bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of two conserved G-quadruplex forming motifs in the Nipah virus genome and their interaction with G-quadruplex specific ligands
Authors: Majee Prativa , Kumar Mishra Subodh , Pandya Nirali , Shankar Uma , Pasadi Sanjeev , Muniyappa K. , Nayak Debasis , Kumar Amit 
Published: January 2020

AbstractThe G-quadruplex (GQ) motifs are considered as potential drug-target sites for several human pathogenic viruses such as Zika, Hepatitis, Ebola, and Human Herpesviruses. The recent outbreaks of Nipah virus (NiV) in India, the highly fatal emerging zoonotic virus is a potential threat to global health security as no anti-viral drug or vaccine in currently available. Therefore, here in the present study, we sought to assess the ability of the putative G-quadruplex forming sequences in the NiV genome to form G-quadruplex structures and act as targets for anti-viral compounds. Bioinformatics analysis underpinned by various biophysical and biochemical techniques (such as NMR, CD, EMSA, DMS footprinting assay) confirmed the presence of two highly conserved G-quadruplex forming sequences (HGQs) in the G and L genes of NiV. These genes encode the cell attachment glycoprotein and RNA-dependent RNA polymerase, respectively and are essential for the virus entry and replication within the host cell. It remains possible that stabilization of these HGQs by the known G-quadruplex binding ligands like TMPyP4 and Braco-19 represents a promising strategy to inhibit the expression of the HGQ harboring genes and thereby stop the viral entry and replication inside the host cell. Accordingly, we report for the first time, that HGQs in Nipah virus genome are targets for G-quadruplex specific ligands; therefore, could serve as potential targets for anti-viral therapy.
Contrasting functional structure of saproxylic beetle assemblages associated to different microhabitats
Authors: Micó Estefanía , Ramilo Pablo , Thorn Simon , Müller Jörg , Galante Eduardo , Carmona Carlos P. 
Published: January 2020

AbstractSaproxylic beetles depend on diverse microhabitats that are exploited by different species assemblages. We focused on analysing the functional trait patterns and functional diversity components of two main assemblages that were collected with window traps (WTs) and hollow emergence traps (HETs) respectively, between three protected areas of the Iberian Peninsula. For that we measured phenological, physiological, morphological, and ecological traits. Results showed that the main microhabitats exploited by each assemblage (WT and HET) constrain most of the morphological traits and trophic guilds. In addition, relative elytra length and predator guild, together with adult activity period, responded to differences at the habitat level (among study areas). HET assemblages were less taxonomically diverse but more functionally diverse than those of WTs, enhancing the functional relevance of tree hollows. Additionally, niche filtering dominated WT assemblages, which were characterised by a narrower functional space and a higher redundancy. In contrast, in the HET assemblages the coexistence of functionally dissimilar species is driven by the niche heterogeneity. HET and WT assemblages differed in the functional space occupied by each within areas, but both assemblages reflected coincident patterns among areas that pointed to a reduction of functional space with management.
Hybridization between subterranean tuco-tucos (Rodentia, Ctenomyidae) with contrasting phylogenetic positions
Authors: Kubiak Bruno Busnello , Kretschmer Rafael , Leipnitz Leonardo Trindade , Maestri Renan , de Almeida Thamara Santos , Borges Leandro Rodrigues , Galiano Daniel , Pereira Jorge C. , de Oliveira Edivaldo Herculano Corrêa , Ferguson-Smith Malcolm A. , de Freitas Thales Renato Ochotorena 
Published: January 2020

AbstractReproductive compatibility usually decreases according to increasing genetic difference and the time of divergence between species. However, the amount of modification required to influence hybridization may vary in different species. Thus, it is extremely important to conduct studies that seek to understand what and how variables influence the reproductive isolation of species. We have explored a system involving two species of subterranean rodents that present morphological, karyotypic, and evolutionary history differences and are capable of generating hybrids. To gain insight into the karyotype organization of genusCtenomys, we examined the chromosome evolution by classical and molecular cytogenetics of both parental species and hybrids. Furthermore, we have used different approaches to analyze the differences between the parental species and the hybrids, and determined the origin of the hybrids. The results of our work demonstrate unequivocally that some species that present extensive differences in chromosome organization, phenotype, evolutionary history, sperm morphology and genetic, which are usually associated with reproductive isolation, can generate natural hybrids. The results also demonstrate that females of both species are able to generate hybrids with males of the other species. In addition, the chromosome-specific probes prepared fromCtenomys flamarioniprovide an invaluable tool for comparative cytogenetics in closely related species.
Corticosteroid reduction by addition of cetirizine and montelukast in biopsy-proven minimal-change nephrotic syndrome concomitant with allergic disorders
Authors: Oshima Yoichi , Sumida Keiichi , Yamanouchi Masayuki , Hayami Noriko , Sekine Akinari , Mizuno Hiroki , Kawada Masahiro , Hiramatsu Rikako , Hasegawa Eiko , Suwabe Tatsuya , Hoshino Junichi , Sawa Naoki , Fujii Takeshi , Takaichi Kenmei , Ubara Yoshifumi 
Published: January 2020

AbstractRecent reports suggest helper T-cell abnormalities in minimal-change nephrotic syndrome (MCNS), which often complicate allergic disorders that show a similar helper T-cell profile with Th2/Th17 predominance. However, the effect of anti-allergy therapy on MCNS remains unknown. This retrospective study included 51 patients with biopsy-proven MCNS recruited between November 2012 and October 2015, with follow-up through November 2017. We analyzed relapse and temporal daily corticosteroid dose with and without co-administration of histamine H1 receptor antagonist, cetirizine, and cysteinyl-leukotriene receptor antagonist, montelukast, as well as between baseline and after follow-up. Thirteen patients were treated with cetirizine and montelukast in addition to conventional therapy, whereas 38 patients were treated by conventional therapy only, consisting of corticosteroids and immunosuppressants. To adjust for baseline clinical characteristics, a 1:1 propensity score–matched model was applied. The clinical characteristics of the two groups after matching were similar at baseline. The treatment group showed a significant reduction in the lowest daily dose of oral prednisolone throughout the entire treatment course after the study compared to that of baseline (p < 0.025), which was not observed in the control group (p = 0.37), and showed significantly higher percentage of patients establishing corticosteroid-free state for the first time throughout the entire treatment course by addition of cetirizine and montelukast compared to the control group (p < 0.025). The study shows, for the first time, the steroid sparing effect of cetirizine and montelukast in addition to conventional treatment in MCNS patients with concomitant allergies.
Ganglion Cell – Inner Plexiform Layer Damage in Diabetic Patients: 3-Year Prospective, Longitudinal, Observational Study
Authors: Lim Hyung Bin , Shin Yong Il , Lee Min Woo , Koo Hyungmoon , Lee Woo Hyuk , Kim Jung Yeul 
Published: January 2020

AbstractDiabetes is expected to accelerate age-related ganglion cell–inner plexiform layer (GC-IPL) loss, but there is limited information on the rate of reduction in GC-IPL thicknesses. We aimed to evaluate the reduction rate of GC-IPL thickness in diabetic patients, and to compare the rates between patients without and with diabetic retinopathy (DR). We included 112 eyes of 112 patients with diabetes [49 eyes without DR (no-DR group) and 63 eyes with mild to moderate non-proliferative DR (NPDR group)] and 63 eyes of 63 normal controls (control group) in this study. Macular GC-IPL thickness in all participants was measured for 3 years at 1-year intervals. The reduction rates of GC-IPL thickness were determined by linear mixed models and compared among the three groups. The estimated reduction rates of the average GC-IPL thickness in the no-DR (−0.627 μm/year) and NPDR (−0.987 μm/year) groups were 2.26-fold (p = 0.010) and 3.56-fold (p = 0.001) faster, respectively, than the control group (−0.277 μm/year). Age, duration of diabetes, and baseline average GC-IPL thickness were associated with longitudinal changes in average GC-IPL thickness. The GC-IPL reduction rate was significantly faster in diabetic patients, with and without DR. Physicians should therefore be aware that GC-IPL damage continues even if there is no DR.
Detecting coalitions by optimally partitioning signed networks of political collaboration
Authors: Aref Samin , Neal Zachary 
Published: January 2020

AbstractWe propose new mathematical programming models for optimal partitioning of a signed graph into cohesive groups. To demonstrate the approach’s utility, we apply it to identify coalitions in US Congress since 1979 and examine the impact of polarized coalitions on the effectiveness of passing bills. Our models produce a globally optimal solution to the NP-hard problem of minimizing the total number of intra-group negative and inter-group positive edges. We tackle the intensive computations of dense signed networks by providing upper and lower bounds, then solving an optimization model which closes the gap between the two bounds and returns the optimal partitioning of vertices. Our substantive findings suggest that the dominance of an ideologically homogeneous coalition (i.e. partisan polarization) can be a protective factor that enhances legislative effectiveness.
Arterial Medial Calcification through Enhanced small Extracellular Vesicle Release in Smooth Muscle-Specific Asah1 Gene Knockout Mice
Authors: Bhat Owais M. , Li Guangbi , Yuan Xinxu , Huang Dandan , Gulbins Erich , Kukreja Rakesh C. , Li Pin-Lan 
Published: February 2020

AbstractArterial medial calcification (AMC) involves an increased small extracellular vesicle (sEV) secretion and apatite calcium precipitation in the arterial wall. The mechanisms mediating AMC remain poorly understood. In the present study, smooth muscle-specific acid ceramidase (Ac) gene knockout mice (Asah1fl/fl/SMCre) were used to demonstrate the role of lysosomal ceramide signaling pathway in AMC. Asah1fl/fl/SMCre mice were found to have more severe AMC in both aorta and coronary arteries compared to their littermates (Asah1fl/fl/SMwt and WT/WT mice) after receiving a high dose vitamin D. These mice also had pronounced upregulation of osteopontin and RUNX2 (osteogenic markers), CD63, AnX2 (sEV markers) and ALP expression (mineralization marker) in the arterial media. In cultured coronary arterial smooth muscle cells (CASMCs) from Asah1fl/fl/SMCre mice, high dose of Pi led to a significantly increased calcium deposition, phenotypic change and sEV secretion compared to WT CASMCs, which was associated with reduced lysosome-multivesicular body (MVB) interaction. Also, GW4869, sEV release inhibitor decreased sEV secretion and calcification in these cells. Lysosomal transient receptor potential mucolipin 1 (TRPML1) channels regulating lysosome interaction with MVBs were found remarkably inhibited in Asah1fl/fl/SMCre CASMCs as shown by GCaMP3 Ca2+ imaging and Port-a-Patch patch clamping of lysosomes. Lysosomal Ac in SMCs controls sEV release by regulating lysosomal TRPML1 channel activity and lysosome-MVB interaction, which importantly contributes to phenotypic transition and AMC.
Microbial Diversity and Metabolite Profiles of Palm Wine Produced From Three Different Palm Tree Species in Côte d’Ivoire
Authors: Djeni Theodore N. , Kouame Karen H. , Ake Francine D. M. , Amoikon Laurent S. T. , Dje Marcellin K. , Jeyaram Kumaraswamy 
Published: February 2020

AbstractPalm wine, the most commonly consumed traditional alcoholic beverage in Western Africa, harbours a complex microbiota and metabolites, which plays a crucial role in the overall quality and value of the product. In the present study, a combined metagenomic and metabolomic approach was applied to describe the microbial community structure and metabolites profile of fermented saps from three palm species (Elaeis guineensis, Raphia hookeri, Borassus aethiopum) in Côte d’Ivoire. Lactobacillaceae (47%), Leuconostocaceae (16%) and Acetobacteriaceae (28%) were the most abundant bacteria and Saccharomyces cerevisiae (87%) the predominant yeasts in these beverages. The microbial community structure of Raphia wine was distinctly different from the others. Multivariate analysis based on the metabolites profile clearly separated the three palm wine types. The main differentiating metabolites were putatively identified as gevotroline hydrochloride, sesartemin and methylisocitrate in Elaeis wine; derivative of homoserine, mitoxantrone in Raphia wine; pyrimidine nucleotide sugars (UDP-D-galacturonate) and myo-Inositol derivatives in Borassus wine. The enriched presence of gevotroline (an antipsychotic agent) and mitoxantrone (an anticancer drug) in palm wine supports its therapeutic potential. This work provides a valuable insight into the microbiology and biochemistry of palm wines and a rationale for selecting functional microorganisms for potential biotechnology applications.
Quantitative spatio-temporal characterization of epileptic spikes using high density EEG: Differences between NREM sleep and REM sleep
Authors: Kang Xuan , Boly Melanie , Findlay Graham , Jones Benjamin , Gjini Klevest , Maganti Rama , Struck Aaron F. 
Published: February 2020

AbstractIn this study, we applied high-density EEG recordings (HD-EEG) to quantitatively characterize the fine-grained spatiotemporal distribution of inter-ictal epileptiform discharges (IEDs) across different sleep stages. We quantified differences in spatial extent and duration of IEDs at the scalp and cortical levels using HD-EEG source-localization, during non-rapid eye movement (NREM) sleep and rapid eye movement (REM) sleep, in six medication-refractory focal epilepsy patients during epilepsy monitoring unit admission. Statistical analyses were performed at single subject level and group level across different sleep stages for duration and distribution of IEDs. Tests were corrected for multiple comparisons across all channels and time points. Compared to NREM sleep, IEDs during REM sleep were of significantly shorter duration and spatially more restricted. Compared to NREM sleep, IEDs location in REM sleep also showed a higher concordance with electrographic ictal onset zone from scalp EEG recording. This study supports the localizing value of REM IEDs over NREM IEDs and suggests that HD-EEG may be of clinical utility in epilepsy surgery work-up.
Fine-grained climate velocities reveal vulnerability of protected areas to climate change
Authors: Heikkinen Risto K. , Leikola Niko , Aalto Juha , Aapala Kaisu , Kuusela Saija , Luoto Miska , Virkkala Raimo 
Published: February 2020

AbstractClimate change velocity is an increasingly used metric to assess the broad-scale climatic exposure and climate change induced risks to terrestrial and marine ecosystems. However, the utility of this metric in conservation planning can be enhanced by determining the velocities of multiple climatic drivers in real protected area (PA) networks on ecologically relevant scales. Here we investigate the velocities of three key bioclimatic variables across a nation-wide reserve network, and the consequences of including fine-grained topoclimatic data in velocity assessments. Using 50-m resolution data describing present-day and future topoclimates, we assessed the velocities of growing degree days, the mean January temperature and climatic water balance in the Natura 2000 PA network in Finland. The high-velocity areas for the three climate variables differed drastically, indicating contrasting exposure risks in different PAs. The 50-m resolution climate data revealed more realistic estimates of climate velocities and more overlap between the present-day and future climate spaces in the PAs than the 1-km resolution data. Even so, the current temperature conditions were projected to disappear from almost all the studied PAs by the end of this century. Thus, in PA networks with only moderate topographic variation, far-reaching climate change induced ecological changes may be inevitable.
Integrated metabolomic and transcriptomic analyses identify critical genes in eicosapentaenoic acid biosynthesis and metabolism in the sea urchin Strongylocentrotus intermedius
Authors: Wang Heng , Ding Jun , Ding Siyu , Chang Yaqing 
Published: February 2020

AbstractGonads are the only edible part of the sea urchin and have great potential as a health-promoting food for human consumption. Polyunsaturated fatty acids (PUFAs) are important necessary nutrients that determine not only the nutritional value of sea urchins but guarantee their normal growth and reproduction. However, the information on the molecular mechanisms of PUFA biosynthesis and metabolism in this species remains elusive. In this study, we used Strongylocentrotus intermedius as our model species and conducted integrated metabolomic and transcriptomic analyses of potentially critical genes involved in PUFA biosynthesis and metabolism during gonad growth and development, mainly focusing on eicosapentaenoic acid (EPA). We found six differentially accumulated metabolites associated with PUFA in the metabolomic analysis. More differentially expressed genes (DEGs) were related to PUFA in testis than ovary (1823 DEGs in testis and 1499 DEGs in ovary). We verified 12 DEGs by RNA-Seq results and found that Aldh7a1, Ecm3, Fads2, and Hsd17b12 genes had similar expression patterns in EPA concentration during gonad growth and development. In contrast, the other DEGs were downregulated and we inferred that EPA or PUFA may be metabolized as energy during certain periods. Our metabolic and genetic data will facilitate a better understanding of PUFA regulation networks during gonad growth and development in S. intermedius.
Large‐scale road safety evaluation using extreme value theory
Authors: Orsini Federico , Gecchele Gregorio , Gastaldi Massimiliano , Rossi Riccardo 
Published: February 2020

Emerging international transportation system (ITS) and sensing technologies allow collecting of large amounts of high‐quality traffic data in highways, which can be used for road safety analysis. With this kind of data, it is possible to apply extreme value theory (EVT), which is gaining interest in the field of road safety, thanks to its ability to produce quick and reliable safety evaluations. EVT can estimate the probability of extreme events (i.e. road crashes) from relatively short observation periods, using surrogate measures of safety in place of crash data. In this work, EVT is applied for a large‐scale case study in two motorways, located in north‐eastern Italy. Vehicle‐by‐vehicle information was collected using microwave radars in 19 motorways cross‐sections for one year, and time‐to‐collision was calculated for each pair of consecutive vehicles. A six‐year crash database of the toll road was used to validate model results. For each cross‐section, two traditional approaches, block‐maxima and peak‐over‐threshold, were applied to estimate EVT parameters. Both approaches produced reliable predictions of annual rear‐end collisions; in particular, in about 90% of the cross‐sections, the observed number of crashes fell within the 95% confidence interval of the predicted number of crashes.
AGN jets versus accretion as reionization sources
Authors: Torres-Albà Núria , Bosch-Ramon Valentí , Iwasawa Kazushi 
Published: February 2020

Context. Cosmic reionization put an end to the dark ages that came after the recombination era. Observations seem to favor the scenario of massive-star photons generated in low-mass galaxies being responsible for the bulk of reionization and, whereas a possible contribution from AGN accretion disks has been widely considered, they are currently thought to have had a minor role in reionization.
Aims. We aim to study the possibility of AGN having contributed to reionization not only through their accretion disks, but also through ionizing photons coming from the AGN jets interacting with the intergalactic medium.
Methods. We adopt an empirically derived AGN luminosity function at z ≃ 6, use X-ray observations to correct it for the presence of obscured sources, and estimate the density of jetted AGN. We then use analytical calculations to derive the fraction of jet energy that goes into ionizing photons. Finally, we compute the contribution of AGN jets to the H II volume filling factor at redshifts z ≃ 15−5.
Results. We show that the contribution of the AGN jet lobes to the reionization of the Universe at z ∼ 6 might have been as high as ≳10% of that of star-forming galaxies, under the most favorable conditions of jetted and obscuration fraction.
Conclusions. The contribution of AGN to the reionization, while most likely not dominant, could have been higher than previously assumed, thanks to the radiation originated in the jet lobes.
The Sun at millimeter wavelengths
Authors: Wedemeyer Sven , Szydlarski Mikolaj , Jafarzadeh Shahin , Eklund Henrik , Guevara Gomez Juan Camilo , Bastian Tim , Fleck Bernhard , de la Cruz Rodriguez Jaime , Rodger Andrew , Carlsson Mats 
Published: February 2020

Context. The Atacama Large Millimeter/submillimeter Array (ALMA) started regular observations of the Sun in 2016, first offering receiver Band 3 at wavelengths near 3 mm (100 GHz) and Band 6 at wavelengths around 1.25 mm (239 GHz).
Aims. Here we present an initial study of one of the first ALMA Band 3 observations of the Sun. Our aim is to characterise the diagnostic potential of brightness temperatures measured with ALMA on the Sun.
Methods. The observation covers a duration of 48 min at a cadence of 2 s targeting a quiet Sun region at disc-centre. Corresponding time series of brightness temperature maps are constructed with the first version of the Solar ALMA Pipeline and compared to simultaneous observations with the Solar Dynamics Observatory (SDO).
Results. The angular resolution of the observations is set by the synthesised beam, an elliptical Gaussian that is approximately 1.4″ × 2.1″ in size. The ALMA maps exhibit network patches, internetwork regions, and elongated thin features that are connected to large-scale magnetic loops, as confirmed by a comparison with SDO maps. The ALMA Band 3 maps correlate best with the SDO/AIA 171 Å, 131 Å, and 304 Å channels in that they exhibit network features and, although very weak in the ALMA maps, imprints of large-scale loops. A group of compact magnetic loops is very clearly visible in ALMA Band 3. The brightness temperatures in the loop tops reach values of about 8000−9000 K and in extreme moments up to 10 000 K.
Conclusions. ALMA Band 3 interferometric observations from early observing cycles already reveal temperature differences in the solar chromosphere. The weak imprint of magnetic loops and the correlation with the 171, 131, and 304 SDO channels suggests, however, that the radiation mapped in ALMA Band 3 might have contributions from a wider range of atmospheric heights than previously assumed, but the exact formation height of Band 3 needs to be investigated in more detail. The absolute brightness temperature scale as set by total power measurements remains less certain and must be improved in the future. Despite these complications and the limited angular resolution, ALMA Band 3 observations have a large potential for quantitative studies of the small-scale structure and dynamics of the solar chromosphere.