bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of α-tocopherol on oxidative damage and serum levels of Clara cell protein 16 in aspiration pneumonitis induced by bile acids
Authors: Alaçam H , Karlı R , Alıcı Ö , Avcı B , Güzel A , Kozan A , Mertoğlu C , Murat N , Şalış O , Güzel A , Şahin M 
Published: September 2012

Our aim in this study is to examine the effects of α-tocopherol (AT) on rats with aspiration pneumonitis induced with bile acids (BAs). The animals were divided in to four groups, namely saline group ( n = 7), saline + AT group ( n = 7), BA group ( n = 7), and BA + AT group ( n = 7). Saline and BA groups aspirated intratracheally with 1 ml/kg saline and 1 ml/kg bile acids, respectively. AT was given at 20 mg/kg/day dosage for 7 days to the groups. AT group was given 20 mg/kg/day AT for 7 days. Malondialdehyde (MDA), Clara cell protein 16 (CC-16), catalase (CAT), superoxide dismutase (SOD), as well as peribronchial inflammatory cell infiltration, alveolar septal infiltration, alveolar edema, alveolar exudate, alveolar histiocytes, and necrosis were evaluated. The CAT activity of the BA group was significantly lower than the saline group. In the BA + AT group, there was a significant increase in SOD and CAT activities when compared with that of the BA group. The CC-16 and MDA contents in the BA group were significantly higher than in the saline group. The CC-16 and MDA levels of the BA + AT group were significantly lower than BA group. Histopathologic changes were seen in BA group, and there was a significant decrease in the BA + AT group. In conclusion, AT might be beneficial in the treatment of aspiration pneumonitis induced by BAs because AT decreased oxidative damage and resulted in a decrease in CC-16 levels.
Mental health, service use and social capital among Indian-Australians: findings of a wellbeing survey
Authors: Maheshwari Rajesh , Steel Zachary 
Published: September 2012

Objective: Indian-Australians represent a distinct immigrant group both demographically and culturally. Yet, despite an expanding body of research on transcultural mental health in Australia, there is a paucity of studies regarding mental health of Indian-Australians. This paper explores the extent of psychological morbidity and related service use in a representative sample of Indian-Australians. It further examines the association of mental health with social participation and networking in this ethnic community. Method: Measures to assess current levels of psychological distress, functional disability, service use, and social capital were administered in a random sample of 71 Indian-Australian family groups living in Sydney. Results: Amongst participants, 15% reported high to very high levels of psychological distress. Psychological distress was associated with increased days of functional disability and higher levels of functional impairment, and an increased likelihood of a GP consultation. However, 91% of participants with identifiable mental health needs did not seek any mental health consultation. Social capital was not found to be a significant predictor of psychological health or service use in this sample. Conclusion: Psychological morbidity in the Indian-Australian community is associated with high levels of functional disability, both in number of days and extent of severity, but only a small proportion seeks mental health help.
Attitudes of Medical Oncologists in Qatar Toward Palliative Care
Authors: Zeinah Ghaith F. Abu , Al-Kindi Sadeer G. , Hassan Azza Adel 
Published: September 2012

Objectives: The first and only palliative care (PC) unit in Qatar was established in 2008 to serve adult patients with cancer. As PC was only recently introduced to oncology practice in Qatar and the region, raising awareness among physicians is crucial. This survey study is designed to outline the level of awareness and knowledge of oncologists in Qatar toward PC. Methods: In this cross-sectional survey study, copies of a self-constructed questionnaire were distributed to 49 physicians at the National Center for Cancer Care and Research in Qatar during January 2012 and collected for data analysis. Results: The physician response rate was 100%. Less than half of the responders (36.7%) had official training in PC, but the majority (89.8%) showed interest in the field. Only 57.8% of the physicians reported self-competence in providing good PC to the dying patient. On the other hand, up to 69.4% are aware of the guidelines for pain relief and 58.7% apply them in their clinical practice. The concept of PC hospice was familiar to 77.1% of participants. On one hand, 85.7% of the physicians advocated that every medical center should have PC service, while up to 70.8% preferred that patients with short survival expectancy die in the community, rather than in a hospital setting. Conclusions: There is relatively good awareness and knowledge among health care providers specialized in cancer treatment in our hospital, despite the lack of formal training. Further training and informative sessions are required to raise awareness among oncologists and encourage utilization of PC services and thus optimize patient accessibility to PC.
The p53 pathway in hematopoiesis: lessons from mouse models, implications for humans
Authors: Pant Vinod , Quintás-Cardama Alfonso , Lozano Guillermina 
Published: September 2012

AbstractAberrations in the p53 tumor suppressor pathway are associated with hematologic malignancies. p53-dependent cell cycle control, senescence, and apoptosis functions are actively involved in maintaining hematopoietic homeostasis under normal and stress conditions. Whereas loss of p53 function promotes leukemia and lymphoma development in humans and mice, increased p53 activity inhibits hematopoietic stem cell function and results in myelodysplasia. Thus, exquisite regulation of p53 activity is critical for homeostasis. Most of our understanding of p53 function in hematopoiesis is derived from genetically engineered mice. Here we summarize some of these models, the various mechanisms that disrupt the regulation of p53 activity, and their relevance to human disease.
Self-antigen recognition by follicular lymphoma B-cell receptors
Authors: Sachen Kacey L. , Strohman Michael J. , Singletary Jonathan , Alizadeh Ash A. , Kattah Nicole H. , Lossos Chen , Mellins Elizabeth D. , Levy Shoshana , Levy Ronald 
Published: September 2012

Abstract
Follicular lymphoma is a monoclonal B-cell malignancy with each patient's tumor expressing a unique cell surface immunoglobulin (Ig), or B-cell receptor (BCR), that can potentially recognize antigens and/or transduce signals into the tumor cell. Here we evaluated the reactivity of tumor derived Igs for human tissue antigens. Self-reactivity was observed in 26% of tumor Igs (25 of 98). For one follicular lymphoma patient, the recognized self-antigen was identified as myoferlin. This patient's tumor cells bound recombinant myoferlin in proportion to their level of BCR expression, and the binding to myoferlin was preserved despite ongoing somatic hypermutation of Ig variable regions. Furthermore, BCR-mediated signaling was induced after culture of tumor cells with myoferlin. These results suggest that antigen stimulation may provide survival signals to tumor cells and that there is a selective pressure to preserve antigen recognition as the tumor evolves.
Expression of Myc, but not pSTAT3, is an adverse prognostic factor for diffuse large B-cell lymphoma treated with epratuzumab/R-CHOP
Authors: Gupta Mamta , Maurer Matthew J. , Wellik Linda E. , Law Mark E. , Han Jing Jing , Ozsan Nazan , Micallef Ivana N. , Dogan Ahmet , Witzig Thomas E. 
Published: September 2012

AbstractSTAT3 regulates cell growth by up-regulating downstream targets, such as Myc. The frequency of phosphorylated STAT3 (pSTAT3) and Myc expression and their prognostic relevance is unknown within diffuse large B-cell lymphoma (DLBCL) germinal center B-cell (GCB) and non-GCB subtypes. pSTAT3 and Myc were studied by immunohistochemistry (IHC) on tumors from 40 DLBCL patients uniformly treated on a clinical trial of epratuzumab/rituximab-CHOP. A total of 35% of cases were pSTAT3-positive, and pSTAT3 positivity was more frequent in the non-GCB (P = .06) type but did not correlate with event-free survival (EFS). Myc expression was observed in 50% of cases and was more frequent in non-GCB type (P = .07). Myc-positive cases had inferior EFS in all patients, including the GCB and pSTAT3-positive cases, were more likely to express Myc (P = .06). Myc translocations involving the major breakpoint regions were found in 10% (3 of 29) of cases, and all 3 cases were GCB and had an inferior EFS (P = .09). pSTAT3, but not Myc expression, was correlated with elevated pretreatment serum cytokines, such as IL-10 (P = .05), G-CSF (P = .03), and TNF-α (P = .04). pSTAT3 IHC in DLBCL tumors has the potential to identify patients for STAT3 pathway–directed therapy; Myc IHC is a potential marker for inferior EFS in GCB patients.
γ9 and δ2CDR3 domains regulate functional avidity of T cells harboring γ9δ2TCRs
Authors: Gründer Cordula , van Dorp Suzanne , Hol Samantha , Drent Esther , Straetemans Trudy , Heijhuurs Sabine , Scholten Kirsten , Scheper Wouter , Sebestyen Zsolt , Martens Anton , Strong Roland , Kuball Jürgen 
Published: September 2012

AbstractImmunotherapy with innate immune cells has recently evoked broad interest as a novel treatment option for cancer patients. γ9δ2T cells in particular are emerging as an innate cell population with high frequency and strong antitumor reactivity, which makes them and their receptors promising candidates for immune interventions. However, clinical trials have so far reported only limited tumor control by adoptively transferred γ9δ2T cells. As a potential explanation for this lack of efficacy, we found unexpectedly high variability in tumor recognition within the physiologic human γ9δ2T-cell repertoire, which is substantially regulated by the CDR3 domains of individual γ9δ2TCRs. In the present study, we demonstrate that the reported molecular requirements of CDR3 domains to interact with target cells shape the physiologic γ9δ2T-cell repertoire and, most likely, limit the protective and therapeutic antitumor efficacy of γ9δ2T cells. Based on these findings, we propose combinatorial-γδTCR-chain exchange as an efficient method for designing high-affinity γ9δ2TCRs that mediate improved antitumor responses when expressed in αβT cells both in vitro and in vivo in a humanized mouse model.
BMP9 regulates endoglin-dependent chemokine responses in endothelial cells
Authors: Young Kira , Conley Barbara , Romero Diana , Tweedie Eric , O'Neill Christine , Pinz Ilka , Brogan Louise , Lindner Volkhard , Liaw Lucy , Vary Calvin P. H. 
Published: September 2012

Abstract
BMP9 signaling has been implicated in hereditary hemorrhagic telangiectasia (HHT) and vascular remodeling, acting via the HHT target genes, endoglin and ALK1. This study sought to identify endothelial BMP9-regulated proteins that could affect the HHT phenotype. Gene ontology analysis of cDNA microarray data obtained after BMP9 treatment of primary human endothelial cells indicated regulation of chemokine, adhesion, and inflammation pathways. These responses included the up-regulation of the chemokine CXCL12/SDF1 and down-regulation of its receptor CXCR4. Quantitative mass spectrometry identified additional secreted proteins, including the chemokine CXCL10/IP10. RNA knockdown of endoglin and ALK1 impaired SDF1/CXCR4 regulation by BMP9. Because of the association of SDF1 with ischemia, we analyzed its expression under hypoxia in response to BMP9 in vitro, and during the response to hindlimb ischemia, in endoglin-deficient mice. BMP9 and hypoxia were additive inducers of SDF1 expression. Moreover, the data suggest that endoglin deficiency impaired SDF1 expression in endothelial cells in vivo. Our data implicate BMP9 in regulation of the SDF1/CXCR4 chemokine axis in endothelial cells and point to a role for BMP9 signaling via endoglin in a switch from an SDF1-responsive autocrine phenotype to an SDF1 nonresponsive paracrine state that represses endothelial cell migration and may promote vessel maturation.
Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)
Authors: Cheung Warren A , Ouellette BF Francis , Wasserman Wyeth W 
Published: September 2012

Abstract

Background
MEDLINE®/PubMed® indexes over 20 million biomedical articles, providing curated annotation of its contents using a controlled vocabulary known as Medical Subject Headings (MeSH). The MeSH vocabulary, developed over 50+ years, provides a broad coverage of topics across biomedical research. Distilling the essential biomedical themes for a topic of interest from the relevant literature is important to both understand the importance of related concepts and discover new relationships.

Results
We introduce a novel method for determining enriched curator-assigned MeSH annotations in a set of papers associated to a topic, such as a gene, an author or a disease. We generate MeSH Over-representation Profiles (MeSHOPs) to quantitatively summarize the annotations in a form convenient for further computational analysis and visualization. Based on a hypergeometric distribution of assigned terms, MeSHOPs statistically account for the prevalence of the associated biomedical annotation while highlighting unusually prevalent terms based on a specified background. MeSHOPs can be visualized using word clouds, providing a succinct quantitative graphical representation of the relative importance of terms. Using the publication dates of articles, MeSHOPs track changing patterns of annotation over time. Since MeSHOPs are quantitative vectors, MeSHOPs can be compared using standard techniques such as hierarchical clustering. The reliability of MeSHOP annotations is assessed based on the capacity to re-derive the subset of the Gene Ontology annotations with equivalent MeSH terms.

Conclusions
MeSHOPs allows quantitative measurement of the degree of association between any entity and the annotated medical concepts, based directly on relevant primary literature. Comparison of MeSHOPs allows entities to be related based on shared medical themes in their literature. A web interface is provided for generating and visualizing MeSHOPs.
Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution
Authors: Purves Joanne , Blades Matthew , Arafat Yasrab , Malik Salman A , Bayliss Christopher D , Morrissey Julie A 
Published: September 2012

Abstract

Background

Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates.

Results
Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another.

Conclusions
The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.
Adenylate kinase 2 (AK2) promotes cell proliferation in insect development
Authors: Chen Ru-Ping , Liu Chun-Yan , Shao Hong-Lian , Zheng Wei-Wei , Wang Jin-Xing , Zhao Xiao-Fan 
Published: September 2012

Abstract

Background
Adenylate kinase 2 (AK2) is a phosphotransferase that catalyzes the reversible reaction 2ADP(GDP) ↔ ATP(GTP) + AMP and influences cellular energy homeostasis. However, the role of AK2 in regulating cell proliferation remains unclear because AK2 has been reported to be involved in either cell proliferation or cell apoptosis in different cell types of various organisms.

Results
This study reports AK2 promotion of cell proliferation using the lepidopteran insect Helicoverpa armigera and its epidermal cell line HaEpi as models. Western blot analysis indicates that AK2 constitutively expresses in various tissues during larval development. Immunocytochemistry analysis indicates that AK2 localizes in the mitochondria. The recombinant expressed AK2 in E. coli promotes cell growth and viability of HaEpi cell line by 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. AK2 knockdown in larvae by RNA interference causes larval growth defects, including body weight decrease and development delay. AK2 knockdown in larvae also decreases the number of circulating haemocytes. The mechanism for such effects might be the suppression of gene transcription involved in insect development caused by AK2 knockdown.

Conclusion
These results show that AK2 regulates cell growth, viability, and proliferation in insect growth and development.
Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max
Authors: Zabala Gracia , Campos Edhilvia , Varala Kranthi K , Bloomfield Sean , Jones Sarah I , Win Hlaing , Tuteja Jigyasa H , Calla Bernarda , Clough Steven J , Hudson Matthew , Vodkin Lila O 
Published: October 2012

Abstract

Background
Small non-coding RNAs (smRNAs) are known to have major roles in gene regulation in eukaryotes. In plants, knowledge of the biogenesis and mechanisms of action of smRNA classes including microRNAs (miRNAs), short interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs) has been gained mostly through studies with Arabidopsis. In recent years, high throughput sequencing of smRNA populations has enabled extension of knowledge from model systems to plants with larger, more complex genomes. Soybean (Glycine max) now has many genomics resources available including a complete genome sequence and predicted gene models. Relatively little is known, however, about the full complement of its endogenous smRNAs populations and the silenced genes.

Results
Using Illumina sequencing and computational analysis, we characterized eight smRNA populations from multiple tissues and organs of soybean including developing seed and vegetative tissues. A total of 41 million raw sequence reads collapsed into 135,055 unique reads were mapped to the soybean genome and its predicted cDNA gene models. Bioinformatic analyses were used to distinguish miRNAs and siRNAs and to determine their genomic origins and potential target genes. In addition, we identified two soybean TAS3 gene homologs, the miRNAs that putatively guide cleavage of their transcripts, and the derived tasiRNAs that could target soybean genes annotated as auxin response factors. Tissue-differential expression based on the flux of normalized miRNA and siRNA abundances in the eight smRNA libraries was evident, some of which was confirmed by smRNA blotting. Our global view of these smRNA populations also revealed that the size classes of smRNAs varied amongst different tissues, with the developing seed and seed coat having greater numbers of unique smRNAs of the 24-nt class compared to the vegetative tissues of germinating seedlings. The 24-nt class is known to be derived from repetitive elements including transposons. Detailed analysis of the size classes associated with ribosomal RNAs and transposable element families showed greater diversity of smRNAs in the 22- and 24-nt size classes.

Conclusions
The flux of endogenous smRNAs within multiple stages and tissues of seed development was contrasted with vegetative tissues of soybean, one of the dominant sources of protein and oil in world markets. The smRNAs varied in size class, complexity of origins, and possible targets. Sequencing revealed tissue-preferential expression for certain smRNAs and expression differences among closely related miRNA family members.
Variation in dengue virus plaque reduction neutralization testing: systematic review and pooled analysis
Authors: Rainwater-Lovett Kaitlin , Rodriguez-Barraquer Isabel , Cummings Derek AT , Lessler Justin 
Published: September 2012

AbstractBackgroundThe plaque reduction neutralization test (PRNT) remains the gold standard for the detection of serologic immune responses to dengue virus (DENV). While the basic concept of the PRNT remains constant, this test has evolved in multiple laboratories, introducing variation in materials and methods. Despite the importance of laboratory-to-laboratory comparability in DENV vaccine development, the effects of differing PRNT techniques on assay results, particularly the use of different dengue strains within a serotype, have not been fully characterized.MethodsWe conducted a systematic review and pooled analysis of published literature reporting individual-level PRNT titers to identify factors associated with heterogeneity in PRNT results and compared variation between strains within DENV serotypes and between articles using hierarchical models.ResultsThe literature search and selection criteria identified 8 vaccine trials and 25 natural exposure studies reporting 4,411 titers from 605 individuals using 4 different neutralization percentages, 3 cell lines, 12 virus concentrations and 51 strains. Of 1,057 titers from primary DENV exposure, titers to the exposure serotype were consistently higher than titers to non-exposure serotypes. In contrast, titers from secondary DENV exposures (n = 628) demonstrated high titers to exposure and non-exposure serotypes. Additionally, PRNT titers from different strains within a serotype varied substantially. A pooled analysis of 1,689 titers demonstrated strain choice accounted for 8.04% (90% credible interval [CrI]: 3.05%, 15.7%) of between-titer variation after adjusting for secondary exposure, time since DENV exposure, vaccination and neutralization percentage. Differences between articles (a proxy for inter-laboratory differences) accounted for 50.7% (90% CrI: 30.8%, 71.6%) of between-titer variance.ConclusionsAs promising vaccine candidates arise, the lack of standardized assays among diagnostic and research laboratories make unbiased inferences about vaccine-induced protection difficult. Clearly defined, widely accessible reference reagents, proficiency testing or algorithms to adjust for protocol differences would be a useful first step in improving dengue PRNT comparability and quality assurance.