bluuebunny/crossref_metadata_2025_split huggingface dataset:
Posttranscriptional regulation of cancer traits by HuR
Authors: Abdelmohsen Kotb , Gorospe Myriam 
Published: May 2010

AbstractCancer‐related gene expression programs are strongly influenced by posttranscriptional mechanisms. The RNA‐binding protein HuR is highly abundant in many cancers. Numerous HuR‐regulated mRNAs encode proteins implicated in carcinogenesis. Here, we review the collections of HuR target mRNAs that encode proteins responsible for implementing five major cancer traits. By interacting with specific mRNA subsets, HuR enhances the levels of proteins that (1) promote cell proliferation, (2) increase cell survival, (3) elevate local angiogenesis, (4) help the cancer cell evade immune recognition, and (5) facilitate cancer cell invasion and metastasis. We propose that HuR exerts a tumorigenic function by enabling these cancer phenotypes. We discuss evidence that links HuR to several specific cancers and suggests its potential usefulness in cancer diagnosis, prognosis, and therapy. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA Turnover and Surveillance > Regulation of RNA Stability
RNA in Disease and Development > RNA in Disease
Long noncoding RNAs in mammalian cells: what, where, and why?
Authors: Chen Ling‐Ling , Carmichael Gordon G. 
Published: May 2010

AbstractNot all long, polyadenylated cellular RNAs encode polypeptides. In recent years, it has become apparent that a number of organisms express abundant amounts of transcripts that lack open reading frames or that are retained in the nucleus. Rather than accumulating silently in the cell, we now know that many of these long noncoding RNAs (lncRNAs) play important roles in nuclear architecture or in the regulation of gene expression. Here, we discuss some recent progress in our understanding of the functions of a number of important lncRNAs in mammalian cells. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA Processing > RNA Editing and Modification
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
RNA in Disease and Development > RNA in Development
Plant viruses versus RNAi: Simple pathogens reveal complex insights on plant antimicrobial defense
Authors: Qu Feng 
Published: May 2010

AbstractRNA interference (RNAi) and related processes serve as a nucleic‐acid‐mediated surveillance system conserved in almost all eukaryotic organisms. This surveillance system detects various forms of double‐stranded RNA (dsRNA) in cells and initiates a cascade of events that degrades dsRNAs into small interfering RNAs (siRNAs) or microRNAs (miRNAs). These small RNAs in turn serve as sequence‐specific guides to interfere with the function of other nucleic acids through degradation or translational repression of homologous RNAs, or modification of homologous genome segments. One of the major roles of RNAi in plants and invertebrates is antiviral defense. Conversely, viruses have also evolved to encode suppressors of RNAi (VSRs), which disrupt RNAi at various steps. Research activities focusing on the relationship between plant viruses and RNAi have been essential to our current understanding of RNAi mechanisms. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action
RNA in Disease and Development > RNA in Disease
Lessons learnt from animal models: pathophysiology of neuropathic lysosomal storage disorders
Authors: Hemsley Kim M. , Hopwood John J. 
Published: May 2010

AbstractApproximately 50 inborn errors of metabolism known as lysosomal storage disorders have been discovered to date, most of which are due to a single mutation in a gene encoding a soluble lysosomal enzyme. Consequently, inadequate enzyme activity results in the accumulation of substrates for that enzyme, invariably accompanied by a wide variety of secondary pathological changes. Many of these conditions remain untreatable, and therefore, research into pathogenic processes and potential treatment strategies is intense. A key tool for researchers in this area is the availability of clinically relevant animal models in which to study disease manifestation and evaluate therapeutic outcomes. Large numbers of both naturally occurring and genetically modified animal models of neurodegenerative lysosomal storage disorders are in existence, with spontaneous models occurring in both large domestic (e.g., cat, dog, sheep) and small (e.g., mouse) animal species. Many have undergone rigorous phenotypic characterization and are now providing us with insights into neurological disease processes. The purpose of this review is to highlight some of the major lessons learnt from these studies.
Effects of root diameter and root nitrogen concentration on in situ root respiration among different seasons and tree species
Authors: Chen Dima , Zhou Lixia , Rao Xingquan , Lin Yongbiao , Fu Shenglei 
Published: May 2010

AbstractKnowledge of root respiration is a prerequisite for a better understanding of ecosystem carbon budget and carbon allocation. However, there are not many relevant data in the literature on direct measurements of in situ root respiration by root chamber method. Furthermore, few studies have been focused on the effects of root diameter (Dr) and root nitrogen concentration (Nr) on in situ root respiration among different seasons and tree species. To address these goals, we used a simplified root‐chamber system to measure in situ root respiration rates of Acacia crassicarpa and Eucalyptus urophylla in subtropical plantations of south China. We found that the species and season variation in root respiration were affected by Dr and Nr. Also, the root respiration per unit dry mass (Rr, nmol CO2 g−1 s−1) and root respiration per unit N (Rn, nmol CO2 g N−1 s−1) were affected by Dr and Nr. The Rr, Rn, Nr and soil temperature sensitivity (Q10) of Rr for the two species significantly decreased with an increase of Dr. The Rr of the two species showed significant an inter‐seasonal and diurnal pattern, and this trend decreased with increasing Dr. Both the Rr and Q10 of the two species increased with increasing Nr. The Dr and Nr explained 54 and 52% of the observed variation in Rr for A. crassicarpa, and 65 and 70% for E. urophylla. The Rr, Nr, and Q10 of A. crassicarpa were significantly higher than those of E. urophylla. Our results indicated that root respiration was dependent on Dr and Nr, and this dependence varied with season and plant species.
Host Proteome Research in HIV Infection
Authors: Zhang Lijun , Zhang Xiaojun , Ma Qing , Zhou Honghao 
Published: May 2010

Abstract
Proteomics has been widely used in the last few years to look for new biomarkers and decipher the mechanism of HIV–host interaction. Herein, we review the recent developments of HIV/AIDS proteomic research, including the samples used in HIV/AIDS related research, the technologies used for proteomic study, the diagnosis biomarkers of HIV-associated disease especially HIV-associated neurocognitive impairment, the mechanisms of HIV–host interaction, HIV-associated dementia, substance abuse, and so on. In the end of this review, we also give some prospects about the limitation and future improvement of HIV/AIDS proteomic research.
Characterization of Evolutionarily Conserved MicroRNAs in Amphioxus
Authors: Wang Lei , Jiang Lan , Hu Songnian , Wang Yejun 
Published: May 2010

Abstract
Amphioxus is an extant species closest to the ancestry of vertebrates. Observation of microRNA (miRNA) distribution of amphioxus would lend some hints for evolutionary research of vertebrates. In this study, using the publicly available scaffold data of the Florida amphioxus (Branchiostoma floridae) genome, we screened and characterized homologs of miRNAs that had been identified in other species. In total, 68 pieces of such homologs were obtained and classified into 33 families. Most of these miRNAs were distributed as clusters in genome. Inter-species comparison showed that many miRNAs, which had been thought as vertebrate- or mammal-specific before, were also present in amphioxus, while some miRNAs that had been considered as protostome-specific before also existed in amphioxus. Compared with ciona, amphioxus had an apparent miRNA gene expansion, but phylogenetic analysis showed that the duplicated miRNAs or clusters of amphioxus had a higher homology level than those duplicated ones in vertebrates.
In Silico Analysis of Sequential, Structural and Functional Diversity of Wheat Cystatins and Its Implication in Plant Defense
Authors: Dutt Shriparna , Singh V.K. , Marla Soma S. , Kumar Anil 
Published: May 2010

Abstract
Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases. Cereal crops like wheat are continuously threatened by a multitude of pathogens, therefore cystatins offer to play a pivotal role in deciding the plant response. In order to study the need of having diverse specificities and activities of various cystatins, we conducted comparative analysis of six wheat cystatins (WCs) with twelve rice, seven barley, one sorghum and ten corn cystatin sequences employing different bioinformatics tools. The obtained results identified highly conserved signature sequences in all the cystatins considered. Several other motifs were also identified, based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering. Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins. Protein-protein interaction of WCs with papain supported the notion that functional diversity is a consequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs. Thus there is a significant conservation at the sequential and structural levels; however, concomitant variations maintain the functional diversity in this protein family, which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.
Quality Assessment of Transcriptome Data Using Intrinsic Statistical Properties
Authors: Brysbaert Guillaume , Pellay François-Xavier , Noth Sebastian , Benecke Arndt 
Published: May 2010

Abstract
In view of potential application to biomedical diagnosis, tight transcriptome data quality control is compulsory. Usually, quality control is achieved using labeling and hybridization controls added at different stages throughout the processing of the biologic RNA samples. These control measures, however, only reflect the performance of the individual technical manipulations during the entire process and have no bearing as to the continued integrity of the RNA sample itself. Here we demonstrate that intrinsic statistical properties of the resulting transcriptome data signal and signal-variance distributions and their invariance can be identified independently of the animal species studied and the labeling protocol used. From these invariant properties we have developed a data model, the parameters of which can be estimated from individual experiments and used to compute relative quality measures based on similarity with large reference datasets. These quality measures add supplementary, non-redundant information to standard quality control estimates based on spike-in and hybridization controls, and are exploitable in data analysis. A software application for analyzing datasets as well as a reference dataset for AB1700 arrays are provided. They should allow AB1700 users to easily integrate this method into their analysis pipeline, and might instigate similar developments for other transcriptome platforms.
A Modified Enrichment Method to Construct Microsatellite Library from Plateau Pika Genome (Ochotona Curzoniae)
Authors: Geng Jianing , Li Kexin , Zhang Yanming , Hu Songnian 
Published: May 2010

Abstract
A microsatellite-enriched library of plateau pika (Ochotona curzoniae) was constructed according to the strong affinity between biotin and streptavidin. Firstly, genomic DNA was fragmented by ultrasonication, which is a major improvement over traditional methods. Linker-ligated DNA fragments were hybridized with biotinylated microsatellite probes, and then were subjected to streptavidin-coated magnetic beads. PCR amplification was performed to obtain double-stranded DNA fragments containing microsatellites. Ligation and transformation were carried out by using the pGEM-T Vector System I and Escherichia coli DH10B competent cells. Sequencing results showed that 80.2% of clones contained microsatellite repeat motif. Several modifications make this protocol time-efficient and technically easier than the traditional ones; particularly, composition and relative abundance of microsatellite repeats in plateau pika genome were truly represented through the optimized PCR conditions. This method has also been successfully applied to construct microsatellite-enriched genomic libraries of Chinese hamster (Cricetulus griseus) and small abalone [Haliotis diversicolor (Reeve)] with high rates of positive clones, demonstrating its feasibility and stability.
Evolution of interspecific variation in size of attachment structures in the large tapeworm genusAcanthobothrium(Tetraphyllidea: Onchobothriidae)
Authors: RANDHAWA H. S. , POULIN R. 
Published: May 2010

SUMMARYParasites have evolved a myriad of attachment structures closely adapted to their hosts and sites of attachment. Here, using members of the genusAcanthobothriumvan Beneden, 1850 (Cestoda: Tetraphyllidea: Onchobothriidae), we (i) examined the influence of host body size and phylogeny, in addition to morphological features of these tapeworms, on the size of 3 structures used in attachment (bothridia, accessory suckers and hooks) by means of general linear models and phylogenetic-independent contrasts methods, and (ii) quantified the scaling exponents of relationships between size of attachment structures and tapeworm body size. Our results indicate that there exists a positive relationship, albeit not directly proportional, between size of attachment structures andAcanthobothriumspp. body size, and hook size and size of bothridia and accessory suckers. These results suggest that the resource investment in whole-body growth is greater than that in attachment structures, and that a greater investment in development of bothridia and accessory suckers is required to maintain an equivalent functional efficacy to hooks. In addition, host body size also influences, though less markedly, the size of attachment structures inAcanthobothriumspp. independently of parasite size itself.Acanthobothriumspecies have evolved a generalized mode of attachment that is successful in maintaining their position on various intestinal mucosal topographies across a variety of hosts exploiting different food resources.
Efficacy of the sequential integration of psychotherapy and pharmacotherapy in major depressive disorder: a preliminary meta-analysis
Authors: Guidi J. , Fava G. A. , Fava M. , Papakostas G. I. 
Published: May 2010

BackgroundPrevention of relapse and recurrence represents an important task in the successful treatment of major depressive disorder (MDD). The aim of this meta-analysis was to examine the efficacy of the sequential integration of psychotherapy and pharmacotherapy in reducing the risk of relapse and recurrence in MDD.MethodKeyword searches were conducted in Medline, EMBASE, PsycINFO and the Cochrane Library from inception of each database to December 2008. Randomized controlled trials examining the efficacy of the administration of psychotherapy after successful response to acute-phase pharmacotherapy in the treatment of adults with MDD were considered for inclusion in the meta-analysis.ResultsEight high-quality studies with 442 patients in a sequential treatment arm and 433 in a control treatment arm were included. The pooled risk ratio (RR) for relapse/recurrence was 0.797 [95% confidence interval (CI) 0.659–0.964] according to the random-effects model, suggesting a relative advantage in preventing relapse/recurrence for the sequential administration of treatments compared with control conditions. Performing subgroup analyses, we found a trend favoring psychotherapy during continuation of antidepressant drugs compared to antidepressants or treatment as usual (RR 0.842, 95% CI 0.674–1.051). Patients randomized to psychotherapy while antidepressants were discontinued were significantly less likely to experience relapse/recurrence compared to controls (RR 0.650, 95% CI 0.463–0.912).ConclusionsWe found evidence that the sequential integration of psychotherapy and pharmacotherapy is a viable strategy for preventing relapse and recurrence in MDD. In addition, our findings suggest that discontinuation of antidepressant drugs may be feasible when psychotherapy is provided.
Controlled cross-over study in normal subjects of naloxone-preceding-lactate infusions; respiratory and subjective responses: relationship to endogenous opioid system, suffocation false alarm theory and childhood parental loss
Authors: Preter M. , Lee S. H. , Petkova E. , Vannucci M. , Kim S. , Klein D. F. 
Published: May 2010

BackgroundThe expanded suffocation false alarm theory (SFA) hypothesizes that dysfunction in endogenous opioidergic regulation increases sensitivity to CO2, separation distress and panic attacks. In panic disorder (PD) patients, both spontaneous clinical panics and lactate-induced panics markedly increase tidal volume (TV), whereas normals have a lesser effect, possibly due to their intact endogenous opioid system. We hypothesized that impairing the opioidergic system by naloxone could make normal controls parallel PD patients' response when lactate challenged. Whether actual separations and losses during childhood (childhood parental loss, CPL) affected naloxone-induced respiratory contrasts was explored. Subjective panic-like symptoms were analyzed although pilot work indicated that the subjective aspect of anxious panic was not well modeled by this specific protocol.MethodRandomized cross-over sequences of intravenous naloxone (2 mg/kg) followed by lactate (10 mg/kg), or saline followed by lactate, were given to 25 volunteers. Respiratory physiology was objectively recorded by the LifeShirt. Subjective symptomatology was also recorded.ResultsImpairment of the endogenous opioid system by naloxone accentuates TV and symptomatic response to lactate. This interaction is substantially lessened by CPL.ConclusionsOpioidergic dysregulation may underlie respiratory pathophysiology and suffocation sensitivity in PD. Comparing specific anti-panic medications with ineffective anti-panic agents (e.g. propranolol) can test the specificity of the naloxone+lactate model. A screen for putative anti-panic agents and a new pharmacotherapeutic approach are suggested. Heuristically, the experimental unveiling of the endogenous opioid system impairing effects of CPL and separation in normal adults opens a new experimental, investigatory area.
The associations of high levels of C-reactive protein with depression and myocardial infarction in 9258 women and men from the HUNT population study
Authors: Bjerkeset O. , Romild U. , Smith G. Davey , Hveem K. 
Published: May 2010

BackgroundElevated levels of circulating C-reactive protein (CRP) have been associated with coronary heart disease and, in some studies, depression. Most studies have been of populations selected by age and/or gender. We investigate these associations with depression, myocardial infarction (MI), or both, in a large general population sample.MethodA cross-sectional population study of 9258 women and men aged ⩾20 years. The study included clinical examination, self-report of MI and depression and factors known to confound their associations. The Hospital Anxiety and Depression Scale was used to assess severity of depressive symptoms. Elevated high sensitive-CRP was defined as values >2.2 mg/l.ResultsThe association of elevated CRP with depression was attenuated towards the null [from odds ratio (OR) 1.28, p=0.001 to OR 1.08, p=0.388] following extensive adjustment, while associations with MI (adjusted OR 1.42, p=0.032) and co-morbid MI and depression (adjusted OR 2.66, p=0.003) persisted. Confounders associated with elevated CRP levels were smoking (OR 1.66; p<0.001), chronic physical illness (OR 1.34, p<0.001), BMI ⩾30 (OR 1.13, p<0.001), employment (OR 0.70, p<0.001) and high coffee consumption (OR 0.83, p=0.017). Interaction tests indicated a lower effect of old age (OR 0.54, p<0.001) and smoking (OR 0.63, p<0.001) on elevated CRP levels in women compared with men.ConclusionsCRP levels were raised in those with MI and co-morbid MI and depression; the positive association with depression was explained by confounding factors. We found new evidence that might help understand gender-specific patterns. Future studies should explore the neurobiological mechanisms underpinning these interrelations and their relevance for treatment of these conditions.
The dynamics of development: Challenges for Bayesian rationality
Authors: Straubinger Nils , Cokely Edward T. , Stevens Jeffrey R. 
Published: May 2010

AbstractOaksford & Chater (O&C) focus on patterns of typical adult reasoning from a probabilistic perspective. We discuss implications of extending the probabilistic approach to lifespan development, considering the role of working memory, strategy use, and expertise. Explaining variations in human reasoning poses a challenge to Bayesian rational analysis, as it requires integrating knowledge about cognitive processes.
VICTORIAN COSMOPOLITANISM, INTERRUPTED
Authors: Robbins Bruce 
Published: May 2010

Readers ofMiddlemarch(1871–1872) willremember the moment when Brooke's bid to win a seat in Parliament abruptly ends, in the middle of the Reform Bill campaign and in the middle of a speech. He tells the crowd how happy he is to be there. He tells the crowd he is a “close neighbor” of theirs. Then he says the following:“I've always gone a good deal into public questions – machinery, now, and machine-breaking – you're many of you concerned with machinery, and I've been going into that lately. It won't do, you know, breaking machines: everything must go on – trade, manufactures, commerce, interchange of staples – that kind of thing – since Adam Smith that must go on. We must look all over the globe: – ‘Observation with extensive view,’ must look everywhere, ‘from China to Peru,’ as somebody says – Johnson, I think, ‘The Rambler,’ you know. That's what I have done up to a certain point – not as far as Peru; but I've not always stayed at home – I saw it wouldn't do. I've been in the Levant, where some of your Middlemarch goods go – and then, again, in the Baltic. The Baltic, now.” (Eliot,Middlemarch349; Book 5, ch. 51)It's when he passes from the Levant to the Baltic that Brooke is interrupted by a laugh-creating echo from the crowd, an echo which, “by the time it said, ‘The Baltic, now'” (350; Book 5, ch. 51), has become fatal.