bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold-inducible RNA-binding protein causes endothelial dysfunction via activation of Nlrp3 inflammasome
Authors: Yang Weng-Lang , Sharma Archna , Wang Zhimin , Li Zhigang , Fan Jie , Wang Ping 
Published: May 2016

AbstractCold-inducible RNA-binding protein (CIRP) is a damage-associated molecular pattern (DAMP) molecule which stimulates proinflammatory cytokine release in hemorrhage and sepsis. Under these medical conditions, disruption of endothelial homeostasis and barrier integrity, typically induced by proinflammatory cytokines, is an important factor contributing to morbidity and mortality. However, the role of CIRP in causing endothelial dysfunction has not been investigated. In this study, we show that intravenous injection of recombinant murine CIRP (rmCIRP) in C57BL/6 mice causes lung injury, evidenced by vascular leakage, edema, increased leukocyte infiltration and cytokine production in the lung tissue. The CIRP-induced lung damage is accompanied with endothelial cell (EC) activation marked by upregulation of cell-surface adhesion molecules E-selectin and ICAM-1. Using in vitro primary mouse lung vascular ECs (MLVECs), we demonstrate that rmCIRP treatment directly increases the ICAM-1 protein expression and activates NAD(P)H oxidase in MLVECs. Importantly, CIRP stimulates the assembly and activation of Nlrp3 inflammasome in MLVECs accompanied with caspase-1 activation, IL-1β release and induction of proinflammatory cell death pyroptosis. Finally, our study demonstrates CIRP-induced EC pyroptosis in the lungs of C57BL/6 mice for the first time. Taken together, the released CIRP in shock can directly activate ECs and induce EC pyroptosis to cause lung injury.
Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing
Authors: Wu Linkun , Chen Jun , Wu Hongmiao , Wang Juanying , Wu Yanhong , Lin Sheng , Khan Muhammad Umar , Zhang Zhongyi , Lin Wenxiong 
Published: May 2016

AbstractUnder consecutive monoculture, the biomass and quality of Pseudostellaria heterophylla declines significantly. In this study, a three-year field experiment was conducted to identify typical growth inhibition effects caused by extended monoculturing of P. heterophylla. Deep pyrosequencing was used to examine changes in the structure and composition of soil fungal community along a three-year gradient of monoculture. The results revealed a distinct separation between the newly planted plot and the two-year, three-year monocultured plots. The Shannon and Simpson diversity indices were significantly higher in the two-year and three-year monoculture soils than in the newly planted soil. Consecutive monoculture of this plant led to a significant increase in relative abundance of Fusarium, Trichocladium and Myrothecium and Simplicillium, etc., but a significant decrease in the relative abundance of Penicillium. Quantitative PCR analysis confirmed a significant increase in Fusarium oxysporum, an agent known to cause wilt and rot disease of P. heterophylla. Furthermore, phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth of pathogenic F. oxysporum. Overall, this study demonstrated that consecutive monoculture of P. heterophylla can alter the fungal community in the rhizosphere, including enrichment of host-specific pathogenic fungi at the expense of plant-beneficial fungi.
Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change
Authors: Qian Chaoju , Yin Hengxia , Shi Yong , Zhao Jiecai , Yin Chengliang , Luo Wanyin , Dong Zhibao , Chen Guoxiong , Yan Xia , Wang Xiao-Ru , Ma Xiao-Fei 
Published: May 2016

AbstractClimate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.
Degenerate seaweed to tilted dendrite transition and their growth dynamics in directional solidification of non-axially oriented crystals: a phase-field study
Authors: Xing Hui , Dong Xianglei , Wu Hongjing , Hao Guanhua , Wang Jianyuan , Chen Changle , Jin Kexin 
Published: May 2016

AbstractWe report the results of a phase-field study of degenerate seaweed to tilted dendrite transition and their growth dynamics during directional solidification of a binary alloy. Morphological selection maps in the planes of (G, Vp) and (ε4, Vp) show that lower pulling velocity, weaker anisotropic strength and higher thermal gradient can enhance the formation of the degenerate seaweed. The tip undercooling shows oscillations in seaweed growth, but it keeps at a constant value in dendritic growth. The M-S instability on the tips and the surface tension anisotropy of the solid-liquid interface are responsible for the formation of the degenerate seaweed. It is evidenced that the place where the interfacial instability occurs determines the morphological transition. The transient transition from degenerate seaweed to tilted dendrite shows that dendrites are dynamically preferred over seaweed. For the tilted dendritic arrays with a large tilted angle, primary spacing is investigated by comparing predicted results with the classical scaling power law, and the growth direction is found to be less sensitive to the pulling velocity and the primary spacing. Furthermore, the effect of the initial interface wavelength on the morphological transition is investigated to perform the history dependence of morphological selection.
Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) α-kinase domain apoenzyme reveals a novel autoinhibited conformation
Authors: Ye Qilu , Yang Yidai , van Staalduinen Laura , Crawley Scott William , Liu Linda , Brennan Stephanie , Côté Graham P. , Jia Zongchao 
Published: May 2016

AbstractThe α-kinases are a family of a typical protein kinases present in organisms ranging from protozoa to mammals. Here we report an autoinhibited conformation for the α-kinase domain of Dictyostelium myosin-II heavy chain kinase A (MHCK-A) in which nucleotide binding to the catalytic cleft, located at the interface between an N-terminal and C-terminal lobe, is sterically blocked by the side chain of a conserved arginine residue (Arg592). Previous α-kinase structures have shown that an invariant catalytic aspartic acid residue (Asp766) is phosphorylated. Unexpectedly, in the autoinhibited conformation the phosphoryl group is transferred to the adjacent Asp663, creating an interaction network that stabilizes the autoinhibited state. The results suggest that Asp766 phosphorylation may play both catalytic and regulatory roles. The autoinhibited structure also provides the first view of a phosphothreonine residue docked into the phospho-specific allosteric binding site (Pi-pocket) in the C-lobe of the α-kinase domain.
Reproductive concessions between related and unrelated members promote eusociality in bees
Authors: Andrade Aline C. R. , Miranda Elder A. , Del Lama Marco A. , Nascimento Fábio S. 
Published: May 2016

AbstractAnimal societies exhibit remarkable variation in their breeding strategies. Individuals can maximize their fitness by either reproducing or by helping relatives. Social hymenopterans have been key taxa for the study of Hamilton’s inclusive fitness theory because the haplodiploid sex-determination system results in asymmetric relatedness among breeders producing conflict over the partitioning of reproduction. In small cooperative groups of insects, totipotent individuals may maximize their inclusive fitness by controlling reproduction despotically rather than helping their relatives. Here, we demonstrate that the dominant females of the primitively eusocial bee Euglossa melanotricha (Apidae: Euglossini) control reproduction, but concede part of the reproductive output with their related and unrelated subordinates. As expected, a dominant female capitalizes on the direct reproduction of related subordinates, according to her interests. We found that reproductive skew was positively correlated with relatedness. The concessions were highly reduced in mother-daughter and sibling nests (relatedness r ± s.d. = 0.54 ± 0.02 and 0.79 ± 0.02, respectively) but much more egalitarian in unrelated associations (r = −0.10 ± 0.01). We concluded that reproductive skew in these primitively eusocial bees is strongly related to the genetic structure of associations, and also that females are able to assess pairwise relatedness, either directly or indirectly, and use this information to mediate social contracts.
Anemia increases the mortality risk in patients with stroke: A meta-analysis of cohort studies
Authors: Li Zhanzhan , Zhou Tao , Li Yanyan , Chen Peng , Chen Lizhang 
Published: May 2016

AbstractThe impact of anemia on the outcome of patients with stroke remains inconsistent. We performed a meta-analysis of cohort studies to assess the mortality risk in stroke patients with and without anemia. Systematic searches were conducted in the PubMed, China National Knowledge Infrastructure, Web of Science and Wanfang databases to identify relevant studies from inception to November 2015. The estimated odds ratio with a 95% confidence interval was pooled. subgroup analyses and sensitivity analyses were also conducted. We used Begg’s funnel plot and Egger’s test to detect the potential publication bias. Thirteen cohort studies with a total of 19239 patients with stroke were included in this meta-analysis. The heterogeneity among studies was slight (I2 = 59.0%, P = 0.031). The results from a random-effect model suggest that anemia is associated with an increased mortality risk in patients with stroke (adjusted odds ratio = 1.39, 95% confidence interval: 1.22–1.58, P < 0.001). The subgroup analyses are consistent with the total results. This meta-analysis of 13 cohort studies finds that anemia increases the mortality risk in patients with stroke. Future studies should perform longer follow-up to confirm this finding and explore its possible mechanism.
Surface Plasmon Enhanced Photocatalysis of Au/Pt-decorated TiO2 Nanopillar Arrays
Authors: Shuang Shuang , Lv Ruitao , Xie Zheng , Zhang Zhengjun 
Published: May 2016

AbstractThe low quantum yields and lack of visible light utilization hinder the practical application of TiO2 in high-performance photocatalysis. Herein, we present a design of TiO2 nanopillar arrays (NPAs) decorated with both Au and Pt nanoparticles (NPs) directly synthesized through successive ion layer adsorption and reaction (SILAR) at room temperature. Au/Pt NPs with sizes of ~4 nm are well-dispersed on the TiO2 NPAs as evidenced by electron microscopic analyses. The present design of Au/Pt co-decoration on the TiO2 NPAs shows much higher visible and ultraviolet (UV) light absorption response, which leads to remarkably enhanced photocatalytic activities on both the dye degradation and photoelectrochemical (PEC) performance. Its photocatalytic reaction efficiency is 21 and 13 times higher than that of pure TiO2 sample under UV-vis and visible light, respectively. This great enhancement can be attributed to the synergy of electron-sink function of Pt and surface plasmon resonance (SPR) of Au NPs, which significantly improves charge separation of photoexcited TiO2. Our studies demonstrate that through rational design of composite nanostructures one can harvest visible light through the SPR effect to enhance the photocatalytic activities initiated by UV-light and thus realize more effectively utilization of the whole solar spectrum for energy conversion.
Clinical Nomogram for Predicting Survival of Esophageal Cancer Patients after Esophagectomy
Authors: Cao Jinlin , Yuan Ping , Wang Luming , Wang Yiqing , Ma Honghai , Yuan Xiaoshuai , Lv Wang , Hu Jian 
Published: May 2016

AbstractThe aim of this study was to construct an effective clinical nomogram for predicting the survival of esophageal cancer patients after esophagectomy. We identified esophageal cancer patients (n = 4,281) who underwent esophagectomy between 1988 and 2007 from the Surveillance, Epidemiology and End Results (SEER) 18 registries database. Clinically significant parameters for survival were used to construct a nomogram based on Cox regression analyses. The model was validated using bootstrap resampling and a Chinese cohort (n = 145). A total of 4,109 patients from the SEER database were included for analysis. The multivariate analyses showed that the factors of age, race, histology, tumor site, tumor size, grade and depth of invasion and the numbers of metastases and retrieved nodes were independent prognostic factors. All of these factors were selected into the nomogram. The nomogram showed a clear prognostic superiority over the seventh AJCC-TNM classification (C-index: SEER cohort, 0.716 vs 0.693, respectively; P < 0.01; Chinese cohort, 0.699 vs 0.680, respectively; P < 0.01). Calibration of the nomogram predicted the probabilities of 3- and 5-year survival, which corresponded closely with the actual survival rates. This novel prognostic model may improve clinicians’ abilities to predict individualized survival and to make treatment recommendations.
Nano-SPRi Aptasensor for the Detection of Progesterone in Buffer
Authors: Zeidan Effat , Shivaji Renuka , Henrich Vincent C. , Sandros Marinella G. 
Published: May 2016

AbstractProgesterone is a steroid hormone that plays a central role in the female reproductive processes such as ovulation and pregnancy with possible effects on other organs as well. The measurement of progesterone levels in bodily fluids can assist in early pregnancy diagnosis and can provide insight for other reproductive functions. In this work, the detection of progesterone was examined by integrating novel aptamer development with a nanoEnhanced surface plasmon resonance imaging sensor. First, we developed X-aptamers and selected them for binding to progesterone. Then, we took advantage of the multi-array feature of SPRi to develop an optimized biosensor capable of simultaneously screening the 9 X-aptamers developed to determine the binding capabilities of each aptamer. The sensor surface design conditions were further optimized for the sandwich assay, which employed nanoEnhancers (NIR-streptavidin coated quantum dots) for ultrasensitive detection of progesterone molecules. The assay designed was examined over a concentration range of 1.575 ng/mL to 126 μg/mL resulting in a limit of detection (LOD) of 1.575 ng/mL (5 nM) in phosphate buffer.
Involvement of Auxin and Brassinosteroid in Dwarfism of Autotetraploid Apple (Malus × domestica)
Authors: Ma Yue , Xue Hao , Zhang Lei , Zhang Feng , Ou Chunqing , Wang Feng , Zhang Zhihong 
Published: May 2016

AbstractThe plant height is an important trait in fruit tree. However, the molecular mechanism on dwarfism is still poorly understood. We found that colchicine-induced autotetraploid apple plants (Malus × domestica) exhibited a dwarf phenotype. The vertical length of cortical parenchyma cells was shorter in autotetraploids than in diploids, by observing paraffin sections. Hormone levels of indoleacetic acid (IAA) and brassinosteroid (BR) were significantly decreased in 3- and 5-year-old autotetraploid plants. Digital gene expression (DGE) analysis showed that the differentially expressed genes were mainly involved in IAA and BR pathways. microRNA390 was significantly upregulated according to microarray analysis. Exogenous application of IAA and BR promoted stem elongation of both apple plants grown in medium. The results show that dwarfing in autotetraploid apple plants is most likely regulated by IAA and BR. The dwarf phenotype of autotetraploid apple plants could be due to accumulation of miR390 after genome doubling, leading to upregulation of apple trans-acting short-interfering RNA 3 (MdTAS3) expression, which in turn downregulates the expression of MdARF3. Overall, this leads to partial interruption of the IAA and BR signal transduction pathway. Our study provides important insights into the molecular mechanisms underlying dwarfism in autopolyploid apple plants.
A novel polysaccharide from Sargassum integerrimum induces apoptosis in A549 cells and prevents angiogensis in vitro and in vivo
Authors: Liu Ge , Kuang Shan , Wu Shimei , Jin Weihua , Sun Chaomin 
Published: May 2016

AbstractMany polysaccharides isolated from plants have exhibited promising antitumor activities. The aim of this study is to investigate the antitumor activity of the novel polysaccharide named SPS from Sargassum integerrimum, elucidate the underlying anticancer mechanism in a human lung cancer cell line A549 and evaluate its anti-angiogenic activity both in vitro and in vivo. The results show that SPS significantly reduces A549 cells viability in a dose- and time-dependent manner via MTT method. Flow cytometry analysis indicates that SPS could induce cell apoptosis, the loss of mitochondrial membrane potential (MMP), generation of reactive oxygen species (ROS) and G2/M phase cell cycle arrest of A549 cells. Up-regulation of the expressions of P53 and Bax, down-regulation of the expression of Bcl-2 and activation of cleaved caspase-3, caspase-9 and PARP are also detected by western blotting after the treatment of SPS. In addition, SPS inhibits the proliferation, migration and cord formation of human umbilical vein endothelial cells (HUVECs) in vitro and prevents the vascular development of zebrafish embryos in vivo. Altogether, our data prove the anticancer and anti-angiogenesis properties of SPS and provide further insights into the potential pharmacological application of SPS as antitumor and anti-angiogenic agent against lung cancer.
Nanospherical arabinogalactan proteins are a key component of the high-strength adhesive secreted by English ivy
Authors: Huang Yujian , Wang Yongzhong , Tan Li , Sun Leming , Petrosino Jennifer , Cui Mei-Zhen , Hao Feng , Zhang Mingjun 
Published: May 2016

SignificanceDespite the significant progress that has been made in exploring the molecular basis for multiple adhesive events in the animal kingdom, the exceptional adhesion behaviors of climbing plants, such as English ivy, are still poorly understood. In this study, the spheroidal nanoparticles observed in the mucilage exuded by the English ivy were identified to be predominantly composed of arabinogalactan proteins (AGPs). The roles of these AGP-rich nanoparticles in favoring the generation of strong adhesion strength are elucidated. The Ca2+-driven electrostatic interactions among uronic acids within AGPs and pectin upon curing could be exploited as guidelines in the design and fabrication of novel synthetic adhesives, and the ivy-derived adhesive composite is capable of serving as a template for inspiring the development of diverse adhesive biomaterials.
Differential rhythmicity: detecting altered rhythmicity in biological data
Authors: Thaben Paul F , Westermark Pål O 
Published: May 2016

Abstract

Motivation
Biological rhythms, such as rhythms in gene expression controlled by the cell cycle or the circadian clock, are important in cell physiology. A common type of experiment compares rhythmicity in tissues or cells either kept under different conditions or having different genotypes. Such investigations provide insights into underlying mechanisms as well as functions of rhythms.

Results
We present and benchmark a set of statistical and computational methods for this type of analysis, here termed differential rhythmicity analysis. The methods detect alterations in rhythm amplitude, phase and signal to noise ratio in one set of measurements compared to another. Using these methods, we compared circadian rhythms in liver mRNA expression in mice held under two different lighting conditions: constant darkness and light-dark cycles, respectively. This analysis revealed widespread and reproducible amplitude increases in mice kept in light-dark cycles. Further analysis of the subset of differentially rhythmic transcripts implied the immune system in mediating ambient light-dark cycles to rhythmic transcriptional activities. The methods are suitable for genome- or proteome-wide studies, and provide rigorous P values against well-defined null hypotheses.

Availability and Implementation
The methods were implemented as the accompanying R software package DODR, available on CRAN.

Contact
pal-olof.westermark@charite.de

Supplementary information
Supplementary data are available at Bioinformatics online.
Focal depth measurements of the vaginal wall: a new method to noninvasively quantify vaginal wall thickness in the diagnosis and treatment of vaginal atrophy
Authors: Weber Maaike A. , Diedrich Chantal M. , Ince Can , Roovers Jan-Paul 
Published: May 2016

AbstractObjective:The aim of the study was to evaluate if vaginal focal depth measurement could be a noninvasive method to quantify vaginal wall thickness.Methods:Postmenopausal women undergoing topical estrogen therapy because of vaginal atrophy (VA) were recruited. VA was diagnosed based on the presence of symptoms and vaginal pH at least 5.5. The control group consisted of women above 40 years without VA. Focal depth measurements were performed before and after treatment using the Cytocam-Incident Dark Field device assessing the distance between the subepithelial microcirculation and the epithelial surface. Measurements were performed before and after treatment in the intervention group and at two different time points in the control group. Vaginal pH was measured. Symptoms were evaluated using the most bothersome symptom approach.Results:Eight women with VA and nine controls were included. Pretreatment median focal depth was not significantly different between both groups. Pretreatment focal depth more than doubled after a median of 7 weeks of topical estrogen treatment (80 μm [interquartile range 80-120 μm] vs 220 μm [148-248 μm],P = 0.02), whereas the measurements in the control group did not change. Pretreatment vaginal pH differed between both groups (5.5 vs 5.1, respectively,P < 0.01). Vaginal pH did not change after treatment.Conclusions:Using in vivo microscopy we introduced a new noninvasive measure of vaginal wall thickness. A significant increase in vaginal focal depth was observed in participants with VA treated with topical estrogens. This innovative measurement of vaginal wall thickness could become the preferred objective measure to evaluate treatment effect. Moreover, it has great potential for other applications in the field of urogynecology.