implications

The circular economy can be realized through remanufacturing if the attitude of consumers is shaped positively toward remanufactured products through the dissemination of comprehensive product information.

Originality/value

This research is the first attempt to assess the PI of Indian consumers by developing and testing the conceptual model. Further, this research provides guidelines to remanufacturing firms for attracting the consumers toward the purchase of remanufactured products.