bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exclusive use of digital PCR allows an absolute assay of heat-killed Lactobacilli in foods targeting multiple copies of 16S rDNA
Authors: Soejima Takashi , Tanaka Miyuki , Yamauchi Koji , Abe Fumiaki 
Published: July 2020

AbstractThe real-time PCR (qPCR) and digital PCR (dPCR) to amplify a single-copy of house-keeping genes (i.e.,hsp60, pheSortuf) are used for the assay of limited microbial species. In general, with a single-copy gene, there are obviously varied DNA sequences for even the same microbial species, which could cause difficulties with design of primers and probes for PCR when targeting various single copy genes. In general, for identification by dPCR (as a representative case:Lactobacillus paracasei), accumulated DNA sequence information of 16S rDNA, which is much more frequently used, should be targeted. In contrast, next-generation sequencing revealed that there are five copies of 16S rDNA in a liveL. paracaseiMCC1849. Therefore, we aimed to reveal, if heat-killedL. paracaseisupplemented in nutritional foods that aid the host immune system have the relevant five copies per chromosomal DNA, and if the relevant copies remain unchanged on the same chromosomal DNA or remain to be different chromosomal DNA fragments. So, we revealed the actual distribution of the potential original five copies of 16S rDNA using our innovative dPCR, in which both 16S rDNA andhsp60genes were simultaneously elongated. The molecular ratios of 16S rDNA/hsp60dispersed in the dPCR chip were then estimated. The 16S rDNA/hsp60molecular ratios of the heat-killedL. paracaseiin foods, resultantly ranged from 5.0 to 7.2, being the same or higher than that of the five copies determined by next-generation sequencing. The 16S rDNA copy number/ratio indicated the chromosomal DNA molecular number and the associated cell number. As significance, different nutritional foods could potentially cause the loss of chromosomal DNA of supplemented beneficial microbes to a much greater degree. Our absolute dPCR does not require standard correlative samples for the estimation of final products. The estimation principle of the ratio of 16S rDNA/a house-keeping single-copy gene by our absolute dPCR could lead to a useful and accurate assay for various nutritional foods.
PPARG (Pro12Ala) genetic variant and risk of T2DM: a systematic review and meta-analysis
Authors: Sarhangi Negar , Sharifi Farshad , Hashemian Leila , Hassani Doabsari Maryam , Heshmatzad Katayoun , Rahbaran Marzieh , Jamaldini Seyed Hamid , Aghaei Meybodi Hamid Reza , Hasanzad Mandana 
Published: July 2020

AbstractType 2 diabetes mellitus (T2DM) is a complex disease caused by the interaction between genetic and environmental factors. A growing number of evidence suggests that the peroxisome proliferator-activated receptor gamma (PPARG) gene plays a major role in T2DM development. Meta-analysis of genetic association studies is an efficient tool to gain a better understanding of multifactorial diseases and potentially to provide valuable insights into gene-disease interactions. The present study was focused on assessing the association between Pro12Ala variation in the PPARG and T2DM risk through a comprehensive meta-analysis. We searched PubMed, WoS, Embase, Scopus and ProQuest from 1990 to 2017. The fixed-effect or random-effect model was used to evaluate the pooled odds ratios (ORs) and 95% confidence intervals (CIs) depending on the heterogeneity among studies. The sources of heterogeneity and publication bias among the included studies were assessed using I2 statistics and Egger's tests. A total of 73 studies, involving 62,250 cases and 69,613 controls were included. The results showed that the minor allele (G) of the rs1801282 variant was associated with the decreased risk of T2DM under different genetic models. Moreover, the protective effect of minor allele was detected to be significantly more in some ethnicities including the European (18%), East Asian (20%), and South East Asian (18%). And the reduction of T2DM risk in Ala12 carriers was stronger in individuals from North Europe rather than Central and South Europe. Our findings indicated that the rs1801282 variant may contribute to decrease of T2DM susceptibility in different ancestries.
Nanoparticle size distribution from inversion of wide angle X-ray total scattering data
Authors: Ferri Fabio , Bertolotti Federica , Guagliardi Antonietta , Masciocchi Norberto 
Published: July 2020

AbstractAn increasingly important issue in nanoscience and nanotechnology is the accurate determination of nanoparticle sizing. Wide angle X-ray total scattering (WAXTS) data are frequently used to retrieve the Particle Size Distributions (PSDs) of nanocrystals of highly technological relevance; however, the PSD shape typically relies on an a-priori assumption. Here, we propose a modified version of the classical iterative Lucy-Richardson (LR) algorithm, which is simple, fast and highly reliable against noise, and demonstrate that the inversion of WAXTS data can be profitably used for recovering accurate PSD regardless of its shape. Computer simulations based on the use of the Debye Scattering Equation (DSE) modelling WAXTS data show that the algorithm is capable of recovering accurate PSDs even when the sample is made of a mixture of different polymorphs and/or exhibits microstrain effects. When applied to the inversion of WAXTS data taken on real samples, the method requires accurate modelling of the nanoparticle crystal structure, which includes structural defects, microstrain and surface induced distortions. Provided that this information is correctly fed to the program, the inversion algorithm reconstructs the WAXTS data with high accuracy and recovers highly robust (against noise) PSDs. Two examples reporting the characterization of Magnetite-Maghemite and commercial P25-Titania nanopowders, are discussed. We demonstrate that pre-assumption of wrong PSD shape leads to inaccurate number-based average sizes in highly polydisperse samples.
Against all odds: a tale of marine range expansion with maintenance of extremely high genetic diversity
Authors: Robalo Joana I. , Francisco Sara M. , Vendrell Catarina , Lima Cristina S. , Pereira Ana , Brunner Benedikt P. , Dia Mamadou , Gordo Leonel , Castilho Rita 
Published: July 2020

AbstractThe displacement of species from equatorial latitudes to temperate locations following the increase in sea surface temperatures is among the significant reported consequences of climate change. Shifts in the distributional ranges of species result in fish communities tropicalisation, i.e., high latitude colonisations by typically low latitude distribution species. These movements create new interactions between species and new trophic assemblages. The Senegal seabream,Diplodus bellottii, may be used as a model to understand the population genetics of these invasions. In the last decades, this species has undergone an outstanding range expansion from its African area of origin to the Atlantic coast of the Iberian Peninsula, where now occurs abundantly. Mitochondrial and nuclear markers revealed a striking high haplotypic nucleotide and genetic diversity values, along with significant population differentiation throughout the present-day geographical range of the Senegal seabream. These results are not consistent with the central-marginal hypothesis, nor with the expectations of a leptokurtic distribution of individuals, asD. bellottiiseems to be able to retain exceptional levels of diversity in marginal and recently colonised areas. We discuss possible causes for hyperdiversity and lack of geographical structure and subsequent implications for fisheries.
Correlation among photoluminescence and the electronic and atomic structures of Sr2SiO4:xEu3+ phosphors: X-ray absorption and emission studies
Authors: Zheng Shi-Yan , Chiou Jau-Wern , Li Yueh-Han , Yang Cheng-Fu , Ray Sekhar Chandra , Chen Kuan-Hung , Chang Chun-Yu , Shelke Abhijeet R. , Wang Hsiao-Tsu , Yeh Ping-Hung , Lai Chun-Yen , Hsieh Shang-Hsien , Pao Chih-Wen , Chen Jeng-Lung , Lee Jyh-Fu , Tsai Huang-Ming , Fu Huang-Wen , Hua Chih-Yu , Lin Hong-Ji , Chen Chien-Te , Pong Way-Faung 
Published: July 2020

AbstractA series of Eu3+-activated strontium silicate phosphors, Sr2SiO4:xEu3+ (SSO:xEu3+, x = 1.0, 2.0 and 5.0%), were synthesized by a sol–gel method, and their crystalline structures, photoluminescence (PL) behaviors, electronic/atomic structures and bandgap properties were studied. The correlation among these characteristics was further established. X-ray powder diffraction analysis revealed the formation of mixed orthorhombic α'-SSO and monoclinic β-SSO phases of the SSO:xEu3+ phosphors. When SSO:xEu3+ phosphors are excited under ultraviolet (UV) light (λ = 250 nm, ~ 4.96 eV), they emit yellow (~ 590 nm), orange (~ 613 nm) and red (~ 652 and 703 nm) PL bands. These PL emissions typically correspond to 4f–4f electronic transitions that involve the multiple excited 5D0 → 7FJ levels (J = 1, 2, 3 and 4) of Eu3+ activators in the host matrix. This mechanism of PL in the SSO:xEu3+ phosphors is strongly related to the local electronic/atomic structures of the Eu3+–O2− associations and the bandgap of the host lattice, as verified by Sr K-edge and Eu L3-edge X-ray absorption near-edge structure (XANES)/extended X-ray absorption fine structure, O K-edge XANES and Kα X-ray emission spectroscopy. In the synthesis of SSO:xEu3+ phosphors, interstitial Eu2O3-like structures are observed in the host matrix that act as donors, providing electrons that are nonradiatively transferred from the Eu 5d and/or O 2p–Eu 4f/5d states (mostly the O 2p–Eu 5d states) to the 5D0 levels, facilitating the recombination of electrons that have transitioned from the 5D0 level to the 7FJ level in the bandgap. This mechanism is primarily responsible for the enhancement of PL emissions in the SSO:xEu3+ phosphors. This PL-related behavior indicates that SSO:xEu3+ phosphors are good light-conversion phosphor candidates for use in near-UV chips and can be very effective in UV-based light-emitting diodes.
Mandibular sawing in a snail-eating snake
Authors: Kojima Yosuke , Fukuyama Ibuki , Kurita Takaki , Hossman Mohamad Yazid Bin , Nishikawa Kanto 
Published: July 2020

AbstractThe jaws of vertebrates display a striking diversity in form and function, but they typically open and close like a trapdoor rather than sliding like a saw. Here, we report unique feeding behaviour in the blunt-headed snail-eating snake, Aplopeltura boa (family Pareidae), where the snake cuts off and circumvents the indigestible part (the operculum) of its prey in the mouth using long sliding excursions of one side of the mandible, while the upper jaws and the mandible on the other side maintain a stable grasp on the prey. This behaviour, which we call ‘mandibular sawing’, is made possible by extraordinarily independent movements of the jaw elements and is a surprising departure from usual feeding behaviour in vertebrates.
Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis
Authors: Kalmankar Neha V. , Venkatesan Radhika , Balaram Padmanabhan , Sowdhamini Ramanathan 
Published: July 2020

AbstractClitoria ternatea a perennial climber of the Fabaceae family, is well known for its agricultural and medical applications. It is also currently the only known member of the Fabaceae family that produces abundant amounts of the ultra-stable macrocyclic peptides, cyclotides, across all tissues. Cyclotides are a class of gene-encoded, disulphide-rich, macrocyclic peptides (26–37 residues) acting as defensive metabolites in several plant species. Previous transcriptomic studies have demonstrated the genetic origin of cyclotides from the Fabaceae plant family to be embedded in the albumin-1 genes, unlike its counterparts in other plant families. However, the complete mechanism of its biosynthesis and the repertoire of enzymes involved in cyclotide folding and processing remains to be understood. In this study, using RNA-Seq data and de novo transcriptome assembly of Clitoria ternatea, we have identified 71 precursor genes of cyclotides. Out of 71 unique cyclotide precursor genes obtained, 51 sequences display unique cyclotide domains, of which 26 are novel cyclotide sequences, arising from four individual tissues. MALDI-TOF mass spectrometry analysis of fractions from different tissue extracts, coupled with precursor protein sequences obtained from transcriptomic data, established the cyclotide diversity in this plant species. Special focus in this study has also been on identifying possible enzymes responsible for proper folding and processing of cyclotides in the cell. Transcriptomic mining for oxidative folding enzymes such as protein-disulphide isomerases (PDI), ER oxidoreductin-1 (ERO1) and peptidylprolyl cis-trans isomerases (PPIases)/cyclophilins, and their levels of expression are also reported. In particular, it was observed that the CtPDI genes formed plant-specific clusters among PDI genes as compared to those from other plant species. Collectively, this work provides insights into the biogenesis of the medicinally important cyclotides and establishes the expression of certain key enzymes participating in peptide biosynthesis. Also, several novel cyclotide sequences are reported and precursor sequences are analysed in detail. In the absence of a published reference genome, a comprehensive transcriptomics approach was adopted to provide an overview of diverse properties and constituents of C. ternatea.
Development of the FAST-DOSE assay system for high-throughput biodosimetry and radiation triage
Authors: Wang Qi , Lee Younghyun , Shuryak Igor , Pujol Canadell Monica , Taveras Maria , Perrier Jay R. , Bacon Bezalel A. , Rodrigues Matthew A. , Kowalski Richard , Capaccio Christopher , Brenner David J. , Turner Helen C. 
Published: July 2020

AbstractFollowing a large-scale radiological incident, there is a need for FDA-approved biodosimetry devices and biomarkers with the ability to rapidly determine past radiation exposure with sufficient accuracy for early population triage and medical management. Towards this goal, we have developed FAST-DOSE (Fluorescent Automated Screening Tool for Dosimetry), an immunofluorescent, biomarker-based system designed to reconstruct absorbed radiation dose in peripheral blood samples collected from potentially exposed individuals. The objective of this study was to examine the performance of the FAST-DOSE assay system to quantify intracellular protein changes in blood leukocytes for early biodosimetry triage from humanized NOD-scid-gamma (Hu-NSG) mice and non-human primates (NHPs) exposed to ionizing radiation up to 8 days after radiation exposure. In the Hu-NSG mice studies, the FAST-DOSE biomarker panel was able to generate delivered dose estimates at days 1, 2 and 3 post exposure, whereas in the NHP studies, the biomarker panel was able to successfully classify samples by dose categories below or above 2 Gy up to 8 days after total body exposure. These results suggest that the FAST-DOSE bioassay has large potential as a useful diagnostic tool for rapid and reliable screening of potentially exposed individuals to aid early triage decisions within the first week post-exposure.
A non-invasive soil-based setup to study tomato root volatiles released by healthy and infected roots
Authors: Gulati Sneha , Ballhausen Max-Bernhard , Kulkarni Purva , Grosch Rita , Garbeva Paolina 
Published: July 2020

AbstractThe role of root exudates in mediating plant–microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant–microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.
Association between inflammatory bowel disease and bullous pemphigoid: a population-based case–control study
Authors: Chen Yi-Ju , Juan Chao-Kuei , Chang Yun-Ting , Wu Chun-Ying , Ho Hsiu J. , Tseng Hsiao-Ching 
Published: July 2020

AbstractThe coexistence of inflammatory bowel disease (IBD) and bullous pemphigoid (BP) has been reported. No large-scale study to date has explored the relationship between these diseases. This population-based case-control study examined the association between IBD and BP by using a nationwide database. A total of 5,263 BP patients and 21,052 age- and gender-, hospital visit number-matched controls were identified in the National Health Insurance Research Database of Taiwan (1997–2013). Demographic characteristics and comorbidities including IBD were compared. Logistic regression was conducted to examine the predicting factors for BP. The mean age at diagnosis was 74.88 years and 54.3% of subjects were male. BP patients tended to have more cardiovascular risk factors, autoimmune and neurologic comorbidities, and hematologic cancers than matched controls. There were 20 cases of IBD (0.38%), mostly ulcerative colitis (N = 17, 0.32%) among BP patients, compared to 33 IBD cases (0.16%) among controls (p < 0.001). Ulcerative colitis was found to be significantly associated with BP [adjusted odds ratio (OR) 3.60, 95% confidence interval (CI) 1.91–6.77, p < 0.001] on multivariate analysis. Treatment for IBD was not associated with BP development. Information about diet, lifestyle, alcohol consumption, and smoking habit was not available. We concluded that UC is independently associated with BP.
Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace
Authors: Chessa Daniela , Murgia Manuela , Sias Emanuela , Deligios Massimo , Mazzarello Vittorio , Fiamma Maura , Rovina Daniela , Carenti Gabriele , Ganau Giulia , Pintore Elisabetta , Fiori Mauro , Kay Gemma L. , Ponzeletti Alessandro , Cappuccinelli Piero , Kelvin David J. , Wain John , Rubino Salvatore 
Published: July 2020

AbstractThis study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.
Characterization of highly pathogenic avian influenza H5Nx viruses in the ferret model
Authors: Pulit-Penaloza Joanna A. , Brock Nicole , Pappas Claudia , Sun Xiangjie , Belser Jessica A. , Zeng Hui , Tumpey Terrence M. , Maines Taronna R. 
Published: July 2020

AbstractHighly pathogenic avian influenza (HPAI) H5 viruses, of the A/goose/Guangdong/1/1996 lineage, have exhibited substantial geographic spread worldwide since the first detection of H5N1 virus in 1996. Accumulation of mutations in the HA gene has resulted in several phylogenetic clades, while reassortment with other avian influenza viruses has led to the emergence of new virus subtypes (H5Nx), notably H5N2, H5N6, and H5N8. H5Nx viruses represent a threat to both the poultry industry and human health and can cause lethal human disease following virus exposure. Here, HPAI H5N6 and H5N2 viruses (isolated between 2014 and 2017) of the 2.3.4.4 clade were assessed for their capacity to replicate in human respiratory tract cells, and to cause disease and transmit in the ferret model. All H5N6 viruses possessed increased virulence in ferrets compared to the H5N2 virus; however, pathogenicity profiles varied among the H5N6 viruses tested, from mild infection with sporadic virus dissemination beyond the respiratory tract, to severe disease with fatal outcome. Limited transmission between co-housed ferrets was observed with the H5N6 viruses but not with the H5N2 virus. In vitro evaluation of H5Nx virus replication in Calu-3 cells and the identification of mammalian adaptation markers in key genes associated with pathogenesis supports these findings.
Geographic variation in cardiometabolic risk factor prevalence explained by area-level disadvantage in the Illawarra-Shoalhaven region of the NSW, Australia
Authors: Toms Renin , Mayne Darren J. , Feng Xiaoqi , Bonney Andrew 
Published: July 2020

AbstractCardiometabolic risk factors (CMRFs) demonstrate significant geographic variation in their distribution. The study aims to quantify the general contextual effect of the areas on CMRFs; and the geographic variation explained by area-level socioeconomic disadvantage. A cross sectional design and multilevel logistic regression methods were adopted. Data included objectively measured routine pathology test data between years 2012 and 2017 on: fasting blood sugar level; glycated haemoglobin; total cholesterol; high density lipoprotein; urinary albumin creatinine ratio; estimated glomerular filtration rate; and body mass index. The 2011 Australian census based Index of Relative Socioeconomic Disadvantage (IRSD) were the area-level study variables, analysed at its smallest geographic unit of reporting. A total of 1,132,029 CMRF test results from 256,525 individuals were analysed. After adjusting for individual-level covariates, all CMRFs significantly associated with IRSD and the probability of higher risk CMRFs increases with greater area-level disadvantage. Though the specific contribution of IRSD in the geographic variation of CMRF ranged between 57.8 and 14.71%, the general contextual effect of areas were found minimal (ICCs 0.6–3.4%). The results support universal interventions proportional to the need and disadvantage level of populations for the prevention and control of CMRFs, rather than any area specific interventions as the contextual effects were found minimal in the study region.
Evidence for long-term seamount-induced chlorophyll enhancements
Authors: Leitner Astrid B. , Neuheimer Anna B. , Drazen Jeffrey C. 
Published: July 2020

AbstractSeamounts are ubiquitous global features often characterized by biological hotspots of diversity, biomass, and abundance, though the mechanisms responsible are poorly understood. One controversial explanation suggests seamount-induced chlorophyll enhancements (SICE) subsidize seamount ecosystems. Using a decade of satellite chlorophyll data, we report substantial long-term chlorophyll enhancements around 17% of Pacific seamounts and 45% of shallow (< 100 m) seamounts, with the highest probability of detection at shallow, low-latitude seamounts. SICE is shown to enhance chlorophyll concentrations by up to 56% relative to oceanic conditions, and SICE seamounts have two-fold higher fisheries catch relative to non-enhancing seamounts. Therefore, seamount-induced bottom-up trophic subsidies are not rare, occurring most often at shallow, heavily exploited seamounts, suggesting an important subset of seamounts experience fundamentally different trophic dynamics than previously thought.