bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urinary Exosomes Contain MicroRNAs Capable of Paracrine Modulation of Tubular Transporters in Kidney
Authors: Gracia Tannia , Wang Xiaonan , Su Ya , Norgett Elizabeth E. , Williams Timothy L. , Moreno Pablo , Micklem Gos , Karet Frankl Fiona E. 
Published: January 2017

AbstractExosomes derived from all nephron segments are present in human urine, where their functionality is incompletely understood. Most studies have focused on biomarker discovery rather than exosome function. Through sequencing we identified the miRNA repertoire of urinary exosomes from healthy volunteers; 276 mature miRNAs and 345 pre-miRNAs were identified (43%/7% of reads). Among the most abundant were members of the miR-10, miR-30 and let-7 families. Targets for the identified miRNAs were predicted using five different databases; genes encoding membrane transporters and their regulators were enriched, highlighting the possibility that these miRNAs could modulate key renal tubular functions in a paracrine manner. As proof of concept, cultured renal epithelial cells were exposed to urinary exosomes and cellular exosomal uptake was confirmed; thereafter, reduced levels of the potassium channel ROMK and kinases SGK1 and WNK1 were observed in a human collecting duct cell line, while SPAK was unaltered. In proximal tubular cells, mRNA levels of the amino acid transporter gene SLC38A2 were diminished and reflected in a significant decrement of its encoded protein SNAT2. Protein levels of the kinase SGK1 did not change. Thus we demonstrated a novel potential function for miRNA in urinary exosomes.
Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX
Authors: Liu Lin-lin , Liu Pei-jin , Hu Song-qi , He Guo-qiang 
Published: January 2017

AbstractNO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10−10 s−1) when the temperature was less than 1000 K.
Methylation specific targeting of a chromatin remodeling complex from sponges to humans
Authors: Cramer Jason M. , Pohlmann Deborah , Gomez Fernando , Mark Leslie , Kornegay Benjamin , Hall Chelsea , Siraliev-Perez Edhriz , Walavalkar Ninad M. , Sperlazza M. Jeannette , Bilinovich Stephanie , Prokop Jeremy W. , Hill April L. , Williams David C. 
Published: January 2017

AbstractDNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find thatEphydatia muellerihas genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development ofE. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution.
Relationship of hyposalivation and xerostomia in Mexican elderly with socioeconomic, sociodemographic and dental factors
Authors: Islas-Granillo Horacio , Borges-Yáñez Aida , Fernández-Barrera Miguel Ángel , Ávila-Burgos Leticia , Patiño-Marín Nuria , Márquez-Corona María de Lourdes , Mendoza-Rodríguez Martha , Medina-Solís Carlo Eduardo 
Published: January 2017

AbstractWe determined the prevalence of hyposalivation and xerostomia in older Mexicans (≥60 years), and its relationship with diverse factors. A cross-sectional study was realized in elderly subjects from Pachuca, Mexico. Chewing-stimulated saliva was collected under standardized conditions and salivary flow was measured; subjects were considered to have hyposalivation if their stimulated salivary flow was less than 0.7 mL per minute. Xerostomia was evaluated by asking subjects ‘Does your mouth feel dry?’. Hyposalivation was present in 59.7%, and xerostomia in 25.2% of subjects. 16.5% of subjects had both conditions. Xerostomia was present in 27.7% of subjects with hyposalivation and 21.4% of subjects without hyposalivation, but the difference was not significant (p > 0.05). Thus, 68.3% of older Mexicans had xerostomia and/or hyposalivation. Factors associated with hyposalivation were: using fewer devices in oral hygiene, lacking social benefits for retirement/pension, living in a public retirement home, brushing teeth less than twice a day and lacking teeth without dentures. None of the factors included in this study were associated with xerostomia. We concluded that several variables studied were associated with hyposalivation, but none for xerostomia. Additional research should examine the amount of hyposalivation and factors associated with hyposalivation especially in elderly with increased risk for hyposalivation.
Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa
Authors: Alam Intikhab , Yang Yan-Qing , Wang Yong , Zhu Mei-Lan , Wang Heng-Bo , Chalhoub Boulos , Lu Yun-Hai 
Published: January 2017

AbstractMore and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.
Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts
Authors: Forkus Brittany , Ritter Seth , Vlysidis Michail , Geldart Kathryn , Kaznessis Yiannis N. 
Published: January 2017

AbstractDespite the arsenal of technologies employed to control foodborne nontyphoidal Salmonella (NTS), infections have not declined in decades. Poultry is the primary source of NTS outbreaks, as well as the fastest growing meat sector worldwide. With recent FDA rules for phasing-out antibiotics in animal production, pressure is mounting to develop new pathogen reduction strategies. We report on a technology to reduce Salmonella enteritidis in poultry. We engineered probiotic E. coli Nissle 1917, to express and secrete the antimicrobial peptide, Microcin J25. Using in vitro experiments and an animal model of 300 turkeys, we establish the efficacy of this technology. Salmonella more rapidly clear the ceca of birds administered the modified probiotic than other treatment groups. Approximately 97% lower Salmonella carriage is measured in a treated group, 14 days post-Salmonella challenge. Probiotic bacteria are generally regarded as safe to consume, are bile-resistant and can plausibly be modified to produce a panoply of antimicrobial peptides now known. The reported systems may provide a foundation for platforms to launch antimicrobials against gastrointestinal tract pathogens, including ones that are multi-drug resistant.
Activation of Wnt/β-catenin signalling via GSK3 inhibitors direct differentiation of human adipose stem cells into functional hepatocytes
Authors: Huang Jieqiong , Guo Xinyue , Li Weihong , Zhang Haiyan 
Published: January 2017

AbstractThe generation of hepatocytes that are derived from human adipose stem cells (hASCs) represents an alternative to human hepatocytes for individualized therapeutic and pharmaceutical applications. However, the mechanisms facilitating hepatocyte differentiation from hASCs are not well understood. Here, we show that upon exposure to glycogen synthase kinase 3 (GSK3) inhibitors alone, the expression of definitive endoderm specific genes GATA4, FOXA2, and SOX17 in hASCs significantly increased in a manner with activation of Wnt/β-catenin signalling. Down regulation of the β-catenin expression attenuates the effect of GSK3 inhibitors on the induction of these specific genes. The cells induced using GSK3 inhibitors were directed to differentiate synchronously into hepatocyte-like cells (HLCs) after further combinations of soluble factors by a reproducible three-stage method. Moreover, hASC-HLCs induced using GSK3 inhibitors possess low-density lipoprotein uptake, albumin secretion, and glycogen synthesis ability, express important drug-metabolizing cytochrome P450 (CYP450) enzymes, and demonstrate CYP450 activity. Therefore, our findings suggest that activation of Wnt/β-catenin signalling via GSK3 inhibitors in definitive endoderm specification may represent an important mechanism mediating hASCs differentiated to functional hepatocyte. Furthermore, development of similar compounds may be useful for robust, potentially scalable and cost-effective generation of functional hepatocytes for drug screening and predictive toxicology platforms.
Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12
Authors: Chen Chi , Lu Ziheng , Ciucci Francesco 
Published: January 2017

AbstractUnderstanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations.
The occurrence rate of acute-onset postoperative endophthalmitis after cataract surgery in Chinese small- and medium-scale departments of ophthalmology
Authors: Zhu Yanan , Chen Xinyi , Chen Peiqing , Wu Jianjun , Hua Huixia , Yao Ke 
Published: January 2017

AbstractEndophthalmitis can be a devastating complication after cataract surgery. Therefore, this study sought to better understand the occurrence rate of acute-onset postoperative endophthalmitis after cataract surgery in Chinese small and medium-scale departments of ophthalmology, as well as identify its risk factors and assess the treatment options. This investigation revealed 52 postoperative endophthalmitis cases in 46,185 operations at 30 hospitals from 2011 to 2013, at an occurrence rate of 0.11%. A small cataract surgery volume of less than 500 cases per year (OR 2.21; p = 0.006), the absence of 0.5% povidone iodine (PVP-I) irrigation (OR 1.73; p = 0.046), and intraoperative posterior capsular rupture (PCR) with vitreous loss (OR 4.40; p = 0.034) showed statistically significant associations with endophthalmitis in the multivariate analysis. The rate of culture positivity was 44.2%, with Staphylococcus epidermidis being the most common organism isolated in China. More than 40% of the endophthalmitis cases were treated with a nonstandard antibiotics regimen, and only 32.7% of these had a visual acuity of better than 20/40. We concluded that the occurrence rate of acute-onset endophthalmitis following cataract surgery in Chinese small and medium-scale departments of ophthalmology lags behind the level of developed countries, as well as Chinese top eye centers. Overall, the use of 0.5% PVP-I irrigation seemed to be an effective measure to reduce the risk of the development of postoperative endophthalmitis.
A new type of two-dimensional carbon crystal prepared from 1,3,5-trihydroxybenzene
Authors: Du Qi-Shi , Tang Pei-Duo , Huang Hua-Lin , Du Fang-Li , Huang Kai , Xie Neng-Zhong , Long Si-Yu , Li Yan-Ming , Qiu Jie-Shan , Huang Ri-Bo 
Published: January 2017

AbstractA new two-dimensional (2D) carbon crystal, different from graphene, has been prepared from 1,3,5-trihydroxybenzene, consisting of 4-carbon and 6-carbon rings in 1:1 ratio, named 4–6 carbophene by authors, in which all carbon atoms possess sp2hybrid orbitals with some distortion, forming an extensive conjugated π-bonding planar structure. The angles between the three σ-bonds of the carbon sp2orbitals are roughly 120°, 90°, and 150°. Each of the three non-adjacent sides of a 6C-ring is shared with a 4C-ring; and each of the two opposite sides of a 4C-ring is shared with a 6C-ring. Dodecagonal holes with a diameter of approximate 5.8 Å are regularly located throughout the 2D carbon crystal. Even though the bond energies in 4–6 carbophene are weaker than those in the graphene, the new planar crystal is quite stable in ambient conditions. The 4–6 carbophene can be synthetized from 1,3,5-trihydroxybenzene or other benzene derivatives through dehydration and polymerization reactions, and may possess several possible patterns that form a family of 2D carbon crystals. A possible side reaction involving 1,3,5-trihydroxybenzene is also discussed, which may produce a carbon-oxygen two dimensional crystal.
Optimizing isothiocyanate formation during enzymatic glucosinolate breakdown by adjusting pH value, temperature and dilution in Brassica vegetables and Arabidopsis thaliana
Authors: Hanschen Franziska S. , Klopsch Rebecca , Oliviero Teresa , Schreiner Monika , Verkerk Ruud , Dekker Matthijs 
Published: January 2017

AbstractConsumption of glucosinolate-rich Brassicales vegetables is associated with a decreased risk of cancer with enzymatic hydrolysis of glucosinolates playing a key role. However, formation of health-promoting isothiocyanates is inhibited by the epithiospecifier protein in favour of nitriles and epithionitriles. Domestic processing conditions, such as changes in pH value, temperature or dilution, might also affect isothiocyanate formation. Therefore, the influences of these three factors were evaluated in accessions of Brassica rapa, Brassica oleracea, and Arabidopsis thaliana. Mathematical modelling was performed to determine optimal isothiocyanate formation conditions and to obtain knowledge on the kinetics of the reactions. At 22 °C and endogenous plant pH, nearly all investigated plants formed nitriles and epithionitriles instead of health-promoting isothiocyanates. Response surface models, however, clearly demonstrated that upon change in pH to domestic acidic (pH 4) or basic pH values (pH 8), isothiocyanate formation considerably increases. While temperature also affects this process, the pH value has the greatest impact. Further, a kinetic model showed that isothiocyanate formation strongly increases due to dilution. Finally, the results show that isothiocyanate intake can be strongly increased by optimizing the conditions of preparation of Brassicales vegetables.
Helminth-induced Ly6Chi monocyte-derived alternatively activated macrophages suppress experimental autoimmune encephalomyelitis
Authors: Terrazas Cesar , de Dios Ruiz-Rosado Juan , Amici Stephanie A. , Jablonski Kyle A. , Martinez-Saucedo Diana , Webb Lindsay M. , Cortado Hanna , Robledo-Avila Frank , Oghumu Steve , Satoskar Abhay R. , Rodriguez-Sosa Miriam , Terrazas Luis I. , Guerau-de-Arellano Mireia , Partida-Sánchez Santiago 
Published: January 2017

AbstractHelminths cause chronic infections and affect the immune response to unrelated inflammatory diseases. Although helminths have been used therapeutically to ameliorate inflammatory conditions, their anti-inflammatory properties are poorly understood. Alternatively activated macrophages (AAMϕs) have been suggested as the anti-inflammatory effector cells during helminth infections. Here, we define the origin of AAMϕs during infection with Taenia crassiceps, and their disease-modulating activity on the Experimental Autoimmune Encephalomyelitis (EAE). Our data show two distinct populations of AAMϕs, based on the expression of PD-L1 and PD-L2 molecules, resulting upon T. crassiceps infection. Adoptive transfer of Ly6C+ monocytes gave rise to PD-L1+/PD-L2+, but not PD-L1+/PD-L2− cells in T. crassiceps-infected mice, demonstrating that the PD-L1+/PD-L2+ subpopulation of AAMϕs originates from blood monocytes. Furthermore, adoptive transfer of PD-L1+/PD-L2+ AAMϕs into EAE induced mice reduced disease incidence, delayed disease onset, and diminished the clinical disability, indicating the critical role of these cells in the regulation of autoimmune disorders.
Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration
Authors: Zinkernagel Martin S. , Zysset-Burri Denise C. , Keller Irene , Berger Lieselotte E. , Leichtle Alexander B. , Largiadèr Carlo R. , Fiedler Georg M. , Wolf Sebastian 
Published: January 2017

AbstractAge-related macular degeneration (AMD) is the most frequent cause of blindness in the elderly. There is evidence that nutrition, inflammation and genetic risk factors play an important role in the development of AMD. Recent studies suggest that the composition of the intestinal microbiome is associated with metabolic diseases through modulation of inflammation and host metabolism. To investigate whether compositional and functional alterations of the intestinal microbiome are associated with AMD, we sequenced the gut metagenomes of patients with AMD and controls. The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with AMD, whereas Bacteroides eggerthii was enriched in controls. Patient’s intestinal microbiomes were enriched in genes of the L-alanine fermentation, glutamate degradation and arginine biosynthesis pathways and decreased in genes of the fatty acid elongation pathway. These findings suggest that modifications in the intestinal microbiome are associated with AMD, inferring that this common sight threatening disease may be targeted by microbiome-altering interventions.
Aberrant development of intrinsic brain activity in a rat model of caregiver maltreatment of offspring
Authors: Yan C-G , Rincón-Cortés M , Raineki C , Sarro E , Colcombe S , Guilfoyle D N , Yang Z , Gerum S , Biswal B B , Milham M P , Sullivan R M , Castellanos F X 
Published: January 2017

AbstractCaregiver maltreatment induces vulnerability to later-life psychopathology. Clinical and preclinical evidence suggest changes in prefrontal and limbic circuitry underlie this susceptibility. We examined this question using a rat model of maternal maltreatment and methods translated from humans, resting-state functional magnetic resonance imaging (R-fMRI). Rat pups were reared by mothers provided with insufficient or abundant bedding for nest building from postnatal (PN) days 8 to 12 and underwent behavioral assessments of affect-related behaviors (forced swim, sucrose preference and social interaction) in adolescence (PN45) and early adulthood (PN60). R-fMRI sessions were conducted under light anesthesia at both ages. Offspring reared with insufficient bedding (that is, maltreated) displayed enduring negative affective behaviors. Amygdala-prefrontal cortex (PFC) functional connectivity increased significantly from adolescence to adulthood in controls, but not in maltreated animals. We computed the fractional amplitude of low-frequency fluctuations (fALFF), an index of intrinsic brain activity, and found that fALFF in medial prefrontal cortex and anterior cingulate cortex (MPFC/ACC) increased significantly with age in controls but remained unchanged in maltreated animals during adolescence and adulthood. We used a seed-based analysis to explore changes in functional connectivity between this region and the whole brain. Compared with controls, maltreated animals demonstrated reduced functional connectivity between MPFC/ACC and left caudate/putamen across both ages. Functional connectivity between MPFC/ACC and right caudate/putamen showed a group by age interaction: decreased in controls but increased in maltreated animals. These data suggest that maltreatment induces vulnerability to psychopathology and is associated with differential developmental trajectories of prefrontal and subcortical circuits underlying affect regulation.