bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circular RNAs expression profiles in human gastric cancer
Authors: Dang Yuan , Ouyang Xiaojuan , Zhang Fan , Wang Kai , Lin Youdong , Sun Baochang , Wang Yu , Wang Lie , Huang Qiaojia 
Published: August 2017

AbstractCircular RNAs (circRNAs) are implicated in a variety of cancers. However, the roles of circRNAs in gastric cancer (GC) remain largely unknown. In the current study, circRNAs expression profiles were screened in GC, using 5 pairs of GC and matched non-GC tissues with circRNA chip. Preliminary results were verified with quantitative PCR (qRT-PCR). Briefly, total of 713 circRNAs were differentially expressed in GC tissues vs. non-GC tissues (fold change ≥ 2.0, p < 0.05): 191 were upregulated, whereas 522 were downregulated in GC tissues. qRT-PCR analysis of randomly selected 7 circRNAs from the 713 circRNAs in 50 paired of GC vs. non-GC control tissues confirmed the microarray data. Gene ontology (GO) and KEGG pathway analyses showed that many circRNAs are implicated in carcinogenesis. Among differentially expressed circRNAs, hsa_circ_0076304, hsa_circ_0035431, and hsa_circ_0076305 had the highest magnitude of change. These results provided a preliminary landscape of circRNAs expression profile in GC.
Increased peripheral blood inflammatory cytokine levels in amyotrophic lateral sclerosis: a meta-analysis study
Authors: Hu Yang , Cao Chang , Qin Xiao-Yan , Yu Yun , Yuan Jing , Zhao Yu , Cheng Yong 
Published: August 2017

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with poorly understood etiology. Increasing evidence suggest that inflammation may play a critical role in the pathogenesis of ALS. Several studies have demonstrated altered levels of blood cytokines in ALS, but results were inconsistent. Therefore, we did a systematic review of studies comparing blood inflammatory cytokines between ALS patients and control subjects, and quantitatively combined the clinical data with a meta-analysis. The systematic review of Pubmed and Web of Science identified 25 studies encompassing 812 ALS patients and 639 control subjects. Random-effects meta-analysis demonstrated that blood tumor necrosis factor-α (TNF; Hedges’ g = 0.655; p = 0.001), TNF receptor 1 (Hedges’ g = 0.741; p < 0.001), interleukin 6 (IL-6; Hedges’ g = 0.25; p = 0.005), IL-1β (Hedges’ g = 0.296; p = 0.038), IL-8 (Hedges’ g = 0.449; p < 0.001) and vascular endothelial growth factor (Hedges’ g = 0.891; p = 0.003) levels were significantly elevated in patients with ALS compared with control subjects. These results substantially enhance our knowledge of the inflammatory response in ALS, and peripheral blood inflammatory cytokines may be used as diagnostic biomarkers for ALS in the future.
Composition formulas of Fe-based transition metals-metalloid bulk metallic glasses derived from dual-cluster model of binary eutectics
Authors: Naz Gul Jabeen , Dong Dandan , Geng Yaoxiang , Wang Yingmin , Dong Chuang 
Published: August 2017

AbstractIt is known that bulk metallic glasses follow simple composition formulas [cluster](glue atom)1 or 3 with 24 valence electrons within the framework of the cluster-plus-glue-atom model. Though the relevant nearest-neighbor cluster can be readily identified from a devitrification phase, the glue atoms remains poorly defined. The present work is devoted to understanding the composition rule of Fe-(B,P,C) based multi-component bulk metallic glasses, by introducing a cluster-based eutectic liquid model. This model regards a eutectic liquid to be composed of two stable liquids formulated respectively by cluster formulas for ideal metallic glasses from the two eutectic phases. The dual cluster formulas are first established for binary Fe-(B,C,P) eutectics: [Fe-Fe14]B2Fe + [B-B2Fe8]Fe ≈ Fe83.3B16.7 for eutectic Fe83B17, [P-Fe14]P + [P-Fe9]P2Fe≈Fe82.8P17.2 for Fe83P17, and [C-Fe6]Fe3 + [C-Fe9]C2Fe ≈ Fe82.6C17.4 for Fe82.7C17.3. The second formulas in these dual-cluster formulas, being respectively relevant to devitrification phases Fe2B, Fe3P, and Fe3C, well explain the compositions of existing Fe-based transition metals-metalloid bulk metallic glasses. These formulas also satisfy the 24-electron rule. The proposition of the composition formulas for good glass formers, directly from known eutectic points, constitutes a new route towards understanding and eventual designing metallic glasses of high glass forming abilities.
Time-Resolved Spectroscopic Study on the Photoredox Reaction of 2-(p-Hydroxymethyl)phenylAnthraquinone
Authors: Song Qingqing , Zhang Xiting , Ma Jiani , Guo Yan , Phillips David Lee 
Published: August 2017

AbstractIn this work, we report a combined time-resolved spectroscopic and density functional theory computational study on 2-(p-hydroxymethyl)phenylanthraquinone (PPAQ) in which the benzyl alcohol moiety is significantly farther away from the AQ ketone group compared to the compound 2-(1-hydroxyethyl) 9,10-anthraquinone (HEAQ) so as to investigate the photophysical and photochemical reactions of PPAQ in several solvents, especially for the photoredox reaction in a pH 2 aqueous solution. The results here indicate that PPAQ undergoes the photoredox reaction via a two-step pathway and that the low efficiency of the photoredox reaction of PPAQ compared to the related HEAQ molecule is caused by the longer distance between the benzyl alcohol moiety and the AQ ketone moieties.
Ecological and evolutionary consequences of alternative sex-change pathways in fish
Authors: Benvenuto C. , Coscia I. , Chopelet J. , Sala-Bozano M. , Mariani S. 
Published: August 2017

AbstractSequentially hermaphroditic fish change sex from male to female (protandry) or vice versa (protogyny), increasing their fitness by becoming highly fecund females or large dominant males, respectively. These life-history strategies present different social organizations and reproductive modes, from near-random mating in protandry, to aggregate- and harem-spawning in protogyny. Using a combination of theoretical and molecular approaches, we compared variance in reproductive success (Vk*) and effective population sizes (Ne) in several species of sex-changing fish. We observed that, regardless of the direction of sex change, individuals conform to the same overall strategy, producing more offspring and exhibiting greater Vk* in the second sex. However, protogynous species show greater Vk*, especially pronounced in haremic species, resulting in an overall reduction of Ne compared to protandrous species. Collectively and independently, our results demonstrate that the direction of sex change is a pivotal variable in predicting demographic changes and resilience in sex-changing fish, many of which sustain highly valued and vulnerable fisheries worldwide.
Reversible inactivation of a peptidoglycan transpeptidase by a β-lactam antibiotic mediated by β-lactam-ring recyclization in the enzyme active site
Authors: Edoo Zainab , Arthur Michel , Hugonnet Jean-Emmanuel 
Published: August 2017

Abstractβ-lactam antibiotics act as suicide substrates of transpeptidases responsible for the last cross-linking step of peptidoglycan synthesis in the bacterial cell wall. Nucleophilic attack of the β-lactam carbonyl by the catalytic residue (Ser or Cys) of transpeptidases results in the opening of the β-lactam ring and in the formation of a stable acyl-enzyme. The acylation reaction is considered as irreversible due to the strain of the β-lactam ring. In contradiction with this widely accepted but poorly demonstrated premise, we show here that the acylation of the L,D-transpeptidase Ldtfm from Enterococcus faecium by the β-lactam nitrocefin is reversible, leading to limited antibacterial activity. Experimentally, two independent methods based on spectrophotometry and mass spectrometry provided evidence that recyclization of the β-lactam ring within the active site of Ldtfm regenerates native nitrocefin. Ring strain is therefore not sufficient to account for irreversible acylation of peptidoglycan transpeptidases observed for most β-lactam antibiotics.
Identification of novel molecular signatures of IgA nephropathy through an integrative -omics analysis
Authors: Krochmal Magdalena , Cisek Katryna , Filip Szymon , Markoska Katerina , Orange Clare , Zoidakis Jerome , Gakiopoulou Chara , Spasovski Goce , Mischak Harald , Delles Christian , Vlahou Antonia , Jankowski Joachim 
Published: August 2017

AbstractIgA nephropathy (IgAN) is the most prevalent among primary glomerular diseases worldwide. Although our understanding of IgAN has advanced significantly, its underlying biology and potential drug targets are still unexplored. We investigated a combinatorial approach for the analysis of IgAN-relevant -omics data, aiming at identification of novel molecular signatures of the disease. Nine published urinary proteomics datasets were collected and the reported differentially expressed proteins in IgAN vs. healthy controls were integrated into known biological pathways. Proteins participating in these pathways were subjected to multi-step assessment, including investigation of IgAN transcriptomics datasets (Nephroseq database), their reported protein-protein interactions (STRING database), kidney tissue expression (Human Protein Atlas) and literature mining. Through this process, from an initial dataset of 232 proteins significantly associated with IgAN, 20 pathways were predicted, yielding 657 proteins for further analysis. Step-wise evaluation highlighted 20 proteins of possibly high relevance to IgAN and/or kidney disease. Experimental validation of 3 predicted relevant proteins, adenylyl cyclase-associated protein 1 (CAP1), SHC-transforming protein 1 (SHC1) and prolylcarboxypeptidase (PRCP) was performed by immunostaining of human kidney sections. Collectively, this study presents an integrative procedure for -omics data exploitation, giving rise to biologically relevant results.
A pulsed-air model of blue whale B call vocalizations
Authors: Dziak R. P. , Haxel J. H. , Lau T.-K. , Heimlich S. , Caplan-Auerbach J. , Mellinger D. K. , Matsumoto H. , Mate B. 
Published: August 2017

AbstractBlue whale sound production has been thought to occur by Helmholtz resonance via air flowing from the lungs into the upper respiratory spaces. This implies that the frequency of blue whale vocalizations might be directly proportional to the size of their sound-producing organs. Here we present a sound production mechanism where the fundamental and overtone frequencies of blue whale B calls can be well modeled using a series of short-duration (<1 s) wavelets. We propose that the likely source of these wavelets are pneumatic pulses caused by opening and closing of respiratory valves during air recirculation between the lungs and laryngeal sac. This vocal production model is similar to those proposed for humpback whales, where valve open/closure and vocal fold oscillation is passively driven by airflow between the lungs and upper respiratory spaces, and implies call frequencies could be actively changed by the animal to center fundamental tones at different frequency bands during the call series.
Mapping the spatial variability of HIV infection in Sub-Saharan Africa: Effective information for localized HIV prevention and control
Authors: Cuadros Diego F. , Li Jingjing , Branscum Adam J. , Akullian Adam , Jia Peng , Mziray Elizabeth N. , Tanser Frank 
Published: August 2017

AbstractUnder the premise that in a resource-constrained environment such as Sub-Saharan Africa it is not possible to do everything, to everyone, everywhere, detailed geographical knowledge about the HIV epidemic becomes essential to tailor programmatic responses to specific local needs. However, the design and evaluation of national HIV programs often rely on aggregated national level data. Against this background, here we proposed a model to produce high-resolution maps of intranational estimates of HIV prevalence in Kenya, Malawi, Mozambique and Tanzania based on spatial variables. The HIV prevalence maps generated highlight the stark spatial disparities in the epidemic within a country, and localize areas where both the burden and drivers of the HIV epidemic are concentrated. Under an era focused on optimal allocation of evidence-based interventions for populations at greatest risk in areas of greatest HIV burden, as proposed by the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the United States President’s Emergency Plan for AIDS Relief (PEPFAR), such maps provide essential information that strategically targets geographic areas and populations where resources can achieve the greatest impact.
Increasing the doping efficiency by surface energy control for ultra-transparent graphene conductors
Authors: Chang Kai-Wen , Hsieh Ya-Ping , Ting Chu-Chi , Su Yen-Hsun , Hofmann Mario 
Published: August 2017

AbstractGraphene’s attractiveness in many applications is limited by its high resistance. Extrinsic doping has shown promise to overcome this challenge but graphene’s performance remains below industry requirements. This issue is caused by a limited charge transfer efficiency (CTE) between dopant and graphene. Using AuCl3 as a model system, we measure CTE as low as 5% of the expected values due to the geometrical capacitance of small adsorbate clusters. We here demonstrate a strategy for enhancing the CTE by a two-step optimization of graphene’s surface energy prior to AuCl3 doping. First, exposure to UV ozone modified the hydrophilicity of graphene and was found to decrease the cluster’s geometric capacitance, which had a direct effect on the CTE. Occurrence of lattice defects at high UV exposure, however, deteriorated graphene’s transport characteristics and limited the effectiveness of this pretreatment step. Thus, prior to UV exposure, a functionalized polymer layer was introduced that could further enhance graphene’s surface energy while protecting it from damage. Combination of these treatment steps were found to increase the AuCl3 charge transfer efficiency to 70% and lower the sheet resistance to 106 Ω/γ at 97% transmittance which represents the highest reported performance for doped single layer graphene and is on par with commercially available transparent conductors.
The open architecture of HD-PTP phosphatase provides new insights into the mechanism of regulation of ESCRT function
Authors: Gahloth Deepankar , Heaven Graham , Jowitt Thomas A. , Mould A. Paul , Bella Jordi , Baldock Clair , Woodman Philip , Tabernero Lydia 
Published: August 2017

AbstractHD-PTP is a tumour suppressor phosphatase that controls endocytosis, down-regulation of mitogenic receptors and cell migration. Central to its role is the specific recruitment of critical endosomal sorting complexes required for transport (ESCRTs). However, the molecular mechanisms that enable HD-PTP to regulate ESCRT function are unknown. We have characterised the molecular architecture of the entire ESCRT binding region of HD-PTP using small angle X-ray scattering and hydrodynamic analyses. We show that HD-PTP adopts an open and extended conformation, optimal for concomitant interactions with multiple ESCRTs, which contrasts with the compact conformation of the related ESCRT regulator Alix. We demonstrate that the HD-PTP open conformation is functionally competent for binding cellular protein partners. Our analyses rationalise the functional cooperation of HD-PTP with ESCRT-0, ESCRT-I and ESCRT-III and support a model for regulation of ESCRT function by displacement of ESCRT subunits, which is crucial in determining the fate of ubiquitinated cargo.
Spacial Energy Distribution Manipulation with Multi-focus Huygens Metamirror
Authors: Wang Zhuochao , Ding Xumin , Zhang Kuang , Wu Qun 
Published: August 2017

AbstractHuygens metasurface is a planar array of crossed electric and magnetic dipoles, which provide specific surface current to tailor the electromagnetic field distribution. By changing the geometrical parameters of the proposed unit cell, the manipulation range of reflection phase can achieve 2π, while the amplitude of the reflection coefficient can keep above 0.993. Based on the designed Huygens meta-atoms, a novel multi-focus Huygens metamirror is proposed at microwave range in this paper. Utilizing the meta-atoms with the desired reflection phase distribution as calculated, the incident plane wave can be converged to designated points in any desired fashion including focal number, location and intensity distribution, which exhibits outstanding manipulation capability. Our research on Huygens metamirror provides a fascinating design of multi-focus imaging in microwave region, which makes it potential applications in antenna and imaging systems.
Controlling congestion on complex networks: fairness, efficiency and network structure
Authors: Buzna Ľuboš , Carvalho Rui 
Published: August 2017

AbstractWe consider two elementary (max-flow and uniform-flow) and two realistic (max-min fairness and proportional fairness) congestion control schemes, and analyse how the algorithms and network structure affect throughput, the fairness of flow allocation, and the location of bottleneck edges. The more realistic proportional fairness and max-min fairness algorithms have similar throughput, but path flow allocations are more unequal in scale-free than in random regular networks. Scale-free networks have lower throughput than their random regular counterparts in the uniform-flow algorithm, which is favoured in the complex networks literature. We show, however, that this relation is reversed on all other congestion control algorithms for a region of the parameter space given by the degree exponent γ and average degree 〈k〉. Moreover, the uniform-flow algorithm severely underestimates the network throughput of congested networks, and a rich phenomenology of path flow allocations is only present in the more realistic α-fair family of algorithms. Finally, we show that the number of paths passing through an edge characterises the location of a wide range of bottleneck edges in these algorithms. Such identification of bottlenecks could provide a bridge between the two fields of complex networks and congestion control.
Rate of entropy model for irreversible processes in living systems
Authors: Zivieri R. , Pacini N. , Finocchio G. , Carpentieri M. 
Published: August 2017

AbstractIn living systems, it is crucial to study the exchange of entropy that plays a fundamental role in the understanding of irreversible chemical reactions. However, there are not yet works able to describe in a systematic way the rate of entropy production associated to irreversible processes. Hence, here we develop a theoretical model to compute the rate of entropy in the minimum living system. In particular, we apply the model to the most interesting and relevant case of metabolic network, the glucose catabolism in normal and cancer cells. We show, (i) the rate of internal entropy is mainly due to irreversible chemical reactions, and (ii) the rate of external entropy is mostly correlated to the heat flow towards the intercellular environment. The future applications of our model could be of fundamental importance for a more complete understanding of self-renewal and physiopatologic processes and could potentially be a support for cancer detection.
Comparative Genomic and Regulatory Analyses of Natamycin Production of Streptomyces lydicus A02
Authors: Wu Huiling , Liu Weicheng , Shi Lingling , Si Kaiwei , Liu Ting , Dong Dan , Zhang Taotao , Zhao Juan , Liu Dewen , Tian Zhaofeng , Yue Yuesen , Zhang Hong , Xuelian Bai , Liang Yong 
Published: August 2017

AbstractStreptomyces lydicus A02 is used by industry because it has a higher natamycin-producing capacity than the reference strain S. natalensis ATCC 27448. We sequenced the complete genome of A02 using next-generation sequencing platforms, and to achieve better sequence coverage and genome assembly, we utilized single-molecule real-time (SMRT) sequencing. The assembled genome comprises a 9,307,519-bp linear chromosome with a GC content of 70.67%, and contained 8,888 predicted genes. Comparative genomics and natamycin biosynthetic gene cluster (BGC) analysis showed that BGC are highly conserved among evolutionarily diverse strains, and they also shared closer genome evolution compared with other Streptomyces species. Forty gene clusters were predicted to involve in the secondary metabolism of A02, and it was richly displayed in two-component signal transduction systems (TCS) in the genome, indicating a complex regulatory systems and high diversity of metabolites. Disruption of the phoP gene of the phoR-phoP TCS and nsdA gene confirmed phosphate sensitivity and global negative regulation of natamycin production. The genome sequence and analyses presented in this study provide an important molecular basis for research on natamycin production in Streptomyces, which could facilitate rational genome modification to improve the industrial use of A02.
Nm23-H1-stabilized hnRNPA2/B1 promotes internal ribosomal entry site (IRES)-mediated translation of Sp1 in the lung cancer progression
Authors: Hung Chia-Yang , Wang Yi-Chang , Chuang Jian-Ying , Young Ming-Jer , Liaw Hungjiun , Chang Wen-Chang , Hung Jan-Jong 
Published: August 2017

AbstractOur recent studies have indicated that specificity protein-1 (Sp1) accumulates substantially in the early stage of lung cancer but is partially decreased in the late stages, which is an important factor in the progression of the cancer. In this study, we found that Nm23-H1 and hnRNPA2/B1 could be recruited to the 5′UTR of Sp1 mRNA. In investigating the clinical relevance of Nm23-H1/Sp1 levels, we found a positive correlation between lung cancer patients with poor prognosis and low levels of Sp1 and Nm23-H1, suggesting an association between Nm23-H1/Sp1 levels and survival rate. Knockdown of Nm23-H1 inhibits lung cancer growth but increases lung cancer cell malignancy, which could be rescued by overexpression of Sp1, indicating that Nm23-H1-induced Sp1 expression is critical for lung cancer progression. We also found that Nm23-H1 increases the protein stability of hnRNPA2/B1and is thereby co-recruited to the 5′UTR of Sp1 mRNA to regulate cap-independent translational activity. Since the Sp1 level is tightly regulated during lung cancer progression, understanding the molecular mechanisms underlying the regulation by Nm23-H1/hnRNPA2B1 of Sp1 expression in the various stages of lung cancer will be beneficial for lung cancer therapy in the future.
A miR-SNP biomarker linked to an increased lung cancer survival by miRNA-mediated down-regulation of FZD4 expression and Wnt signaling
Authors: Lin Jing , Zandi Roza , Shao Ruping , Gu Jian , Ye Yuanqin , Wang Jing , Zhao Yang , Pertsemlidis Alexander , Wistuba Ignacio I. , Wu Xifeng , Roth Jack A. , Ji Lin 
Published: August 2017

AbstractThrough a new hypothesis-driven and microRNA-pathway-based SNP (miR-SNP) association study we identified a novel miR-SNP (rs713065) in the 3′UTR region of FZD4 gene linked with decreased risk of death in early stage NSCLC patients. We determined biological function and mechanism of action of this FZD4-miR-SNP biomarker in a cellular platform. Our data suggest that FZD4-miR-SNP loci may significantly influence overall survival in NSCLC patients by specifically interacting with miR-204 and modulating FZD4 expression and cellular function in the Wnt-signaling-driven tumor progression. Our findings are bridging the gap between the discovery of epidemiological SNP biomarkers and their biological function and will enable us to develop novel therapeutic strategies that specifically target epigenetic markers in the oncogenic Wnt/FZD signaling pathways in NSCLC.