bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of the functional microRNA–mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression
Authors: Li Yongsheng , Xu Juan , Chen Hong , Bai Jing , Li Shengli , Zhao Zheng , Shao Tingting , Jiang Tao , Ren Huan , Kang Chunsheng , Li Xia 
Published: November 2013

Abstract
Glioma is the most common and fatal primary brain tumour with poor prognosis; however, the functional roles of miRNAs in glioma malignant progression are insufficiently understood. Here, we used an integrated approach to identify miRNA functional targets during glioma malignant progression by combining the paired expression profiles of miRNAs and mRNAs across 160 Chinese glioma patients, and further constructed the functional miRNA–mRNA regulatory network. As a result, most tumour-suppressive miRNAs in glioma progression were newly discovered, whose functions were widely involved in gliomagenesis. Moreover, three miRNA signatures, with different combinations of hub miRNAs (regulations≥30) were constructed, which could independently predict the survival of patients with all gliomas, high-grade glioma and glioblastoma. Our network-based method increased the ability to identify the prognostic biomarkers, when compared with the traditional method and random conditions. Hsa-miR-524-5p and hsa-miR-628-5p, shared by these three signatures, acted as protective factors and their expression decreased gradually during glioma progression. Functional analysis of these miRNA signatures highlighted their critical roles in cell cycle and cell proliferation in glioblastoma malignant progression, especially hsa-miR-524-5p and hsa-miR-628-5p exhibited dominant regulatory activities. Therefore, network-based biomarkers are expected to be more effective and provide deep insights into the molecular mechanism of glioma malignant progression.
Energetic adjustments in freely breeding‐fasting king penguins: does colony density matter?
Authors: Viblanc Vincent A. , Saraux Claire , Malosse Nelly , Groscolas René 
Published: November 2013

Summary

For seabirds that forage at sea but breed while fasting on land, successful reproduction depends on the effective management of energy stores. Additionally, breeding often means aggregating in dense colonies where social stress may affect energy budgets.

Male king penguins (Aptenodytes patagonicus) fast for remarkably long periods (up to 1·5 months) while courting and incubating ashore. Although their fasting capacities have been well investigated in captivity, we still know very little about the energetics of freely breeding birds.

We monitored heart rate (HR, a proxy to energy expenditure), body temperature and physical activity of male king penguins during their courtship and first incubation shift in a colony of some 24 000 freely breeding pairs. Males were breeding either under low but increasing colony density (early breeders) or at high and stable density (late breeders).

In early breeders, daily mean and resting HR decreased during courtship but increased again 3 days before egg laying and during incubation. In late breeders, HR remained stable throughout this same breeding period. Interestingly, the daily increase in resting HR we observed in early breeders was strongly associated with a marked increase in colony density over time. This finding remained significant even after controlling for climate effects.

In both early and late breeders, courtship and incubation were associated with a progressive decrease in physical activity, whereas core body temperature remained unchanged.

We discuss the roles of decreased physical activity and thermoregulatory strategies in sustaining the long courtship–incubation fast of male king penguins. We also draw attention to a potential role of conspecific density in affecting the energetics of breeding‐fasting seabirds, that is, a potential energy cost to coloniality.
Non‐native acylated homoserine lactones reveal that LuxIR quorum sensing promotes symbiont stability
Authors: Studer Sarah V. , Schwartzman Julia A. , Ho Jessica S. , Geske Grant D. , Blackwell Helen E. , Ruby Edward G. 
Published: November 2013

SummaryQuorum sensing, a group behaviour coordinated by a diffusible pheromone signal and a cognate receptor, is typical of bacteria that form symbioses with plants and animals. LuxIR‐type N‐acyl L‐homoserine (AHL) quorum sensing is common in Gram‐negative Proteobacteria, and many members of this group have additional quorum‐sensing networks. The bioluminescent symbiont Vibrio fischeri encodes two AHL signal synthases: AinS and LuxI. AinS‐dependent quorum sensing converges with LuxI‐dependent quorum sensing at the LuxR regulatory element. Both AinS‐ and LuxI‐mediated signalling are required for efficient and persistent colonization of the squid host, Euprymna scolopes. The basis of the mutualism is symbiont bioluminescence, which is regulated by both LuxI‐ and AinS‐dependent quorum sensing, and is essential for maintaining a colonization of the host. Here, we used chemical and genetic approaches to probe the dynamics of LuxI‐ and AinS‐mediated regulation of bioluminescence during symbiosis. We demonstrate that both native AHLs and non‐native AHL analogues can be used to non‐invasively and specifically modulate induction of symbiotic bioluminescence via LuxI‐dependent quorum sensing. Our data suggest that the first day of colonization, during which symbiont bioluminescence is induced by LuxIR, is a critical period that determines the stability of the V. fischeri population once symbiosis is established.
HmsC, a periplasmic protein, controls biofilm formation via repression of HmsD, a diguanylate cyclase in Yersinia pestis
Authors: Ren Gai‐Xian , Yan Hai‐Qin , Zhu Hui , Guo Xiao‐Peng , Sun Yi‐Cheng 
Published: November 2013

SummaryYersinia pestis, the cause of plague, forms a biofilm in the foregut of its flea vector to enhance transmission. Biofilm formation in Y. pestis is controlled by the intracellular levels of the second messenger molecule cyclic diguanylate (c‐di‐GMP). HmsT and Y3730, the two diguanylate cyclases (DGC) in Y. pestis, are responsible for the synthesis of c‐di‐GMP. Y3730, which we name here as HmsD, has little effect on in vitro biofilms, but has a major effect on biofilm formation in the flea. The mechanism by which HmsD plays differential roles in vivo and in vitro is not understood. In this study, we show that hmsD is part of a three‐gene operon (y3729‐31), which we designate as hmsCDE. Deletion of hmsC resulted in increased, hmsD‐dependent biofilm formation, while deletion or overexpression of hmsE did not affect biofilm formation. Localization experiments suggest that HmsC resides in the periplasmic space. In addition, we provide evidence that HmsC might interact directly with the periplasmic domain of HmsD and cause the proteolysis of HmsD. We propose that HmsC senses the environmental signals, which in turn regulates HmsD, and controls the c‐di‐GMP synthesis and biofilm formation in Y. pestis.
Careful science? Bodywork and care practices in randomised clinical trials
Authors: Jespersen Astrid P. , Bønnelycke Julie , Eriksen Hanne H. 
Published: November 2013

AbstractConcern about obesity has prompted numerous public health campaigns that urge people to be more physically active. The campaigns often include normative statements and attempt to impose restrictions on individuals' lives without considering the complexities of daily life. We suggest that broadening the focus to reflect everyday practices would foster better targeted public health campaigns. This article is based on our participation inFINE, a multidisciplinary Danish research project. The core methodology ofFINEwas a randomised controlled trial in which 61 moderately overweight men were put into different exercise groups. In this article we analyse the scientific work of the trial as representing entangled processes of bodywork, where data are extracted and objectified bodies are manipulated and care practices address the emotional, social and mundane aspects of the participants' everyday lives. Care practices are an inherent part of producing scientific facts but they are removed from the recognised results of scientific practice and thus from common public health recommendations. However, knowledge about the strategic use of care practices in lifestyle interventions is important for public health initiatives and future efforts should incorporate this aspect.
The role of thiopurine metabolites in inflammatory bowel disease and rheumatological disorders
Authors: Friedman Antony B. , Sparrow Miles P. , Gibson Peter R. 
Published: November 2013

AbstractThiopurines have been a cornerstone of medical management of patients with inflammatory bowel disease (IBD) and many rheumatological disorders. The thiopurines are metabolized to their end products, 6‐methymercaptopurine (6MMP) and the 6‐thioguanine nucleotides (6TGN), with 6TGN being responsible for thiopurine efficacy by causing apoptosis and preventing activation and proliferation of T‐lymphocytes. In IBD, conventional weight‐based dosing with thiopurines leads to an inadequate response in many patients. Utilizing measurement of these metabolites and then employing dose optimization strategies has led to markedly improved outcomes in IBD. Switching between thiopurines as well as the addition of low‐dose allopurinol can overcome adverse events and elevate 6TGN levels into the therapeutic window. There is a paucity of data on thiopurine metabolites in rheumatological diseases and further research is required.
Stability of soil microbial structure and activity depends on microbial diversity
Authors: Tardy Vincent , Mathieu Olivier , Lévêque Jean , Terrat Sébastien , Chabbi Abad , Lemanceau Philippe , Ranjard Lionel , Maron Pierre‐Alain 
Published: November 2013

SummaryDespite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species‐rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current ‘global changes’ context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.
Sociable robots, jazz music, and divination: Contingency as a cultural resource for negotiating problems of intentionality
Authors: WILF EITAN 
Published: November 2013

ABSTRACTIn practices that range from mechanical divination in Central Africa to gamelike interactions among jazz students and the development of a jazz‐improvising humanoid robot marimba player in the United States, contextually meaningful contingency is widely used as a cultural resource for negotiating problems of intentionality. Whereas anthropologists have been concerned with the use of contingency mostly as a cultural resource for increasing predictability of intentions in conflictual situations, I highlight contexts pervaded by modern normative ideals of creativity in which predictability of intentions constitutes a problem, for which contextually meaningful contingency is used as a solution.
Senses of care: Embodying inequality and sustaining personhood in the home care of older adults in Chicago
Authors: BUCH ELANA D. 
Published: November 2013

ABSTRACTIn paid home care—one of the fastest‐growing occupations in the United States—low‐wage workers help elderly clients living in their own homes remain independent by embodying and then reproducing the elders’ lifetimes of experience. Exploring the bodily and moral consequences of everyday home care practices in Chicago, I show that in this context, sustaining independent personhood depended on and intensified unequal social relations. To sustain clients’ personhood, workers developed a deeply embodied empathy that enabled them to imagine and re‐create the elders’ social and sensory worlds. Home care practices involved unreciprocated circulations of bodily experience that led some workers to feel that the needs and preferences of their clients took priority over their own comfort and well‐being. Care workers’ bodily practices thus became one way in which social hierarchies shaped individual subjectivities and came to seem morally legitimate.
Religious cosmopolitanisms: Media, transnational Santería, and travel between the United States and Cuba
Authors: BELISO‐DE JESUS AISHA 
Published: November 2013

ABSTRACTSantería religious travel and media circulations between Cuba and the United States have created new multilateral transnational linkages since the mid‐1990s. U.S.‐based Santería travelers and the Cuban priests who engage with them draw on global–local theoretical models in their interactions, in which video recording of rituals, a putatively prohibited practice in Santería, is becoming increasingly common. I suggest that ontological formations are shifting understandings and uses of religious media. Videos are used as sources of ritual knowledge and as part of rituals themselves and are thought of as ways to virtually and spiritually “travel.” I show how U.S. and Cuban practitioners draw on shared but uneven “religious cosmopolitanisms,” whereby they reconfigure notions of “mobility” through travel‐by‐video and infuse transnational experiences with new spiritual–religious meanings.
The hybrid state: Crime and citizenship in urban Jamaica
Authors: JAFFE RIVKE 
Published: November 2013

ABSTRACTIn inner‐city neighborhoods in Kingston, Jamaica, criminal “dons” have taken on a range of governmental functions. While such criminal actors have sometimes been imagined as heading “parallel states,” I argue that they are part of a hybrid state, an emergent political formation in which multiple governmental actors—in this case, criminal organizations, politicians, police, and bureaucrats—are entangled in a relationship of collusion and divestment, sharing control over urban spaces and populations. Extending recent scholarship on variegated sovereignty and neoliberal shifts in governance, I consider the implications of this diversification of governmental actors for the ways that citizenship is experienced and enacted. The hybrid state both produces and relies on distinct political subjectivities. It is accompanied by a reconfigured, hybrid citizenship, in which multiple practices and narratives related to rule and belonging, to rights and responsibilities, are negotiated by a range of actors.
Omnibus Risk Assessment via Accelerated Failure Time Kernel Machine Modeling
Authors: Sinnott Jennifer A. , Cai Tianxi 
Published: November 2013

Summary
Integrating genomic information with traditional clinical risk factors to improve the prediction of disease outcomes could profoundly change the practice of medicine. However, the large number of potential markers and possible complexity of the relationship between markers and disease make it difficult to construct accurate risk prediction models. Standard approaches for identifying important markers often rely on marginal associations or linearity assumptions and may not capture non-linear or interactive effects. In recent years, much work has been done to group genes into pathways and networks. Integrating such biological knowledge into statistical learning could potentially improve model interpretability and reliability. One effective approach is to employ a kernel machine (KM) framework, which can capture nonlinear effects if nonlinear kernels are used (Scholkopf and Smola, 2002; Liu et al., 2007, 2008). For survival outcomes, KM regression modeling and testing procedures have been derived under a proportional hazards (PH) assumption (Li and Luan, 2003; Cai, Tonini, and Lin, 2011). In this article, we derive testing and prediction methods for KM regression under the accelerated failure time (AFT) model, a useful alternative to the PH model. We approximate the null distribution of our test statistic using resampling procedures. When multiple kernels are of potential interest, it may be unclear in advance which kernel to use for testing and estimation. We propose a robust Omnibus Test that combines information across kernels, and an approach for selecting the best kernel for estimation. The methods are illustrated with an application in breast cancer.
Bayesian Latent-Class Mixed-Effect Hybrid Models for Dyadic Longitudinal Data with Non-Ignorable Dropouts
Authors: Ahn Jaeil , Liu Suyu , Wang Wenyi , Yuan Ying 
Published: November 2013

SummaryThe analysis of longitudinal dyadic data is challenging due to the complicated correlations within and between dyads, as well as possibly non-ignorable dropouts. Based on a mixed-effects hybrid model, we propose an approach to analyze longitudinal dyadic data with non-ignorable dropouts. We factorize the joint distribution of the measurement and dropout processes into three components: the marginal distribution of random effects, the conditional distribution of the dropout process given the random effects, and the conditional distribution of the measurement process given the random effects and missing data patterns. We model the conditional dropout process using a discrete survival model, and the conditional measurement process using a latent-class pattern-mixture model. These models account for the dyadic interdependence using the “actor” and “partner” effects and dyad-specific random effects. We use the latent-dropout-class approach to address the problem of a large number of missing data patterns caused by the dyadic data structure. We evaluate the performance of the proposed method using a simulation study, and apply our method to a longitudinal dyadic data set that arose from a prostate cancer trial.
Methyl jasmonate sensitizes human bladder cancer cells to gambogic acid‐induced apoptosis through down‐regulation of EZH2 expression by miR‐101
Authors: Wang Yongjun , Xiang Wei , Wang Miao , Huang Tao , Xiao Xingyuan , Wang Liang , Tao Dan , Dong Liyun , Zeng Fuqing , Jiang Guosong 
Published: November 2013

Background and PurposeGambogic acid (GA) and methyl jasmonate (MJ) are increasingly being recognized as novel natural anticancer compounds. Here, we investigated the antitumour effects of GA in combination with MJ on human bladder cancer cells.Experimental ApproachCell viability was detected by cell counting kit‐8 assay. Cell apoptosis was assessed by Hoechst 33258 staining and flow cytometry. Protein levels were determined by immunoblotting and expressions of mRNA and miRNAs by RT‐PCR. Differential expressions of a group of downstream genes were identified using microarray analysis.Key ResultsMJ significantly sensitized bladder cancer cells to GA‐induced growth inhibition and apoptosis while sparing normal fibroblasts. MJ enhanced GA‐induced activation of caspase‐3 and caspase‐9, and down‐regulated the expression of XIAP. Furthermore, treatment of bladder cancer cells with a combination of GA and MJ induced synergistic inhibition of the enhancer of zeste homologue 2 (EZH2) expression, whereas miR‐101 expression was up‐regulated. Conversely, knockdown of miR‐101 restored this decreased expression of EZH2 and suppressed the inhibitory effect of GA and MJ on the growth of bladder cancer cells. Microarray analysis showed that genes closely associated with bladder cancer development were significantly down‐regulated by GA and MJ. In a s.c. xenograft mouse model of human bladder carcinoma, the combination of GA and MJ exerted an increased antitumour effect compared with GA alone.Conclusion and ImplicationsMJ sensitizes bladder cancer cells to GA‐induced apoptosis by down‐regulating the expression of EZH2 induced by miR‐101. Thus, the combination of selective anti‐cancer agents MJ and GA could provide a novel strategy for treating human bladder cancer.
TRP channels in lower urinary tract dysfunction
Authors: Franken J , Uvin P , De Ridder D , Voets T 
Published: November 2013

Lower urinary tract dysfunction (LUTd) represents a major healthcare problem. Although it is mostly not lethal, associated social disturbance, medical costs, loss of productivity and especially diminished quality of life should not be underestimated. Although more than 15% of people suffer from a form of LUTd to some extent, pathophysiology often remains obscure. In the past 20 years, transient receptor potential (TRP) channels have become increasingly important in this field of research. These intriguing ion channels are believed to be the main molecular sensors that generate bladder sensation. Therefore, they are intensely pursued as new drug targets for both curative and symptomatic treatment of different forms of LUTd. TRPV1 was the first of its class to be investigated. Actually, even before this channel was cloned, it had already been targeted in the bladder, with clinical trials of intravesical capsaicin instillations. Several other polymodally gated TRP channels, particularly TRPM8, TRPA1 and TRPV4, also appear to play a prominent role in bladder (patho)physiology. With this review, we provide a brief overview of current knowledge on the role of these TRP channels in LUTd and their potential as molecular targets for treatment.Linked ArticlesThis article is part of a themed section on the pharmacology of TRP channels. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue‐10