bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring the robustness of link prediction algorithms under noisy environment
Authors: Zhang Peng , Wang Xiang , Wang Futian , Zeng An , Xiao Jinghua 
Published: January 2016

AbstractLink prediction in complex networks is to estimate the likelihood of two nodes to interact with each other in the future. As this problem has applications in a large number of real systems, many link prediction methods have been proposed. However, the validation of these methods is so far mainly conducted in the assumed noise-free networks. Therefore, we still miss a clear understanding of how the prediction results would be affected if the observed network data is no longer accurate. In this paper, we comprehensively study the robustness of the existing link prediction algorithms in the real networks where some links are missing, fake or swapped with other links. We find that missing links are more destructive than fake and swapped links for prediction accuracy. An index is proposed to quantify the robustness of the link prediction methods. Among the twenty-two studied link prediction methods, we find that though some methods have low prediction accuracy, they tend to perform reliably in the “noisy” environment.
Aliskiren Reduces Hepatic steatosis and Epididymal Fat Mass and Increases Skeletal Muscle Insulin Sensitivity in High-Fat Diet-Fed Mice
Authors: Lee Kuei-Chuan , Hsieh Yun-Cheng , Yang Ying-Ying , Chan Che-Chang , Huang Yi-Hsiang , Lin Han-Chieh 
Published: January 2016

AbstractAliskiren has been found to reduce chronic injury and steatosis in the liver of methionine-choline-deficient (MCD) diet-fed mice. This study investigated whether aliskiren has an anti-steatotic effect in HFD-fed mice, which are more relevant to human patients with non-alcoholic fatty liver disease than MCD mice. Mice fed with 4-week normal chow or HFD randomly received aliskiren (50 mg/kg/day) or vehicle via osmotic minipumps for further 4 weeks. Aliskiren reduced systemic insulin resistance, hepatic steatosis, epididymal fat mass and increased gastrocnemius muscle glucose transporter type 4 levels with lower tissue angiotensin II levels in the HFD-fed mice. In addition, aliskiren lowered nuclear peroxisome proliferator-activated receptor gamma and its down-signaling molecules and increased cytochrome P450 4A14 and carnitine palmitoyltransferase 1A (CPT1a) in liver. In epididymal fat, aliskiren inhibited expressions of lipogenic genes, leading to decrease in fat mass, body weight and serum levels of leptin and free fatty acid. Notably, in the gastrocnemius muscle, aliskiren increased phosphorylation of insulin receptor substrate 1 and Akt. Based on these beneficial effects on liver, peripheral fat and skeletal muscle, aliskiren is a promising therapeutic agent for patients with NAFLD.
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining
Authors: Yu Lan , Shao Chaogang , Ye Xinghuo , Meng Yijun , Zhou Yincong , Chen Ming 
Published: January 2016

AbstractMicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA–target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.
Terahertz beat oscillation of plasmonic electrons interacting with femtosecond light pulses
Authors: Zhang Xinping , He Jianfang , Wang Yimeng , Liu Feifei 
Published: January 2016

AbstractPlasmon resonance in nanostructured metals is in essence collective oscillation of free electrons, which is driven by optical electric fields and oscillates at nearly the same frequency as the excitation photons. This is the basic physics for the currently extensively interested topics in optical metamaterials, optical switching and logic optical “circuits” with potential applications in optical communication and optical computation. We present here an interference effect between photons and plasmon electrons, which is observed as multi-cycle beat-oscillation. The beat frequency is in the range of 3~4 THz, which is equal to the difference between optical frequency of the photons and oscillation frequency of the plasmon electrons. Such beat oscillation evolves in a time scale of more than 1 ps, which is much longer than the optical pulse length, implying interaction between photons and pure damping plasmon-electrons. The discovered mechanisms might be important for exploring new approaches for THz generation.
A New Method to Jointly Estimate the Mortality Risk of Long-Term Exposure to Fine Particulate Matter and its Components
Authors: Crouse Dan L. , Philip Sajeev , van Donkelaar Aaron , Martin Randall V. , Jessiman Barry , Peters Paul A. , Weichenthal Scott , Brook Jeffrey R. , Hubbell Bryan , Burnett Richard T. 
Published: January 2016

AbstractMost studies on the association between exposure to fine particulate matter (PM2.5) and mortality have considered only total concentration of PM2.5 or individual components of PM2.5 and not the combined effects of concentration and particulate composition. We sought to develop a method to estimate the risk of death from long-term exposure to PM2.5 and the distribution of its components, namely: sulphate, nitrate, ammonium, organic mass, black carbon and mineral dust. We decomposed PM2.5 exposure into the sum of total concentration and the proportion of each component. We estimated the risk of death due to exposure using a cohort of ~2.4 million Canadians who were followed for vital status over 16 years. Modelling the concentration of PM2.5 with the distribution of the proportions of components together was a superior predictor for mortality than either total PM2.5 concentration alone, or all component concentrations modelled together. Our new approach has the advantage of characterizing the toxicity of the atmosphere in its entirety. This is required to fully understand the health benefits associated with strategies to improve air quality that may result in complex changes not only in PM2.5 concentration, but also in the distribution of particle components.
Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites
Authors: Xue Xiao-Feng , Guo Jing-Feng , Dong Yan , Hong Xiao-Yue , Shao Renfu 
Published: January 2016

AbstractThe subclass Acari (mites and ticks) comprises two super-orders: Acariformes and Parasitiformes. Most species of the Parasitiformes known retained the ancestral pattern of mitochondrial (mt) gene arrangement of arthropods and their mt tRNAs have the typical cloverleaf structure. All of the species of the Acariformes known, however, have rearranged mt genomes and truncated mt tRNAs. We sequenced the mt genomes of two species of Eriophyoidea:Phyllocoptes taishanensisandEpitrimerus sabinae. The mt genomes ofP. taishanensisandE. sabinaeare 13,475 bp and 13,531 bp, respectively, are circular and contain the 37 genes typical of animals; most mt tRNAs are highly truncated in both mites. On the other hand, these two eriophyoid mites have the least rearranged mt genomes seen in the Acariformes. Comparison between eriophyoid mites and other Aacariformes mites showed that: 1) the most recent common ancestor of Acariformes mites retained the ancestral pattern of mt gene arrangement of arthropods with slight modifications; 2) truncation of tRNAs for cysteine, phenylalanine and histidine occurred once in the most recent common ancestor of Acariformes mites whereas truncation of other tRNAs occurred multiple times; and 3) the placement of eriophyoid mites in the order Trombidiformes needs to be reviewed.
Unplanned pregnancy after ultrasound-guided percutaneous microwave ablation of uterine fibroids: A follow-up study
Authors: Bing-song Zhang , Jing Zhang , Zhi-yu Han , Chang-tao Xu , Rui-fang Xu , Xiu-mei Li , Hui Liu 
Published: January 2016

AbstractA follow-up study was performed with 169 women of childbearing age who underwent ultrasound-guided percutaneous microwave ablation (UPMWA) therapy for symptomatic uterine fibroids in the Chinese PLA General Hospital from June 2007 to December 2014. This study aimed to observe the incidence of unplanned pregnancies in these women after UPMWA treatment in order to evaluate its effect on natural conception. Ten unplanned pregnancies in nine women were occurred. Of the nine patients, six did not want the pregnancy and chose for induced abortion to end the pregnancy at an early stage. Three chose to continue with the pregnancy and gave birth to a healthy term infant delivered by cesarean section (of these three patients, two had been previously diagnosed as infertility). None of the patients had any serious obstetric complications. After UPMWA treatment for uterine fibroids, patients may conceive naturally, the impact of the procedure on fertility and pregnancy outcomes is worthy of further prospective study in larger sample.
Evolutionary mechanism of the defects in the fluoride-containing phosphate based glasses induced by gamma radiation
Authors: Wang Pengfei , He Quanlong , Lu Min , Li Weinan , Peng Bo 
Published: January 2016

AbstractIn the laser driven inertial confinement fusion (ICF) experimental target chamber, like the 3ω (351 nm) laser irradiation, the irradiation of gamma ray and X-rays, will also cause the formation and increase of various defects in the investigated series of fluoride-containing phosphate based glasses that have potential use in novel high performance color separation optics. The induced defects contribute to the increase of absorption in the UV region, which will make the UV performance of these laser glasses deteriorated. Some of the induced defects can be bleached to some extent through the subsequent thermal treatment process, resulting from the release and capture of the electrons in conduction band. Through the gamma radiation and post-heat treatment experiments, a general model of the evolutionary mechanism of the defects in these fluoride-containing phosphate based glasses was proposed.
Effects of calcitriol on random skin flap survival in rats
Authors: Zhou Kai-liang , Zhang Yi-hui , Lin Ding-sheng , Tao Xian-yao , Xu Hua-zi 
Published: January 2016

AbstractCalcitriol, a metabolite of vitamin D, is often used in osteoporosis clinics. However, the material has other bioactivities; for example, it accelerates angiogenesis, has anti-inflammatory properties and inhibits oxidative stress. We investigated the effects of calcitriol in a random skin flap rat model. “McFarlane flap” models were established in 84 male Sprague Dawley rats, divided into two groups. One group received intraperitoneal injections of calcitriol (2 μg/kg/day) whereas control rats received intraperitoneal injections of saline. The percentage flap survival area and tissue water content were measured 7 days later, which showed that calcitriol improved flap survival area and reduced tissue edema. It also increased the mean vessel density and upregulated levels of VEGF mRNA/protein, both of which promote flap angiogenesis. Moreover, it decreased leukocyte and macrophage infiltration, reduced the inflammatory proteins IL1β and IL6, increased SOD activity, decreased MDA content and upregulated the level of autophagy. Overall, our results suggest that calcitriol promotes skin flap survival by accelerating angiogenesis, having anti-inflammatory effects, reducing oxidative stress and promoting autophagy.
Genome-wide identification of calcium-dependent protein kinases in soybean and analyses of their transcriptional responses to insect herbivory and drought stress
Authors: Hettenhausen Christian , Sun Guiling , He Yanbiao , Zhuang Huifu , Sun Ting , Qi Jinfeng , Wu Jianqiang 
Published: January 2016

AbstractCalcium-dependent protein kinases (CDPKs) are plant-specific calcium sensors that play important roles in various aspects of plant physiology. Here, we investigated phylogenic relationships, chromosomal locations, gene structures and tissue-specific, herbivory- and drought-induced expression profiles of soybean (Glycine max) GmCDPKs. Fifty GmCDPK genes were identified, which phylogenetically grouped into 4 distinct clusters and distributed across 13 sub-clusters. Individual classes of GmCDPKs harbor highly conserved mRNA splicing sites and their exon numbers and lengths were consistent with the phylogenetic relationships, suggesting that at least 13 ancestral CDPK genes had emerged before the split of monocots and eudicots. Gene expression analysis indicated that several GmCDPKs were tissue-specific expressed. GmCDPKs’ transcript levels changed after wounding, exhibited specific expression patterns after simulated Spodoptera exigua feeding or soybean aphid (Aphis glycines) herbivory and were largely independent of the phytohormones jasmonic acid and salicylic acid. The most pronounced transcriptional responses were detected after drought and abscisic acid treatments with more than half of all GmCDPKs being upregulated, suggesting their important roles during abiotic stress responses in soybean. Our data provide an important foundation for further functional dissection of GmCDPKs, especially in the context of soybean-insect interactions and drought stress adaptation.
Improved Li storage performance in SnO2 nanocrystals by a synergetic doping
Authors: Wan Ning , Lu Xia , Wang Yuesheng , Zhang Weifeng , Bai Ying , Hu Yong-Sheng , Dai Sheng 
Published: January 2016

AbstractTin dioxide (SnO2) is a widely investigated lithium (Li) storage material because of its easy preparation, two-step storage mechanism and high specific capacity for lithium-ion batteries (LIBs). In this contribution, a phase-pure cobalt-doped SnO2 (Co/SnO2) and a cobalt and nitrogen co-doped SnO2 (Co-N/SnO2) nanocrystals are prepared to explore their Li storage behaviors. It is found that the morphology, specific surface area and electrochemical properties could be largely modulated in the doped and co-doped SnO2 nanocrystals. Gavalnostatic cycling results indicate that the Co-N/SnO2 electrode delivers a specific capacity as high as 716 mAh g−1 after 50 cycles and the same outstanding rate performance can be observed in subsequent cycles due to the ionic/electronic conductivity enhancement by co-doping effect. Further, microstructure observation indicates the existence of intermediate phase of Li3N with high ionic conductivity upon cycling, which probably accounts for the improvements of Co-N/SnO2 electrodes. The method of synergetic doping into SnO2 with Co and N, with which the electrochemical performances is enhanced remarkably, undoubtedly, will have an important influence on the material itself and community of LIBs as well.
Luminopsins integrate opto- and chemogenetics by using physical and biological light sources for opsin activation
Authors: Berglund Ken , Clissold Kara , Li Haofang E. , Wen Lei , Park Sung Young , Gleixner Jan , Klein Marguerita E. , Lu Dongye , Barter Joseph W. , Rossi Mark A. , Augustine George J. , Yin Henry H. , Hochgeschwender Ute 
Published: January 2016

Significance
Although conventional optogenetics utilizing microbial photosensitive channels or pumps to control activity of neurons has enabled great progress in neuroscience, reliance on delivery of light by optic fibers implanted into the brain imposes certain logistical burdens and thus limits application of optogenetics. To expand their utility, we fused optogenetic probes with luciferase that emits biological light in the presence of a substrate and showed that the activity of neurons in vitro, ex vivo, and in vivo could be controlled by biological light in addition to physical light. Such fusion proteins, termed luminopsins, could prove invaluable for experimental and clinical neuroscience.
Highly efficient delivery of functional cargoes by the synergistic effect of GAG binding motifs and cell-penetrating peptides
Authors: Dixon James E. , Osman Gizem , Morris Gavin E. , Markides Hareklea , Rotherham Michael , Bayoussef Zahia , El Haj Alicia J. , Denning Chris , Shakesheff Kevin M. 
Published: January 2016

Significance
Efficient delivery of therapeutic molecules inside cells by nontransgenic approaches is key as gene editing/correction, directed differentiation, and in vivo cell modulation/tracking are translated for regenerative medicine applications. Here we describe a peptide-based system engineered to enhance the activity of cell-penetrating peptides to achieve exceptional intracellular transduction. Glycosaminoglycan-binding enhanced transduction (GET) uses peptides that interact with cell membrane heparan sulfates and promote cell-penetrating peptide-mediated endocytosis into cells. The system is not dependent on extensive positive charge and can be tailored to deliver peptides, recombinant proteins, nucleic acids, nanoparticles, and antibodies. Importantly, this approach does not affect cell proliferation and viability and can be used to deliver a plethora of functional cargoes.
Region effects influence local tree species diversity
Authors: Ricklefs Robert E. , He Fangliang 
Published: January 2016

Significance
The number of species in local ecological assemblages is constrained by competition and other local interactions between populations. However, ecologists have not agreed on the degree to which the unique history and geography of continental regions also influence local species richness. Here, based on forest plots distributed throughout the world, we show that the species richness of forest trees varies among continental regions independently of local climate. In particular, forest plots in Europe and North America contain fewer species than expected from the statistical relationship of diversity to present-day local climate. Thus, the number of species co-occurring locally reflects, to a significant extent, region characteristics, including geographic and geologic history, that influence evolutionary diversification and regional extinction.
Cross-talk among flesh-eatingAeromonas hydrophilastrains in mixed infection leading to necrotizing fasciitis
Authors: Ponnusamy Duraisamy , Kozlova Elena V. , Sha Jian , Erova Tatiana E. , Azar Sasha R. , Fitts Eric C. , Kirtley Michelle L. , Tiner Bethany L. , Andersson Jourdan A. , Grim Christopher J. , Isom Richard P. , Hasan Nur A. , Colwell Rita R. , Chopra Ashok K. 
Published: January 2016

SignificanceNecrotizing fasciitis (NF) is a rapidly progressing fatal skin and muscle tissue lesion. We studied a human case of NF and found that the infection was caused by multiple strains ofA. hydrophila(NF1–NF4). The latter three strains constitute a clonal group, whereas NF1 is phylogenetically distinct. We tested these strains individually in a mouse intramuscular model of infection and observed NF1 to be less virulent than NF2. However, when NF1 and NF2 were mixed, NF1 exhibited more virulence and it decreased NF2 virulence. The cross-talk between NF1 and NF2 was due to the presence of ExoA toxin in NF2, ability of NF1 and NF2 to differentially modulate innate immune mechanism(s), and direct killing of NF2 by NF1.
Sildenafil in Heart Failure with Reactive Pulmonary Hypertension (Sildenafil HF) Clinical Trial (Rationale and Design)
Authors: Guglin Maya , Rajagopalan Navin , Anaya Paul , Charnigo Richard 
Published: January 2016

In this article, we present the rationale and design of the Sildenafil HF trial (ClinicalTrials.gov identifier: NCT02304705). We will randomize patients with heart failure and reactive pulmonary hypertension (pulmonary capillary wedge pressure > 15 mmHg, pulmonary vascular resistance > 3 Wood units) into two groups: the treatment group receiving sildenafil 20 mg 3 times a day and a matching placebo group. The duration of intervention will be 3 months. The primary outcome is 6‐minute walk distance. Key features of this trial include (1) that reactive pulmonary hypertension is an inclusion criterion, (2) that patients will be enrolled regardless of left ventricular ejection fraction, and (3) that clinical stability in the 3 months preceding enrollment is not required.
Characterizing the Pain Narratives of Parents of Youth With Chronic Pain
Authors: Noel Melanie , Beals-Erickson Sarah E. , Law Emily F. , Alberts Nicole M. , Palermo Tonya M. 
Published: January 2016

Objectives:
Questionnaire-based research has shown that parents exert a powerful influence on and are profoundly influenced by living with a child with chronic pain. Examination of parents’ pain narratives through an observational lens offers an alternative approach to understanding the complexity of pediatric chronic pain; however, the narratives of parents of youth with chronic pain have been largely overlooked. The present study aimed to characterize the vulnerability-based and resilience-based aspects of the pain narratives of parents of youth with chronic pain.

Methods:
Pain narratives of 46 parents were recorded during the baseline session as part of 2 clinical trials evaluating a behavioral intervention for parents of youth with chronic pain. The narratives were coded for aspects of pain-related vulnerability and resilience.

Results:
Using exploratory cluster analysis, 2 styles of parents’ pain narratives were identified. Distress narratives were characterized by more negative affect and an exclusively unresolved orientation toward the child’s diagnosis of chronic pain, whereas resilience narratives were characterized by positive affect and a predominantly resolved orientation toward the child’s diagnosis. Preliminary support for the validity of these clusters was provided through our finding of differences between clusters in parental pain catastrophizing about child pain (helplessness).

Discussion:
Findings highlight the multidimensional nature of parents’ experience of their child’s pain problem. Clinical implications in terms of assessment and treatment are discussed.