bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bilateral adrenal EBV-associated smooth muscle tumors in a child with a natural killer cell deficiency
Authors: Shaw Rachel K. , Issekutz Andrew C. , Fraser Robert , Schmit Pierre , Morash Barb , Monaco-Shawver Linda , Orange Jordan S. , Fernandez Conrad V. 
Published: March 2012

Abstract
EBV-associated smooth muscle tumors are found in immunocompromised patients, most commonly HIV/AIDS. We present a 12-year-old girl with the first documented case of EBV-related smooth muscle tumors in the presence of a rare classic NK cell deficiency. This sheds light on the role of NK cells in controlling EBV-related smooth muscle tumors.
Salidroside stimulates DNA repair enzyme Parp-1 activity in mouse HSC maintenance
Authors: Li Xue , Sipple Jared , Pang Qishen , Du Wei 
Published: March 2012

Abstract
Salidroside is a phenylpropanoid glycoside isolated from the medicinal plant Rhodiola rosea, which has potent antioxidant properties. Here we show that salidroside prevented the loss of hematopoietic stem cells (HSCs) in mice under oxidative stress. Quiescent HSCs were recruited into cell cycling on in vivo challenge with oxidative stress, which was blocked by salidroside. Surprisingly, salidroside does not prevent the production of reactive oxygen species but reduces hydrogen peroxide–induced DNA-strand breaks in bone marrow cells enriched for HSCs. We tested whether salidroside enhances oxidative DNA damage repair in mice deficient for 5 DNA repair pathways known to be involved in oxidative DNA damage repair; we found that salidroside activated poly(ADP-ribose)polymerase-1 (PARP-1), a component of the base excision repair pathway, in mouse bone marrow HSCs as well as primary fibroblasts and human lymphoblasts. PARP-1 activation by salidroside protects quiescent HSCs from oxidative stress–induced cycling in native animals and self-renewal defect in transplanted recipients, which was abrogated by genetic ablation or pharmacologic inhibition of PARP-1. Together, these findings suggest that activation of PARP-1 by salidroside could affect the homeostasis and function of HSCs and contribute to the antioxidant effects of salidroside.
β3-integrin is required for differentiation in OC-2 cells derived from mammalian embryonic inner ear
Authors: Brunetta Ivan , Casalotti Stefano O , Hart Ian R , Forge Andrew , Reynolds Louise E 
Published: March 2012

Abstract

Background
The mammalian inner ear contains the organ of Corti which is responsible for the conversion of sound into neuronal signals. This specialised epithelial tissue is the product of a complex developmental process where a common precursor cell type differentiates into the sound transducing hair cells and the non-innervated supporting cells. We hypothesised that integrin proteins, which are involved in cell attachment to extracellular matrix proteins and cellular signalling, play a role in the differentiation process of the precursor inner ear epithelial cells. To test our hypothesis we have utilised a cell line (OC-2) derived from E13 embryonic immortomouse inner ears. In vitro, by switching the incubation temperature from 33°C to 39°C, the OC-2 cells can be induced to differentiate and express hair cells markers, such as Myosin VIIa. The OC-2 cells are thus a useful model system for testing mechanism of hair cells differentiation.

Results
We have identified 4 integrin subunits which are expressed in OC-2 cells: α6, αv, β1 and β3. Among these, the relative level of expression of the αv, β1 and β3 subunits increased in a time dependent manner when the cells were exposed to the differentiating temperature of 39°C, most notably so for β3 which was not detectable at 33°C. Treatment of fully differentiated OC-2 cells with siRNA against the four integrin subunits reduced the expression of not only the respective integrin proteins but also of the hair cell marker Myosin VIIa. Conversely over-expression of β3 was sufficient to induce the expression of Myosin VIIa at 33°C.

Conclusions
Our data demonstrate that modulation of integrin expression is associated with the differentiation process of the OC-2 cells. This suggests that the maturation of the organ of Corti, from where OC-2 cells are derived, may also depend on changes of gene expression associated with integrin expression.
Functional interconnections of HY1 with MYC2 and HY5 in Arabidopsis seedling development
Authors: Prasad Babu Rajendra V , Kumar Selva V , Nandi Ashis , Chattopadhyay Sudip 
Published: March 2012

Abstract
Arabidopsis seedling development is controlled by many regulatory genes involved in multiple signaling pathways. The functional relationships of these genes working in multiple signaling cascades have started to be unraveled. Arabidopsis HY1/HO1 is a rate-limiting enzyme involved in biosynthesis of phytochrome chromophore. HY5 (a bZIP protein) promotes photomorphogenesis, however ZBF1/MYC2 (a bHLH protein) works as a negative regulator of photomorphogenic growth and light regulated gene expression. Further, MYC2 and HY1 have been shown to play important roles in jasmonic acid (JA) signaling pathways. Here, we show the genetic interactions of HY1 with two key transcription factor genes of light signaling, HY5 and MYC2, in Arabidopsis seedling development. Our studies reveal that although HY1 acts in an additive manner with HY5, it is epistatic to MYC2 in light-mediated seedling growth and gene expression. This study further demonstrates that HY1 additively or synergistically functions with HY5, however it works upstream to MYC2 in JA signaling pathways. Taken together, this study demonstrates the functional interrelations of HY1, MYC2 and HY5 in light and JA signaling pathways.
Polymorphic genes of detoxification and mitochondrial enzymes and risk for progressive supranuclear palsy: a case control study
Authors: Potts Lisa F , Cambon Alex C , Ross Owen A , Rademakers Rosa , Dickson Dennis W , Uitti Ryan J , Wszolek Zbigniew K , Rai Shesh N , Farrer Matthew J , Hein David W , Litvan Irene 
Published: March 2012

AbstractBackgroundThere are no known causes for progressive supranuclear palsy (PSP). Themicrotubule associated protein tau(MAPT)H1 haplotype is the major genetic factor associated with risk of PSP, with both oxidative stress and mitochondrial dysfunction also implicated. We investigated whether specific single nucleotide polymorphisms (SNPs) in genes encoding enzymes of xenobiotic detoxification, mitochondrial functioning, or oxidative stress response, includingdebrisoquine 4-hydroxylase, paraoxonase 1and2, N-acetyltransferase 1and2 (NAT2), superoxide dismutase 1and2, and PTEN-induced putative kinaseare associated with PSP.MethodsDNA from 553 autopsy-confirmed Caucasian PSP cases (266 females, 279 males; age at onset 68 ± 8 years; age at death 75 ± 8) from the Society for PSP Brain Bank and 425 clinical control samples (197 females, 226 males; age at draw 72 ± 11 years) from healthy volunteers were genotyped using Taqman PCR and the SequenomiPLEX Gold assay.ResultsThe proportion of NAT2 rapid acetylators compared to intermediate and slow acetylators was larger in cases than in controls (OR = 1.82, p < 0.05). There were no allelic or genotypic associations with PSP for any other SNPs tested with the exception ofMAPT(p < 0.001).ConclusionsOur results show that NAT2 rapid acetylator phenotype is associated with PSP, suggesting that NAT2 may be responsible for activation of a xenobiotic whose metabolite is neurotoxic. Although our results need to be further confirmed in an independent sample, NAT2 acetylation status should be considered in future genetic and epidemiological studies of PSP.
The impact of population-based disease management services for selected chronic conditions: the Costs to Australian Private Insurance - Coaching Health (CAPICHe) study protocol
Authors: Byrnes Joshua M , Goldstein Stan , Venator Benjamin , Pollicino Christine , Ng Shu-Kay , Veroff David , Bennett Christine , Scuffham Paul A 
Published: March 2012

Abstract

Background
Recent evidence from a large scale trial conducted in the United States indicates that enhancing shared decision-making and improving knowledge, self-management, and provider communication skills to at-risk patients can reduce health costs and utilisation of healthcare resources. Although this trial has provided a significant advancement in the evidence base for disease management programs it is still left for such results to be replicated and/or generalised for populations in other countries and other healthcare environments. This trial responds to the limited analyses on the effectiveness of providing chronic disease management services through telephone health coaching in Australia. The size of this trial and it's assessment of cost utility with respect to potentially preventable hospitalisations adds significantly to the body of knowledge to support policy and investment decisions in Australia as well as to the international debate regarding the effect of disease management programs on financial outcomes.

Methods
Intention to treat study applying a prospective randomised design comparing usual care with extensive outreach to encourage use of telephone health coaching for those people identified from a risk scoring algorithm as having a higher likelihood of future health costs. The trial population has been limited to people with one or more of the following selected chronic conditions: namely, low back pain, diabetes, coronary artery disease, heart failure, and chronic obstructive pulmonary disease. This trial will enrol at least 64,835 sourced from the approximately 3 million Bupa Australia private health insured members located across Australia. The primary outcome will be the total (non-maternity) cost per member as reported to the private health insurer (i.e. charged to the insurer) 12 months following entry into the trial for each person. Study recruitment will be completed in early 2012 and the results will be available in late 2013.

Discussion
If positive, CAPICHe will represent a potentially cost-effective strategy to improve health outcomes in higher risk individuals with a chronic condition, in a private health insurance setting.

Trial Registration
Australian New Zealand Clinical Trials Registry reference: ACTRN12611000580976
Inhibiting Mer receptor tyrosine kinase suppresses STAT1, SOCS1/3, and NF-κB activation and enhances inflammatory responses in lipopolysaccharide-induced acute lung injury
Authors: Lee Ye-Ji , Han Ji-Young , Byun Jiyeon , Park Hyun-Jeong , Park Eun-Mi , Chong Young Hae , Cho Min-Sun , Kang Jihee Lee 
Published: March 2012

ABSTRACTMer signaling participates in a novel inhibitory pathway in TLR activation. The purpose of the present study was to examine the role of Mer signaling in the down-regulation of TLR4 activation-driven immune responses in mice, i.t.-treated with LPS, using the specific Mer-blocking antibody. At 4 h and 24 h after LPS treatment, expression of Mer protein in alveolar macrophages and lung tissue decreased, sMer in BALF increased significantly, and Mer activation increased. Pretreatment with anti-Mer antibody did not influence the protein levels of Mer and sMer levels. Anti-Mer antibody significantly reduced LPS-induced Mer activation, phosphorylation of Akt and FAK, STAT1 activation, and expression of SOCS1 and -3. Anti-Mer antibody enhanced LPS-induced inflammatory responses, including activation of the NF-κB pathway; the production of TNF-α, IL-1β, and MIP-2 and MMP-9 activity; and accumulation of inflammatory cells and the total protein levels in BALF. These results indicate that Mer plays as an intrinsic feedback inhibitor of the TLR4- and inflammatory mediator-driven immune responses during acute lung injury.
Coordinated DNA methylation and gene expression changes in smoker alveolar macrophages: specific effects on VEGF receptor 1 expression
Authors: Philibert Robert A , Sears Rory A , Powers Linda S , Nash Emma , Bair Thomas , Gerke Alicia K , Hassan Ihab , Thomas Christie P , Gross Thomas J , Monick Martha M 
Published: March 2012

Abstract
Altered CpG DNA methylation contributes to phenotypic changes in smokerˈs alveolar macrophages.
Cigarette smoking is implicated in numerous diseases, including emphysema and lung cancer. The clinical expression of lung disease in smokers is not well explained by currently defined variations in gene expression or simple differences in smoking exposure. Alveolar macrophages play a critical role in the inflammation and remodeling of the lung parenchyma in smoking-related lung disease. Significant gene expression changes in alveolar macrophages from smokers have been identified. However, the mechanism for these changes remains unknown. One potential mechanism for smoking-altered gene expression is via changes in cytosine methylation in DNA regions proximal to gene-coding sequences. In this study, alveolar macrophage DNA from heavy smokers and never smokers was isolated and methylation status at 25,000 loci determined. We found differential methylation in genes from immune-system and inflammatory pathways. Analysis of matching gene expression data demonstrated a parallel enrichment for changes in immune-system and inflammatory pathways. A significant number of genes with smoking-altered mRNA expression had inverse changes in methylation status. One gene highlighted by this data was the FLT1, and further studies found particular up-regulation of a splice variant encoding a soluble inhibitory form of the receptor. In conclusion, chronic cigarette smoke exposure altered DNA methylation in specific gene promoter regions in human alveolar macrophages.
The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity
Authors: Razeto-Barry Pablo , Díaz Javier , Vásquez Rodrigo A 
Published: March 2012

AbstractThe general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population’s phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.
Modular TRAPP Complexes Regulate Intracellular Protein Trafficking Through Multiple Ypt/Rab GTPases in Saccharomyces cerevisiae
Authors: Zou Shenshen , Liu Yutao , Zhang Xiu Qi , Chen Yong , Ye Min , Zhu Xiaoping , Yang Shu , Lipatova Zhanna , Liang Yongheng , Segev Nava 
Published: March 2012

Abstract
Ypt/Rab are key regulators of intracellular trafficking in all eukaryotic cells. In yeast, Ypt1 is essential for endoplasmic reticulum (ER)-to-Golgi transport, whereas Ypt31/32 regulate Golgi-to-plasma membrane and endosome-to-Golgi transport. TRAPP is a multisubunit complex that acts as an activator of Ypt/Rab GTPases. Trs85 and Trs130 are two subunits specific for TRAPP III and TRAPP II, respectively. Whereas TRAPP III was shown to acts as a Ypt1 activator, it is still controversial whether TRAPP II acts as a Ypt1 or Ypt31/32 activator. Here, we use GFP-Snc1 as a tool to study transport in Ypt and TRAPP mutant cells. First, we show that expression of GFP-Snc1 in trs85Δ mutant cells results in temperature sensitivity. Second, we suggest that in ypt1ts and trs85Δ, but not in ypt31Δ/32ts and trs130ts mutant cells, GFP-Snc1 accumulates in the ER. Third, we show that overexpression of Ypt1, but not Ypt31/32, can suppress both the growth and GFP-Snc1 accumulation phenotypes of trs85Δ mutant cells. In contrast, overexpression of Ypt31, but not Ypt1, suppresses the growth and GFP-Snc1 transport phenotypes of trs130ts mutant cells. These results provide genetic support for functional grouping of Ypt1 with Trs85-containing TRAPP III and Ypt31/32 with Trs130-containing TRAPP II.
APJ1 and GRE3 Homologs Work in Concert to Allow Growth in Xylose in a Natural Saccharomyces sensu stricto Hybrid Yeast
Authors: Schwartz Katja , Wenger Jared W , Dunn Barbara , Sherlock Gavin 
Published: March 2012

Abstract
Creating Saccharomyces yeasts capable of efficient fermentation of pentoses such as xylose remains a key challenge in the production of ethanol from lignocellulosic biomass. Metabolic engineering of industrial Saccharomyces cerevisiae strains has yielded xylose-fermenting strains, but these strains have not yet achieved industrial viability due largely to xylose fermentation being prohibitively slower than that of glucose. Recently, it has been shown that naturally occurring xylose-utilizing Saccharomyces species exist. Uncovering the genetic architecture of such strains will shed further light on xylose metabolism, suggesting additional engineering approaches or possibly even enabling the development of xylose-fermenting yeasts that are not genetically modified. We previously identified a hybrid yeast strain, the genome of which is largely Saccharomyces uvarum, which has the ability to grow on xylose as the sole carbon source. To circumvent the sterility of this hybrid strain, we developed a novel method to genetically characterize its xylose-utilization phenotype, using a tetraploid intermediate, followed by bulk segregant analysis in conjunction with high-throughput sequencing. We found that this strain’s growth in xylose is governed by at least two genetic loci, within which we identified the responsible genes: one locus contains a known xylose-pathway gene, a novel homolog of the aldo-keto reductase gene GRE3, while a second locus contains a homolog of APJ1, which encodes a putative chaperone not previously connected to xylose metabolism. Our work demonstrates that the power of sequencing combined with bulk segregant analysis can also be applied to a nongenetically tractable hybrid strain that contains a complex, polygenic trait, and identifies new avenues for metabolic engineering as well as for construction of nongenetically modified xylose-fermenting strains.
Synthesis and Characterization of Novel Graphene Silicon Oxide Nanocomposite Material
Authors: Alam Tanvir E , Ram Manoj K. , Ladanov Mikhail , Alvi Farah , Mujumdar Ajit , Kumar Ashok 
Published: March 2012

ABSTRACTThe primary objective of our work is to understand the nanocomposite structure of SiO2 coated over graphene (G) nanoplatelets. An attempt has been made to synthesize G-SiO2 nanocomposite using sol-gel technique. The G-SiO2 nanocomposite is characterized using Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Raman spectroscopy, FTIR spectroscopy, and Electrochemical and Electrical measurement technique, respectively. The G-SiO2 nanocomposite reveals platelets characteristics much larger in size than the graphene nanoplatelets. The conductivity of G-SiO2 has been found to increase with an increase in the graphene ratio to SiO2 in nanocomposite material. The G-SiO2 has revealed interesting feature vibrational bands of graphene with SiO2 by varying the precursor of SiO2 with graphene moieties. The cyclic voltammetry studies have indicated the diffusion controlled system. The G-SiO2 nanocomposite shows interesting current–voltage characteristics with variation of graphene in nanocomposite. Our result is indicative of a transformable and viable G-SiO2 material for energy and electrical relay applications.
Folliculitis Induced by EGFR Inhibitors, Preventive and Curative Efficacy of Tetracyclines in the Management and Incidence Rates According to the Type of EGFR Inhibitor Administered: A Systematic Literature Review
Authors: Bachet Jean-Baptiste , Peuvrel Lucie , Bachmeyer Claude , Reguiai Ziad , Gourraud Pierre A. , Bouché Olivier , Ychou Marc , Bensadoun Rene J. , Dreno Brigitte , André Thierry 
Published: March 2012

Abstract

Introduction.
Folliculitis is the most common side effect of epidermal growth factor receptor (EGFR) inhibitors (EGFRIs). It is often apparent, altering patients' quality of life and possibly impacting compliance. Variations in terms of the treatment-related incidence and intensity have not been fully elucidated. Tetracyclines have been recommended for the prophylaxis and treatment of folliculitis but their efficacy is yet to be established.

Materials and Methods.
We carried out two systematic literature reviews. The first assessed the preventive and curative efficacy of tetracyclines. The second assessed the incidence of grade 3–4 folliculitis in the main clinical studies published.

Results.
In four randomized studies, preventive tetracycline treatment was associated with a significantly lower incidence of grade 2–3 folliculitis and a better quality of life in three of the four studies. In curative terms, tetracycline efficacy was not evaluated in any randomized study, but an improvement in grade ≥2 folliculitis was reported in case series. The frequency and severity of folliculitis seem to be greater with the antibodies than with the tyrosine kinase inhibitors. Analysis restricted to lung cancer studies showed a statistically greater incidence in terms of grade 3–4 folliculitis with cetuximab (9%) and erlotinib (8%) than with gefitinib (2%) (p &lt; .0001).

Conclusion.
Unless contraindicated, a tetracycline should be routinely prescribed prophylactically for patients treated with an EGFRI (level of evidence, B2). In curative therapy, the level of evidence for tetracycline efficacy is low (level of evidence, D). The incidence of grade 3–4 folliculitis induced by EGFRIs appears to be lower with gefitinib.