bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting the regulation rules of cancer-related miRNAs based on network analysis
Authors: Liu Zhongyu , Guo Yanzhi , Pu Xuemei , Li Menglong 
Published: October 2016

AbstractmiRNAs (microRNAs) are a set of endogenous and small non-coding RNAs which specifically induce degradation of target mRNAs or inhibit protein translation to control gene expression. Obviously, aberrant miRNA expression in human cells will lead to a serious of changes in protein-protein interaction network (PPIN), thus to activate or inactivate some pathways related to various diseases, especially carcinogenesis. In this study, we systematically constructed the miRNA-regulated co-expressed protein-protein interaction network (CePPIN) for 17 cancers firstly. We investigated the topological parameters and functional annotation for the proteins in CePPIN, especially for those miRNA targets. We found that targets regulated by more miRNAs tend to play a more important role in the forming process of cancers. We further elucidated the miRNA regulation rules in PPIN from a more systematical perspective. By GO and KEGG pathway analysis, miRNA targets are involved in various cellular processes mostly related to cell cycle, such as cell proliferation, growth, differentiation, etc. Through the Pfam classification, we found that miRNAs belonging to the same family tend to have targets from the same family which displays the synergistic function of these miRNAs. Finally, the case study on miR-519d and miR-21-regulated sub-network was performed to support our findings.
Characterization of Toxin Genes and Antimicrobial Susceptibility of Staphylococcus aureus Isolates in Fishery Products in Iran
Authors: Arfatahery Noushin , Davoodabadi Abolfazl , Abedimohtasab Taranehpeimaneh 
Published: October 2016

AbstractStaphylococcus aureus is one of the most common causes of seafood-borne diseases worldwide, which are attributable to the contamination of food by preformed enterotoxins. In this study, a total of 206 (34.3%) Staphylococcus aureus strains were obtained from 600 fish and shrimp samples and were tested for their antimicrobial susceptibility. We assessed the prevalence of the genes responsible for the staphylococcal enterotoxins (SEA, SEB) and toxic shock syndrome toxin 1 (TSST-1) genes. The results indicated that 34% of aqua food samples were contaminated with S. aureus and 23.8% of these isolates were mec-A-positive. Sixty-four percent of the strains isolated from contaminated seafood was enterotoxigenic S. aureus and 28.2% of SEs were MRSA-positive. The most prevalent genotype was characterized by the presence of the sea gene (45.2%), followed by the seb gene (18.5%) and the tst gene encoding TSST-1 was found in eight strains (3.9%). Of the 206 S. aureus isolates, 189 strains (84.9%) were resistant to at least one antibiotic. Given the frequent outbreaks of enterotoxigenic MRSA, it is necessary to make revisions to mandatory programmes to facilitate improved hygiene practices during fishing, aquaculture, processing and sales to prevent the contamination of fishery products in Iran.
A Statistical Learning Framework for Materials Science: Application to Elastic Moduli of k-nary Inorganic Polycrystalline Compounds
Authors: de Jong Maarten , Chen Wei , Notestine Randy , Persson Kristin , Ceder Gerbrand , Jain Anubhav , Asta Mark , Gamst Anthony 
Published: October 2016

AbstractMaterials scientists increasingly employ machine or statistical learning (SL) techniques to accelerate materials discovery and design. Such pursuits benefit from pooling training data across, and thus being able to generalize predictions over, k-nary compounds of diverse chemistries and structures. This work presents a SL framework that addresses challenges in materials science applications, where datasets are diverse but of modest size, and extreme values are often of interest. Our advances include the application of power or Hölder means to construct descriptors that generalize over chemistry and crystal structure, and the incorporation of multivariate local regression within a gradient boosting framework. The approach is demonstrated by developing SL models to predict bulk and shear moduli (K and G, respectively) for polycrystalline inorganic compounds, using 1,940 compounds from a growing database of calculated elastic moduli for metals, semiconductors and insulators. The usefulness of the models is illustrated by screening for superhard materials.
Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions
Authors: Karlsson O. Andreas , Sundell Gustav N. , Andersson Eva , Ivarsson Ylva , Jemth Per 
Published: October 2016

AbstractThe E6 protein from human papillomavirus (HPV) plays an important role during productive infection and is a potential drug target. We have previously designed a high affinity bivalent protein binder for the E6 protein, a fusion between a helix from the E6 associated protein and PDZØ9, an engineered variant (L391F/K392M) of the second PDZ domain from synapse associated protein 97 (SAP97 PDZ2). How the substitutions improve the affinity of SAP97 PDZ2 for HPV E6 is not clear and it is not known to what extent they affect the specificity for cellular targets. Here, we explore the specificity of wild type SAP97 PDZ2 and PDZØ9 through proteomic peptide phage display. In addition, we employ a double mutant cycle of SAP97 PDZ2 in which the binding kinetics for nine identified potential cellular peptide ligands are measured and compared with those for the C-terminal E6 peptide. The results demonstrate that PDZØ9 has an increased affinity for all peptides, but at the cost of specificity. Furthermore, there is a peptide dependent coupling free energy between the side chains at positions 391 and 392. This corroborates our previous allosteric model for PDZ domains, involving sampling of intramolecular energetic pathways.
Ultrastable glasses portray similar behaviour to ordinary glasses at high pressure
Authors: Rodríguez-Tinoco C. , González-Silveira M. , Barrio M. , Lloveras P. , Tamarit J. Ll , Garden J.-L. , Rodríguez-Viejo J. 
Published: October 2016

AbstractPressure experiments provide a unique opportunity to unravel new insights into glass-forming liquids by exploring its effect on the dynamics of viscous liquids and on the evolution of the glass transition temperature. Here we compare the pressure dependence of the onset of devitrification, Ton, between two molecular glasses prepared from the same material but with extremely different ambient-pressure kinetic and thermodynamic stabilities. Our data clearly reveal that, while both glasses exhibit different dTon/dP values at low pressures, they evolve towards closer calorimetric devitrification temperature and pressure dependence as pressure increases. We tentatively interpret these results from the different densities of the starting materials at room temperature and pressure. Our data shows that at the probed pressures, the relaxation time of the glass into the supercooled liquid is determined by temperature and pressure similarly to the behaviour of liquids, but using stability-dependent parameters.
GDGT distribution in a stratified lake and implications for the application of TEX86 in paleoenvironmental reconstructions
Authors: Zhang Zhaohui , Smittenberg Rienk H. , Bradley Raymond S. 
Published: October 2016

AbstractWe investigated the relationship between distributions of GDGTs, GDGT-based proxies and environmental factors in a stratified lake in northwestern Norway. More than 90% of isoGDGTs were produced at the bottom of the oxycline, indicating a predominance of ammonia-oxidizing Group I.1a of Thaumarchaeota, supported by high crenarchaeol/caldarchaeol ratios. Dissolved oxygen content, rather than temperature, exercised a primary control on TEX86 values. In spite of low BIT value in surface sediment, the reconstructed lake surface temperature was “cold” biased. MBT values in streams and lake surface water were significantly smaller than those in the catchment soil, suggesting in situ production of brGDGTs in streams. A rapid transition of MBT vs. temperature/pH relationships occurring at the bottom of oxycline indicated the differential production of various brGDGTs with D.O. and depths. Only within the oxycline were CBT-based pH values close to in situ pH. Our results confirm earlier studies calling for caution in applying TEX86 as a surface temperature proxy, or MBT and/or CBT for reconstructing pH, in anoxic or euxinic lakes, estuaries and ocean basins. We propose that caldarchaeol/crenarchaeol ratio, an indicator of contributions from methanogenic archaea, together with the BIT and TEX86 proxies, can help reconstruct past levels of stratification.
The Growth Pattern of Tibetan Infants at High Altitudes: a Cohort Study in Rural Tibet region
Authors: Wang Weihua , Liu Feng , Zhang Zhicheng , Zhang Yi , Fan Xiaojing , Liu Ruru , Dang Shaonong 
Published: October 2016

AbstractStudies on growth pattern of Tibetan infants and the difference from other child groups were limited due to its special living environment and unique customs. In this study, 253 Tibetan infants were followed-up from their birth to 12th month in rural Tibet. Five visits were conducted and weight and length were measured at each visit. Mixed model was employed to analyze the growth pattern of Tibetan infants and its comparison to the Han infants. Propensity Scores (PS) technique was adopted to control for the potential confounding factors. The mixed model found that the birth weight/length had a negative impact on the increment of Tibetan infants after birth (weight: β = −0.6819, P < 0.0001, length: β = −0.9571, P < 0.0001). The weight increment of Tibetan infants was greater than Han infant with age (βage*ethnic = 0.0345, P < 0.001), after using PS as a covariant. And another mixed model in which PS was used as a matching factor found similar trend. Compared with Chinese Han infants, Tibetan infants were lower weight and shorter length within one year after birth but they had greater increment of weight, suggesting that Tibetan infants might have a significant catch-up growth within the first year of life.
Tea polyphenols inhibit the activation of NF-κB and the secretion of cytokines and matrix metalloproteinases by macrophages stimulated with Fusobacterium nucleatum
Authors: Lagha Amel Ben , Grenier Daniel 
Published: October 2016

AbstractFusobacterium nucleatum has been associated with both periodontal disease and inflammatory bowel disease. This Gram-negative bacterium possesses a high inflammatory potential that may contribute to the disease process. We hypothesized that green and black tea polyphenols attenuate the inflammatory response of monocytes/macrophages mediated by F. nucleatum. We first showed that the tea extracts, EGCG and theaflavins reduce the NF-κB activation induced by F. nucleatum in monocytes. Since NF-κB is a key regulator of genes coding for inflammatory mediators, we tested the effects of tea polyphenols on secretion of IL-1β, IL-6, TNF-α and CXCL8 by macrophages. A pre-treatment of macrophages with the tea extracts, EGCG, or theaflavins prior to a stimulation with F. nucleatum significantly inhibited the secretion of all four cytokines and reduced the secretion of MMP-3 and MMP-9, two tissue destructive enzymes. TREM-1 expressed by macrophages is a cell-surface receptor involved in the propagation of the inflammatory response to bacterial challenges. Interestingly, tea polyphenols inhibited the secretion/shedding of soluble TREM-1 induced by a stimulation of macrophages with F. nucleatum. The anti-inflammatory properties of tea polyphenols identified in the present study suggested that they may be promising agents for the prevention and/or treatment of periodontal disease and inflammatory bowel disease.
Site-specific identification of heparan and chondroitin sulfate glycosaminoglycans in hybrid proteoglycans
Authors: Noborn Fredrik , Gomez Toledo Alejandro , Green Anders , Nasir Waqas , Sihlbom Carina , Nilsson Jonas , Larson Göran 
Published: October 2016

AbstractHeparan sulfate (HS) and chondroitin sulfate (CS) are complex polysaccharides that regulate important biological pathways in virtually all metazoan organisms. The polysaccharides often display opposite effects on cell functions with HS and CS structural motifs presenting unique binding sites for specific ligands. Still, the mechanisms by which glycan biosynthesis generates complex HS and CS polysaccharides required for the regulation of mammalian physiology remain elusive. Here we present a glycoproteomic approach that identifies and differentiates between HS and CS attachment sites and provides identity to the core proteins. Glycopeptides were prepared from perlecan, a complex proteoglycan known to be substituted with both HS and CS chains, further digested with heparinase or chondroitinase ABC to reduce the HS and CS chain lengths respectively and thereafter analyzed by nLC-MS/MS. This protocol enabled the identification of three consensus HS sites and one hybrid site, carrying either a HS or a CS chain. Inspection of the amino acid sequence at the hybrid attachment locus indicates that certain peptide motifs may encode for the chain type selection process. This analytical approach will become useful when addressing fundamental questions in basic biology specifically in elucidating the functional roles of site-specific glycosylations of proteoglycans.
Methyl-CpG binding domain protein acts to regulate the repair of cyclobutane pyrimidine dimers on rice DNA
Authors: Fang Changxun , Chen Weisi , Li Chengxun , Jian Xin , Li Yingzhe , Lin Hongmei , Lin Wenxiong 
Published: October 2016

AbstractUVB radiation causes cyclobutane pyrimidine dimers (CPDs) to form on the DNA of living organisms. This study found that overexpression of the silicon absorbance gene Lsi1 reduced the accumulation of CPDs in rice, which profited from the reactivation by photolyase. The transcript abundance of deoxyribodipyrimidine photolyase (Os10g0167600) was generally correlated with the silicon content of the rice, and the up-regulation of Os10g0167600 was found to be highest in the UVB-treated Lsi1-overexpressed (Lsi1-OX) rice. A trans-acting factor, methyl-CpG binding domain protein (OsMeCP), was found to interact with the cis-element of Os10g0167600. The nucleic location of OsMeCP effectively enabled the transcriptional regulation. Compared with the WT, the level of OsMeCP was lower in the Lsi1-OX rice but higher in the Lsi1-RNAi line. Rice cultured in a high silicate-concentration solution also exhibited less OsMeCP abundance. Overexpression of OsMeCP led to lower Os10g0167600 transcript levels and a higher CPD content than in the WT, but the reverse was true in the OsMeCP-RNAi line. These findings indicate that OsMeCP acts as a negative regulator of silicon, and can mediate the repression of the transcription from Os10g0167600, which inhibits the photoreactivation of the photolyase involved in the repair of CPDs.
Regionalization of Habitat Suitability of Masson’s Pine based on geographic information system and Fuzzy Matter-Element Model
Authors: Zhou Xiuteng , Zhao Manxi , Zhou Liangyun , Yang Guang , Huang Luqi , Yan Cuiqi , Huang Quanshu , Ye Liang , Zhang Xiaobo , Guo Lanpin , Ke Xiao , Guo Jiao 
Published: October 2016

AbstractPine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson’s pine (Pinus massoniana Lamb), as well as ensure effective development of Masson’s pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson’s pine needles accounted for only 7.41% of its distribution area.
Coral recovery in the central Maldives archipelago since the last major mass-bleaching, in 1998
Authors: Pisapia C. , Burn D. , Yoosuf R. , Najeeb A. , Anderson K. D. , Pratchett M. S. 
Published: October 2016

AbstractIncreasing frequency and severity of disturbances is causing global degradation of coral reef ecosystems. This study examined temporal changes in live coral cover and coral composition in the central Maldives from 1997 to 2016, encompassing two bleaching events, a tsunami, and an outbreak of Acanthaster planci. We also examined the contemporary size structure for five dominant coral taxa (tabular Acropora, Acropora muricata, Acropora humilis, Pocillopora spp, and massive Porites). Total coral cover increased throughout the study period, with marked increases following the 1998 mass-bleaching. The relative abundance of key genera has changed through time, where Acropora and Pocillopora (which are highly susceptible to bleaching) were under-represented following 1998 mass-bleaching but increased until outbreaks of A. planci in 2015. The contemporary size-structure for all coral taxa was dominated by larger colonies with peaked distributions suggesting that recent disturbances had a disproportionate impact on smaller colonies, or that recruitment is currently limited. This may suggest that coral resilience has been compromised by recent disturbances, and further bleaching (expected in 2016) could lead to highly protracted recovery times. We showed that Maldivian reefs recovered following the 1998 mass-bleaching event, but it took up to a decade, and ongoing disturbances may be eroding reef resilience.
Quantifying the dilution of the radiocesium contamination in Fukushima coastal river sediment (2011–2015)
Authors: Evrard Olivier , Laceby J. Patrick , Onda Yuichi , Wakiyama Yoshifumi , Jaegler Hugo , Lefèvre Irène 
Published: October 2016

AbstractFallout from the Fukushima Dai-ichi nuclear power plant accident resulted in a 3000-km2 radioactive contamination plume. Here, we model the progressive dilution of the radiocesium contamination in 327 sediment samples from two neighboring catchments with different timing of soil decontamination. Overall, we demonstrate that there has been a ~90% decrease of the contribution of upstream contaminated soils to sediment transiting the coastal plains between 2012 (median – M – contribution of 73%, mean absolute deviation – MAD – of 27%) and 2015 (M 9%, MAD 6%). The occurrence of typhoons and the progress of decontamination in different tributaries of the Niida River resulted in temporary increases in local contamination. However, the much lower contribution of upstream contaminated soils to coastal plain sediment in November 2015 demonstrates that the source of the easily erodible, contaminated material has potentially been removed by decontamination, diluted by subsoils, or eroded and transported to the Pacific Ocean.
Genome shuffling of Lactobacillus plantarum C88 improves adhesion
Authors: Zhao Yujuan , Duan Cuicui , Gao Lei , Yu Xue , Niu Chunhua , Li Shengyu 
Published: October 2016

Abstract
Genome shuffling is an important method for rapid improvement in microbial strains for desired phenotypes. In this study, ultraviolet irradiation and nitrosoguanidine were used as mutagens to enhance the adhesion of the wild-type Lactobacillus plantarum C88. Four strains with better property were screened after mutagenesis to develop a library of parent strains for three rounds of genome shuffling. Fusants F3-1, F3-2, F3-3, and F3-4 were screened as the improved strains. The in vivo and in vitro tests results indicated that the population after three rounds of genome shuffling exhibited improved adhesive property. Random Amplified Polymorphic DNA results showed significant differences between the parent strain and recombinant strains at DNA level. These results suggest that the adhesive property of L. plantarum C88 can be significantly improved by genome shuffling. Improvement in the adhesive property of bacterial cells by genome shuffling enhances the colonization of probiotic strains which further benefits to exist probiotic function.
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease
Authors: Lu Qiongshi , Powles Ryan L. , Abdallah Sarah , Ou Derek , Wang Qian , Hu Yiming , Lu Yisi , Liu Wei , Li Boyang , Mukherjee Shubhabrata , Crane Paul K. , Zhao Hongyu 
Published: October 2016

AbstractContinuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system) increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells) provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer’s disease (LOAD). Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson’s disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available athttp://genocanyon.med.yale.edu/GenoSkyline.Author SummaryAfter years of community efforts, many experimental and computational approaches have been developed and applied for functional annotation of the human genome, yet proper annotation still remains challenging, especially in non-coding regions. As complex disease research rapidly advances, increasing evidence suggests that non-coding regulatory DNA elements may be the primary regions harboring risk variants in human complex diseases. In this paper, we introduce GenoSkyline-Plus, a principled annotation framework to identify tissue and cell type-specific functional regions in the human genome through integration of diverse high-throughput epigenomic and transcriptomic data. Through validation of known non-coding tissue-specific regulatory regions, enrichment analyses on 45 complex traits, and an in-depth case study of neurodegenerative diseases, we demonstrate the ability of GenoSkyline-Plus to accurately identify tissue-specific functionality in the human genome and provide unbiased, genome-wide insights into the genetic basis of human complex diseases.