bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants
Authors: Tapiainen Terhi , Koivusaari Pirjo , Brinkac Lauren , Lorenzi Hernan A. , Salo Jarmo , Renko Marjo , Pruikkonen Hannele , Pokka Tytti , Li Weizhong , Nelson Karen , Pirttilä Anna Maria , Tejesvi Mysore V. 
Published: July 2019

AbstractAltogether, 20–30% of women receive intrapartum antibiotic prophylaxis (IAP) to prevent sepsis in infants and 2–5% of newborn infants receive antibiotics due to suspected sepsis. Caesarean section has a long-term impact on the intestinal microbiome but the effects of perinatal antibiotics on gut microbiome in vaginally delivered infants are not well known. We compared the impact of IAP, postnatal antibiotics, or their combination on the gut microbiome and emergence of antimicrobial resistance in a controlled study of 149 newborn infants recruited within 24 hours after birth. We collected 659 fecal samples, including 426 daily samples from infants before discharge from the hospital and 111 follow-up samples at six months. Penicillin was mostly used for IAP and the combination of penicillin and aminoglycoside for postnatal treatment. Postnatal antibiotic groups received Lactobacillus reuteri probiotic. Newborn gut colonization differed in both IAP and postnatal antibiotics groups as compared to that in control group. The effect size of IAP was comparable to that caused by postnatal antibiotics. The observed differences were still present at six months and not prevented by lactobacilli consumption. Given the present clinical results, the impact of perinatal antibiotics on the subsequent health of newborn infants should be further evaluated.
Building carbon structures inside hollow carbon spheres
Authors: Gangatharan Prakash M. , Maubane-Nkadimeng Manoko S. , Coville Neil J. 
Published: July 2019

AbstractThe synthesis and characterization of helical carbon nanofibers (CNFs) contained within a fully confined nanoreactor is described. In particular, hollow carbon spheres (od = ca. 310 nm; wall thickness ca. 20 nm) were infiltrated with Cu ions (1%) to produce CuO particles (<10 nm) and the CuO was converted to Cu particles at temperature of 300 °C. Acetylene was then used as a carbon source to grow helical CNFs within the hollow carbon spheres. The diameter and helicity of the CNFs was influenced by the Cu content within a hollow carbon sphere, the limited Cu sintering inside a sphere as well as the dimensions of the sphere. The procedures employed suggest that the philosophy of building other structures (and molecules) with any elements within confined nanoreactors is possible.
Non-invasive evaluation of renal structure and function of healthy individuals with multiparametric MRI: Effects of sex and age
Authors: Li Xue-Ming , Yang Ling , Reng Jing , Xu Guo-Hui , Zhou Peng 
Published: July 2019

AbstractClinically, when applying multiparametric magnetic resonance imaging (MRI) examinations in renal diseases, assessment of renal structure and function has to account for age- and sex-related effects. The aim of this study was to investigate the influence of age and sex on multiparametric MRI assessment of renal structure and function in healthy human beings. Studies on 33 healthy volunteers were performed using multiparametric MRI on a 3.0-Tesla MR scanner, including T1-weighted imaging, blood oxygen level-dependent MRI (BOLD MRI), diffusion-weighted imaging (DWI) and diffusion tensor imaging (DTI). Our results revealed that the mean renal cortical thickness (RCT), ratio of cortex to parenchyma (CPR), and cortical R2* values were higher in males than in females. The cortical R2* value was higher in older group than in younger group (18.57 ± 0.99 vs 17.53 ± 0.58, p = 0.001); there was no significant difference in medullary R2* between the older and younger groups (38.18 ± 2.96 vs 36.45 ± 2.47, p = 0.077). The parenchymal thickness (PT) and medullary fractional anisotropy (FA) were lower in older group than in younger group (1.547 ± 0.06 vs 1.604 ± 0.05, p = 0.005 and 0.343 ± 0.03 vs 0.371 ± 0.03, p = 0.016, respectively). Pearson’s correlation analysis showed that PT and medullary FA were inversely related with age (r = −0.483, p = 0.004; r = −0.446, p = 0.009) while cortical R2* values was positively related (r = 0.511, p = 0.002, respectively). The medullary apparent diffusion coefficient (ADC) value had a significant association with PT (r = 0.359, p = 0.04). This study indicated that multiparametric renal MRI parameters are age and sex dependent.
Dissolution of a fibrous peptide by terahertz free electron laser
Authors: Kawasaki Takayasu , Tsukiyama Koichi , Irizawa Akinori 
Published: July 2019

AbstractFibrous peptides such as amyloid fibrils have various roles in biological system, e.g., as causal factor of serious amyloidosis in human and as functional regulator of cell formation in bacteria and eukaryotes. In addition, the fiber-type format is promising as biocompatible scaffold. Therefore, the dissolution method of peptide fibril is potentially useful at many scenes in medical and material fields: as reductive way of pathogenic amyloid, as modification technique of cell structure, and as fabrication tool of biomaterials. However, the fibril structure is generally difficult to be dissociated due to its rigid stacked conformation. Here, we propose a physical engineering technology using terahertz free electron laser (FEL) at far-infrared wavelengths from 70 to 80 μm. Infrared microscopy analysis of the irradiated fibril of calcitonin peptide as a model showed that β-sheet was decreased, and α-helix, turn, and others were increased, compared to those of the fibril before the FEL irradiation. Interestingly, the dissociative effect by the far-infrared laser was remarkable than that by the mid-infrared laser tuned to 6.1 μm that corresponds to amide I. In addition, simple heating at 363 K deformed the fibril state but increased the amount of β-sheet, which was contrast with the action by the FEL, and scanning-electron microscopy and Congo-red staining revealed that the fibril was collapsed power-dependently within a range from 25 to 900 mJ energies supplied with the FEL at 74 μm. It can be considered that irradiation of intense terahertz wave can dissociate fibrous conformation of peptide with little influence of thermal effect.
Tryptophan Oxidation in the UQCRC1 Subunit of Mitochondrial Complex III (Ubiquinol-Cytochrome C Reductase) in a Mouse Model of Myodegeneration Causes Large Structural Changes in the Complex: A Molecular Dynamics Simulation Study
Authors: Unni Sruthi , Thiyagarajan S. , Srinivas Bharath M. M. , Padmanabhan B. 
Published: July 2019

AbstractMuscle diseases display mitochondrial dysfunction and oxidative damage. Our previous study in a cardiotoxin model of myodegeneration correlated muscle damage with mitochondrial dysfunction, which in turn entailed altered mitochondrial proteome and oxidative damage of mitochondrial proteins. Proteomic identification of oxidized proteins in muscle biopsies from muscular dystrophy patients and cardiotoxin model revealed specific mitochondrial proteins to be targeted for oxidation. These included respiratory complexes which displayed oxidative modification of Trp residues in different subunits. Among these, Ubiquinol-Cytochrome C Reductase Core protein 1 (UQCRC1), a subunit of Ubiquinol-Cytochrome C Reductase Complex or Cytochrome b-c1 Complex or Respiratory Complex III displayed oxidation of Trp395, which could be correlated with the lowered activity of Complex III. We hypothesized that Trp395 oxidation might contribute to altered local conformation and overall structure of Complex III, thereby potentially leading to altered protein activity. To address this, we performed molecular dynamics simulation of Complex III (oxidized at Trp395 of UQCRC1 vs. non-oxidized control). Molecular dynamic simulation analyses revealed local structural changes in the Trp395 site. Intriguingly, oxidized Trp395 contributed to decreased plasticity of Complex III due to significant cross-talk among the subunits in the matrix-facing region and subunits in the intermembrane space, thereby leading to impaired electron flow from cytochrome C.
Transcriptomics of a KDELR1 knockout cell line reveals modulated cell adhesion properties
Authors: Blum Andrea , Khalifa Saleem , Nordström Karl , Simon Martin , Schulz Marcel H. , Schmitt Manfred J. 
Published: July 2019

AbstractKDEL receptors (KDELRs) represent transmembrane proteins of the secretory pathway which regulate the retention of soluble ER-residents as well as retrograde and anterograde vesicle trafficking. In addition, KDELRs are involved in the regulation of cellular stress response and ECM degradation. For a deeper insight into KDELR1 specific functions, we characterised a KDELR1-KO cell line (HAP1) through whole transcriptome analysis by comparing KDELR1-KO cells with its respective HAP1 wild-type. Our data indicate more than 300 significantly and differentially expressed genes whose gene products are mainly involved in developmental processes such as cell adhesion and ECM composition, pointing out to severe cellular disorders due to a loss of KDELR1. Impaired adhesion capacity of KDELR1-KO cells was further demonstrated through in vitro adhesion assays, while collagen- and/or laminin-coating nearly doubled the adhesion property of KDELR1-KO cells compared to wild-type, confirming a transcriptional adaptation to improve or restore the cellular adhesion capability. Perturbations within the secretory pathway were verified by an increased secretion of ER-resident PDI and decreased cell viability under ER stress conditions, suggesting KDELR1-KO cells to be severely impaired in maintaining cellular homeostasis.
Evolutionary history of teleost intron-containing and intron-less rhodopsin genes
Authors: Fujiyabu Chihiro , Sato Keita , Utari Ni Made Laksmi , Ohuchi Hideyo , Shichida Yoshinori , Yamashita Takahiro 
Published: July 2019

AbstractRecent progress in whole genome sequencing has revealed that animals have various kinds of opsin genes for photoreception. Among them, most opsin genes have introns in their coding regions. However, it has been known for a long time that teleost retinas express intron-less rhodopsin genes, which are presumed to have been formed by retroduplication from an ancestral intron-containing rhodopsin gene. In addition, teleosts have an intron-containing rhodopsin gene (exo-rhodopsin) exclusively for pineal photoreception. In this study, to unravel the evolutionary origin of the two teleost rhodopsin genes, we analyzed the rhodopsin genes of non-teleost fishes in the Actinopterygii. The phylogenetic analysis of full-length sequences of bichir, sturgeon and gar rhodopsins revealed that retroduplication of the rhodopsin gene occurred after branching of the bichir lineage. In addition, analysis of the tissue distribution and the molecular properties of bichir, sturgeon and gar rhodopsins showed that the abundant and exclusive expression of intron-containing rhodopsin in the pineal gland and the short lifetime of its meta II intermediate, which leads to optimization for pineal photoreception, were achieved after branching of the gar lineage. Based on these results, we propose a stepwise evolutionary model of teleost intron-containing and intron-less rhodopsin genes.
Douglas fir stimulates nitrification in French forest soils
Authors: Zeller Bernd , Legout Arnaud , Bienaimé Séverine , Gratia Bruno , Santenoise Philippe , Bonnaud Pascal , Ranger Jacques 
Published: July 2019

AbstractDouglas fir trees presumable stimulate nitrification in the soil. We studied in 21 French Douglas fir forests if and how nitrification is modulated by soil properties, past land use and current forest management. Soil (0–10 cm depth) was collected and initial concentrations of N-NH4+ and N-NO3−, potential net nitrogen mineralization (PNM) and net nitrification (PNN) rates and microbial biomass were measured. At 11 of the 21 sites, annual nitrate fluxes in the soil were measured using anion exchange resin bags. Soils contained between 2.3 to 29.4 mg N-NO3− kg soil−1. About 86% (±14%) of mineral N was nitrate. The proportion of nitrate increased to almost 100% during incubation. PNN varied from 0.10 mg N kg soil−1 day−1 to 1.05 mg N kg soil−1 day−1 (21 sites). Neither the initial nitrate concentration nor PNN was related to soil chemistry (pH, % C, %N, P, CEC), microbial biomass, texture, past land use or thinning. In situ net nitrate accumulation (NNA) estimated with resins beds varied from 4 to 100 kg N-NO3− ha−1 yr−1 (11 sites). It was positively correlated with base saturation, clay content, ELLENBERG N, temperature and negatively with soil organic N, C/N ratio and precipitation.
Contrasting associations between breeding coloration and parasitism of male Arctic charr relate to parasite species and life cycle stage
Authors: Johansen I. B. , Henriksen E. H. , Shaw J. C. , Mayer I. , Amundsen P.-A. , Øverli Ø. 
Published: July 2019

AbstractConspicuous carotenoid ornamentation is considered a signal of individual “quality” and one of the most intensely studied traits found to co-vary with parasitism. Since it has been suggested that only “high quality” individuals have enough resources to express excessive sexual ornaments and resist parasites, current theory struggles to explain cases where the brightest individuals carry the most parasites. Surprisingly little emphasis has been put on the contrasting routes to fitness utilized by different parasite species inhabiting the same host. Using Arctic charr (Salvelinus alpinus) as model species, we hypothesized that skin redness and allocation of carotenoids between skin and muscle (redness ratio) will be positively and negatively associated with parasites using the fish as an intermediate and final host, respectively. Both pigment parameters were indeed positively associated with abundances of parasites awaiting trophic transmission (Diplostomum sp. and Diphyllobothrium spp.) and negatively associated with the abundance of adult Eubothrium salvelini tapeworms. These empirical data demonstrate that contrasting associations between carotenoid coloration and parasite intensities relates to the specific premises of different parasite species and life cycle stages.
Apelin affects the mouse aging urinary peptidome with minimal effects on kidney
Authors: Vinel Claire , Schanstra Joost P. , Boizard Franck , Péreira Ophélie , Auriau Johanna , Dortignac Alizée , Breuil Benjamin , Feuillet Guylène , Nkuipou-Kenfack Esther , Zürbig Petra , Valet Philippe , Bascands Jean-Loup , Dray Cédric , Denis Colette 
Published: July 2019

AbstractKidney function is altered by age together with a declined filtration capacity of 5–10% per decade after 35 years. Renal aging shares many characteristics with chronic kidney disease. Plasma levels of the bioactive peptide apelin also decline with age and apelin has been shown to be protective in chronic kidney disease. Therefore we evaluated whether apelin could also improve aging-induced renal lesions and function in mice. Since urine is for the major part composed of proteins and peptides originating from the kidney, we first studied apelin-induced changes, in the aging urinary peptidome. Despite the recently published age-associated plasma decrease of apelin, expression of the peptide and its receptor was increased in the kidneys of 24 months old mice. Twenty-eight days treatment with apelin significantly modified the urinary peptidome of 3 and 24 months old mice towards a signature suggesting more advanced age at 3 months, and a younger age at 24 months. The latter was accompanied by a decreased staining of collagen (Sirius red staining) in 24 months old apelin-treated mice, without changing aging-induced glomerular hypertrophy. In addition, apelin was without effect on aging-induced renal autophagy, apoptosis, inflammation and reduced renal function. In conclusion, treatment of aged mice with apelin had a limited effect on kidney lesions although modifying the urinary peptidome towards a younger signature. This supports evidence of apelin inducing more general beneficial effects on other aging organs, muscles in particular, as recently shown for sarcopenia, markers of which end up via the glomerular filtration in urine.
Production and in vivo PET/CT imaging of the theranostic pair 132/135La
Authors: Aluicio-Sarduy Eduardo , Hernandez Reinier , Olson Aeli P. , Barnhart Todd E. , Cai Weibo , Ellison Paul A. , Engle Jonathan W. 
Published: July 2019

AbstractThe present study describes a novel method for the low energy cyclotron production and radiochemical isolation of no-carrier-added 132/135La3+ from bulk natBa. This separation strategy combines precipitation and single-column extraction chromatography to afford an overall radiochemical yield (92 ± 2%) and apparent molar activity (22 ± 4 Mbq/nmol) suitable for the radiolabeling of DOTA-conjugated vectors. The produced 132/135La3+ has a radiochemical and radionuclidic purity amenable for 132La/135La-based cancer theranostic applications. Longitudinal PET/CT images acquired using the positron-emitting 132La and ex vivo biodistribution data separately corroborated the accumulation of unchelated 132/135La3+ ions in bone and the liver.
Modeling the binding of diverse ligands within the Ah receptor ligand binding domain
Authors: Giani Tagliabue Sara , Faber Samantha C. , Motta Stefano , Denison Michael S. , Bonati Laura 
Published: July 2019

AbstractThe Ah receptor (AhR) is a ligand-dependent transcription factor belonging to the basic helix-loop-helix Per-Arnt-Sim (bHLH-PAS) superfamily. Binding to and activation of the AhR by a variety of chemicals results in the induction of expression of diverse genes and production of a broad spectrum of biological and toxic effects. The AhR also plays important roles in several physiological responses, which has led it to become a novel target for the development of therapeutic drugs. Differences in the interactions of various ligands within the AhR ligand binding domain (LBD) may contribute to differential modulation of AhR functionality. We combined computational and experimental analyses to investigate the binding modes of a group of chemicals representative of major classes of AhR ligands. On the basis of a novel computational approach for molecular docking to the homology model of the AhR LBD that includes the receptor flexibility, we predicted specific residues within the AhR binding cavity that play a critical role in binding of three distinct groups of chemicals. The prediction was validated by site-directed mutagenesis and evaluation of the relative ligand binding affinities for the mutant AhRs. These results provide an avenue for understanding ligand modulation of the AhR functionality and for rational drug design.
Tyrosine 51 residue of the syndecan-2 extracellular domain is involved in the interaction with and activation of pro-matrix metalloproteinase-7
Authors: Jang Bohee , Yun Ji-Hye , Choi Sojoong , Park Jimin , Shin Dong Hae , Lee Seung-Taek , Lee Weontae , Oh Eok-Soo 
Published: July 2019

AbstractAlthough syndecan-2 is known to interact with the matrix metalloproteinase-7 (MMP-7), the details of their interaction were unknown. Our experiments with a series of syndecan-2 extracellular domain deletion mutants show that the interaction is mediated through an interaction of the extracellular domain of syndecan-2 (residues 41 to 60) with the α2 helix-loop-α3 helix in the pro-domain of MMP-7. NMR and molecular docking model show that Glu7 of the α1 helix, Glu32 of the α2 helix, and Gly48 and Ser52 of the α2 helix-loop-α3 helix of the MMP-7 pro-domain form the syndecan-2-binding pocket, which is occupied by the side chain of tyrosine residue 51 (Tyr51) of syndecan-2. Consistent with this notion, the expression of a syndecan-2 mutant in which Tyr51 was changed to Ala diminished the interaction between the syndecan-2 extracellular domain and the pro-domain of MMP-7. Furthermore, HT-29 colon adenocarcinoma cells expressing the interaction-defective mutant exhibited reductions in the cell-surface localization of MMP-7, the processing of pro-MMP-7 into active MMP-7, the MMP-7-mediated extracellular domain shedding of both syndecan-2 and E-cadherin, and syndecan-2-mediated anchorage-independent growth. Collectively, these data strongly suggest that Tyr51 of the syndecan-2 extracellular domain mediates its interaction with and activating processing of pro-MMP-7 and regulates MMP-7-dependent syndecan-2 functions.
Enhanced weathering as a trigger for the rise of atmospheric O2 level from the late Ediacaran to the early Cambrian
Authors: Li Wei-Ping , Zhao Yan-Yan , Zhao Ming-Yu , Zha Xiang-Ping , Zheng Yong-Fei 
Published: July 2019

AbstractA shift toward a higher oxygen level in both ocean and atmosphere systems during the late Ediacaran to the early Cambrian has been suggested from multiple indirect proxies. However, the mechanism and magnitude of this oxidation remain unclear. To solve this issue, we measured carbon isotopes in both carbonate and organic matter as well as their trace element compositions for an Ediacaran-Cambrian sequence in the Lower Yangtze basin, South China. The δ13Corg and δ13Ccarb excursions of this sequence are coupled and can be compared with contemporaneous global carbon isotope curves. A 2‰ rise in Δ13Ccarb-org occurred from the late Ediacaran to the early Cambrian, suggesting a substantial increase in atmospheric oxygen level from 16% to 30% of the present atmospheric level (PAL). Furthermore, the distribution pattern of rare earth elements and the concentrations of water-insoluble elements in the carbonates indicate a sudden enhancement in chemical weathering of the continental crust during the early Cambrian, which may be a trigger for the rise of atmospheric O2 level. Both the supply of a large amount of nutrients due to the enhanced continental weathering and the contemporary increase of atmospheric oxygen concentrations may have promoted the appearance of large metazoans in the early Cambrian.
Evaluation of cell viability and metabolic activity of a 3D cultured human epidermal model using a dynamic autoradiographic technique with a PET radiopharmaceutical
Authors: Sasaki Toru , Tamaki Junya , Nishizawa Kentaro , Kojima Takahiro , Tanaka Ryoich , Moriya Ryotaro , Sasaki Haruyo , Maruyama Hiroko 
Published: July 2019

AbstractQuality control of tissues and organs for transplant is important to confirm their safety and effectiveness for regenerative medicine. However, quality evaluation is only carried out using a limited range of inspection criteria, because many of the available evaluation tests are invasive. In order to explore the potential of 2-[18F]fluoro-2-deoxy-D-glucose ([18F]FDG)-bioradiography as a non-invasive test for estimation of the safety, soundness, and effectiveness of tissues for transplantation, [18F]FDG uptake and cell viability or metabolism were investigated using a reconstructed human epidermal model (RHEM). We developed an imaging system, and suitable bioradiographic image acquisition conditions and its effectiveness were investigated. [18F]FDG uptake increased in agreement with DNA content as a marker of cell numbers and for histological assessment during cell proliferation and keratinization. [18F]FDG uptake was significantly decreased in good agreement with the viability of tissues used with various hazardous chemical treatments. [18F]FDG uptake by the tissues was decreased by hypothermia treatment and increased by hypoxia treatment while maintaining cell viability in the tissue. Therefore, [18F]FDG-bioradiography can be useful to estimate cell viability or metabolism in this RHEM. This method might be utilized as a non-invasive test for quality evaluation of tissues for transplantation.