bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomics of Porphyromonas gingivalis within a model oral microbial community
Authors: Kuboniwa Masae , Hendrickson Erik L , Xia Qiangwei , Wang Tiansong , Xie Hua , Hackett Murray , Lamont Richard J 
Published: May 2009

Abstract

Background

Porphyromonas gingivalis is a periodontal pathogen that resides in a complex multispecies microbial biofilm community known as dental plaque. Confocal laser scanning microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell quantitative proteomics, along with mutant construction and analysis, were conducted to investigate how P. gingivalis adapts to this three species community.

Results
1156 P. gingivalis proteins were detected qualitatively during comparison of the three species model community with P. gingivalis incubated alone under the same conditions. Integration of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins were down-regulated and 89 proteins up-regulated. The proteomics results were inspected manually and an ontology analysis conducted using DAVID. Significant decreases were seen in proteins involved in cell shape and the formation of the cell envelope, as well as thiamine, cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-regulated in the community and an hmuR deficient mutant was deficient in three species community formation, but was unimpaired in its ability to form mono- or dual-species biofilms.

Conclusion
Collectively, these results indicate that P. gingivalis can assemble into a heterotypic community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for community structure.
GarlicESTdb: an online database and mining tool for garlic EST sequences
Authors: Kim Dae-Won , Jung Tae-Sung , Nam Seong-Hyeuk , Kwon Hyuk-Ryul , Kim Aeri , Chae Sung-Hwa , Choi Sang-Haeng , Kim Dong-Wook , Kim Ryong Nam , Park Hong-Seog 
Published: May 2009

Abstract

Background

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.

Description
GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at http://garlicdb.kribb.re.kr.

Conclusion
GarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.
Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.)
Authors: Dracatos Peter M , Cogan Noel OI , Sawbridge Timothy I , Gendall Anthony R , Smith Kevin F , Spangenberg German C , Forster John W 
Published: May 2009

AbstractBackgroundQualitative pathogen resistance in both dicotyledenous and monocotyledonous plants has been attributed to the action of resistance (R) genes, including those encoding nucleotide binding site – leucine rich repeat (NBS-LRR) proteins and receptor-like kinase enzymes. This study describes the large-scale isolation and characterisation of candidate R genes from perennial ryegrass. The analysis was based on the availability of an expressed sequence tag (EST) resource and a functionally-integrated bioinformatics database.ResultsAmplification of R gene sequences was performed using template EST data and information from orthologous candidate using a degenerate consensus PCR approach. A total of 102 unique partial R genes were cloned, sequenced and functionally annotated. Analysis of motif structure and R gene phylogeny demonstrated thatLoliumR genes cluster with putative ortholoci, and evolved from common ancestral origins. Single nucleotide polymorphisms (SNPs) predicted through resequencing of amplicons from the parental genotypes of a genetic mapping family were validated, and 26 distinct R gene loci were assigned to multiple genetic maps. Clusters of largely non-related NBS-LRR genes were located at multiple distinct genomic locations and were commonly found in close proximity to previously mapped defence response (DR) genes. A comparative genomics analysis revealed the co-location of several candidate R genes with disease resistance quantitative trait loci (QTLs).ConclusionThis study is the most comprehensive analysis to date of qualitative disease resistance candidate genes in perennial ryegrass. SNPs identified within candidate genes provide a valuable resource for mapping in various ryegrass pair cross-derived populations and further germplasm analysis using association genetics. In parallel with the use of specific pathogen virulence races, such resources provide the means to identify gene-for-gene mechanisms for multiple host pathogen-interactions and ultimately to obtain durable field-based resistance.
Inflammatory (B) symptoms are independent predictors of myelosuppression from chemotherapy in Non-Hodgkin Lymphoma (NHL) patients – analysis of data from a British National Lymphoma Investigation phase III trial comparing CHOP to PMitCEBO
Authors: Sharma Rohini , Cunningham David , Smith Paul , Robertson Graham , Dent Owen , Clarke Stephen J 
Published: May 2009

AbstractBackgroundToxicity from chemotherapy is highly variable, unpredictable and results in substantial morbidity and increased healthcare costs. New predictors of toxicity are required to improve the safety and efficacy of chemotherapy. Inflammatory or B symptoms in lymphoma are associated with elevated plasma inflammatory markers and predict worse treatment response and survival. Recent data suggest that systemic inflammation results in reduced hepatic drug metabolism and increased toxicity from chemotherapy. We investigated whether B symptoms were associated with greater toxicity in patients treated for non-Hodgkin lymphoma (NHL).MethodsThe British National Lymphoma Investigation compared two chemotherapy regimens in older patients with aggressive NHL. Approximately 50% of patients had B symptoms. Demographic and toxicity data on 664 patients were analysed to identify predictors of toxicity by multivariate analysis, with particular reference to B symptoms.ResultsUsing univariate analyses, severe (grades 3–4) leucopenia, anaemia, thrombocytopenia, nausea and vomiting and diarrhoea occurred more frequently in patients with B symptoms. The associations between B symptoms and severe leucopenia (OR 1.7, p = 0.005) and anaemia (OR 2.3, p = 0.025) persisted after adjustment for other prognostic factors in multivariate analyses. The use of granulocyte colony stimulating factor reduced neutropenia in patients with both A and B symptoms.ConclusionFor the first time and in a large NHL cohort we have shown that inflammatory symptoms are independent predictors for myelosuppression from chemotherapy. These data will enable improved prognostication for toxicity and provide individualisation of therapy in NHL and other tumours. These findings also create the potential for strategies used prior to chemotherapy aimed at reducing systemic inflammation in order to improve drug metabolism and reduce treatment-related toxicity.Trial registration numberISRCTN98741793
Occurrence of HSV-1-induced pneumonitis in patients under standard immunosuppressive therapy for rheumatic, vasculitic, and connective tissue disease
Authors: Witt Matthias N , Braun Gerald S , Ihrler Stephan , Schmid Holger 
Published: May 2009

Abstract

Background
Herpes simplex virus type-1 (HSV-1) has been described to cause respiratory tract infections in critically ill patients or in individuals that are immunocompromised. It is a continuing matter of debate under which circumstances HSV-1 is a relevant pathogen for pneumonitis. While its role during critical illness has been investigated by prospective interventional studies, comparatively little systematic data is available on the role of HSV-1 for pneumonitis in outpatients with autoimmune disease under a maintenance regimen of immunosuppression.

Methods
We retrospectively reviewed the charts of ~1400 patients with rheumatoid arthritis, vasculitis, and systemic lupus erythematosus (SLE) that were followed at the outpatient clinic of a German University hospital during the years 2000–2007. Episodes of admission to a ward resulting in the diagnosis of pneumonia/pneumonitis were identified, and the type of pneumonia and clinical features retrospectively studied.

Results
63 patients with rheumatoid arthritis, vasculitis, or SLE were admitted to a ward and diagnosed to have pneumonia/pneumonitis. Using bronchoscopy a total of 6 cases of pulmonary infection associated with HSV-1 in the lower respiratory tract were identified. Among those, 2 cases suggested a causative role of HSV-1 as the sole agent causing pneumonitis that proved clinically responsive to antiviral treatment. In the remaining 4 cases HSV-1 appeared as a bystander of bacterial infection. Maintenance therapy with leflunomide, which inhibits HSV-1 assembly in vitro, was associated with a milder course of pneumonitis in one patient. Detection of HSV-1 was associated with stronger immunosuppressive regimens and vasculitic disease.

Conclusion
The present study analyzed the frequency and hallmarks of cases of HSV-1 associated pneumonitis that occurred in a comparatively large cohort of patients with rheumatologic autoimmune diseases. In an area of controversy, this study provides further evidence that HSV-1 causes isolated pneumonitis in the immunocompromised. The study may provide an estimate on the frequency of relevant HSV-1 infection and bacterial agents in outpatients with autoimmune disease.
An investigation of theory-practice gap in undergraduate paramedic education
Authors: Michau Rebecca , Roberts Samantha , Williams Brett , Boyle Malcolm 
Published: May 2009

Abstract

Background
Bachelor of Emergency Health (Paramedic) (BEH) students at Monash University undertake clinical placements to assist with the transition from student to novice paramedic. Anecdotally, students report a lack of opportunity to practise their clinical skills whilst on placements. The barriers to participation and the theory-practice gap have not been previously documented in Australian paramedic literature. The purpose of this study was to investigate the theory-practice gap for paramedic students by linking education and skill level to case exposure and skills praxis during clinical placements.

Methods
A cross-sectional retrospective study using a convenience sample of second and third year BEH undergraduate students. Ethics approval was granted.

Results
Eighty four second and third year BEH students participated. 59.5% were female (n = 50), 40.5% were male (n = 34). Overall, students most commonly reported exposure to cardiac and respiratory cases and were satisfied with the number of cases encountered during placement. However, over half (n = 46) reported being exposed to < 50% of cases that allowed skills praxis. The most common barrier to participation (34.5%) was the opportunity to participate in patient care and 68% of student's were unsure if paramedics understood their role during clinical placements.

Conclusion
This study demonstrates that the majority of students were satisfied with their clinical placement experience; even though they were exposed to < 50% of cases that allowed skills practice. Identifying these educational barriers will assist in improving the quality and theory-practice gap of paramedic clinical education.
Chloroquine resistance before and after its withdrawal in Kenya
Authors: Mwai Leah , Ochong Edwin , Abdirahman Abdi , Kiara Steven M , Ward Steve , Kokwaro Gilbert , Sasi Philip , Marsh Kevin , Borrmann Steffen , Mackinnon Margaret , Nzila Alexis 
Published: May 2009

Abstract

Background
The spread of resistance to chloroquine (CQ) led to its withdrawal from use in most countries in sub-Saharan Africa in the 1990s. In Malawi, this withdrawal was followed by a rapid reduction in the frequency of resistance to the point where the drug is now considered to be effective once again, just nine years after its withdrawal. In this report, the polymorphisms of markers associated with CQ-resistance against Plasmodium falciparum isolates from coastal Kenya (Kilifi) were investigated, from 1993, prior to the withdrawal of CQ, to 2006, seven years after its withdrawal. Changes to those that occurred in the dihydrofolate reductase gene (dhfr) that confers resistance to the replacement drug, pyrimethamine/sulphadoxine were also compared.

Methods
Mutations associated with CQ resistance, at codons 76 of pfcrt, at 86 of pfmdr1, and at codons 51, 59 and 164 of dhfr were analysed using PCR-restriction enzyme methods. In total, 406, 240 and 323 isolates were genotyped for pfcrt-76, pfmdr1-86 and dhfr, respectively.

Results
From 1993 to 2006, the frequency of the pfcrt-76 mutant significantly decreased from around 95% to 60%, while the frequency of pfmdr1-86 did not decline, remaining around 75%. Though the frequency of dhfr mutants was already high (around 80%) at the start of the study, this frequency increased to above 95% during the study period. Mutation at codon 164 of dhf r was analysed in 2006 samples, and none of them had this mutation.

Conclusion
In accord with the study in Malawi, a reduction in resistance to CQ following official withdrawal in 1999 was found, but unlike Malawi, the decline of resistance to CQ in Kilifi was much slower. It is estimated that, at current rates of decline, it will take 13 more years for the clinical efficacy of CQ to be restored in Kilifi. In addition, CQ resistance was declining before the drug's official withdrawal, suggesting that, prior to the official ban, the use of CQ had decreased, probably due to its poor clinical effectiveness.
Psychometric properties of the Brazilian version of the Child Perceptions Questionnaire (CPQ11–14) – short forms
Authors: Torres Cíntia S , Paiva Saul M , Vale Miriam P , Pordeus Isabela A , Ramos-Jorge Maria L , Oliveira Ana C , Allison Paul J 
Published: May 2009

AbstractBackgroundThe need to evaluate the impact of oral health has led to the development of instruments for measuring oral health-related quality of life (OHQoL). One such instrument is the Child Perceptions Questionnaire (CPQ11–14), developed specifically for 11-to-14-year-old children. As this questionnaire was considered long (37 items), shorter forms were developed with 8 (Impact Short Form: 8 – ISF:8) and 16 items (Impact Short Form: 16 – ISF:16) to facilitate use in the clinical setting and population-based health surveys. The aim of the present study was to translate and cross-culturally adapt these CPQ11–14short forms for Brazilian Portuguese and evaluate the measurement properties of these versions for use on Brazilian children.MethodsFollowing translation and cross-cultural adaptation, the ISF:8 and ISF:16 were tested on 136 children from 11 to 14 years of age in the city of Belo Horizonte, Brazil. The instrument was administered by a trained researcher who also performed clinical examinations. The measurement properties (i.e. criterion validity, construct validity, internal consistency reliability, test-retest reliability) were determined. Discriminant validity was tested between groups, which were divided into children with no cavities and no malocclusion; children with cavities and without malocclusion; and children with malocclusion and without cavities.ResultsThe mean total score was 6.8 [standard deviation (SD) 4.2] for the ISF:8 and 11.9 (SD 7.6) for the ISF:16 (p < 0.001). Statistically significant associations were found between oral abnormalities and the subscales of the ISF:8 and ISF:16 (p< 0.05). Both test-retest stability and internal consistency, as measured by the intra-class correlation coefficient (ICC) (ISF:8 = 0.98 and ISF:16 = 0.97) and Cronbach's alpha (ISF:8 = 0.70 and ISF:16 = 0.84) proved to be adequate. Construct validity was confirmed from the correlation between the short form scores and oral health and overall well-being ratings. The score on the short forms of the CPQ11–14was able to discriminate between different oral conditions. Criterion validity was satisfactory (p < 0.05).ConclusionThe Brazilian versions of CPQ11–14ISF:8 and ISF:16 have satisfactory psychometric properties, similar to those of the original instrument.
Management of appendiceal pseudomyxoma peritonei diagnosed during pregnancy
Authors: Haase Erika , Yoo Dal , Sugarbaker Paul H 
Published: May 2009

Abstract

Background
The incidence of cancer during pregnancy is approximately 1 in 1000. The most common types encountered during pregnancy are cervical, breast and ovarian. Epithelial tumors of the appendix on the other hand are rare and account for only approximately 1% of all colorectal neoplasms; the occurrence of this neoplasm during pregnancy is extremely rare.

Case Presentation
The medical history of a 30 year old woman diagnosed at 17 weeks gestation with an appendiceal mucinous tumor with large volume pseudomyxoma peritonei was presented. Her pregnancy was preserved and she had an early vaginal delivery of a healthy baby at 35 weeks. At 2 1/2 weeks postpartum the patient underwent extensive cytoreductive surgery and intraperitoneal chemotherapy. She remains disease-free 5 years after her initial diagnosis. A literature review of this clinical situation and a discussion of treatment plans were presented.

Conclusion
The management of an appendiceal tumor with pseudomyxoma peritonei diagnosed during pregnancy requires full knowledge of the natural history of this disease to achieve a balance of concern for maternal survival and fetal health.
Antiphospholipid (Hughes) syndrome: beyond pregnancy morbidity and thrombosis
Authors: Mialdea Maria , Sangle Shirish R , D'Cruz David P 
Published: May 2009

Abstract
The antiphospholipid syndrome is an autoimmune disease characterised by recurrent arterial or venous thrombosis, pregnancy morbidity and the persistence of positive antiphospholipid antibodies. Many other clinical manifestations may occur including heart valve disease, livedo reticularis, thrombocytopenia and neurological manifestations such as migraine and seizures. We review a number of other manfestations including stenotic lesions, coronary artery disease and accelerated atherosclerosis, skeletal disorders and the concept of seronegative antiphospholipid syndrome.
Soluble aggregates of the amyloid-β peptide are trapped by serum albumin to enhance amyloid-β activation of endothelial cells
Authors: Reyes Barcelo Adriana A , Gonzalez-Velasquez Francisco J , Moss Melissa A 
Published: May 2009

AbstractBackgroundSelf-assembly of the amyloid-β peptide (Aβ) has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, synthetic molecules capable of inhibiting Aβ self-assembly could serve as therapeutic agents and endogenous molecules that modulate Aβ self-assembly may influence disease progression. However, increasing evidence implicating a principal pathogenic role for small soluble Aβ aggregates warns that inhibition at intermediate stages of Aβ self-assembly may prove detrimental. Here, we explore the inhibition of Aβ1–40self-assembly by serum albumin, the most abundant plasma protein, and the influence of this inhibition on Aβ1–40activation of endothelial cells for monocyte adhesion.ResultsIt is demonstrated that serum albumin is capable of inhibiting in a dose-dependent manner both the formation of Aβ1–40aggregates from monomeric peptide and the ongoing growth of Aβ1–40fibrils. Inhibition of fibrillar Aβ1–40aggregate growth is observed at substoichiometric concentrations, suggesting that serum albumin recognizes aggregated forms of the peptide to prevent monomer addition. Inhibition of Aβ1–40monomer aggregation is observed down to stoichiometric ratios with partial inhibition leading to an increase in the population of small soluble aggregates. Such partial inhibition of Aβ1–40aggregation leads to an increase in the ability of resulting aggregates to activate endothelial cells for adhesion of monocytes. In contrast, Aβ1–40activation of endothelial cells for monocyte adhesion is reduced when more complete inhibition is observed.ConclusionThese results demonstrate that inhibitors of Aβ self-assembly have the potential to trap small soluble aggregates resulting in an elevation rather than a reduction of cellular responses. These findings provide further support that small soluble aggregates possess high levels of physiological activity and underscore the importance of resolving the effect of Aβ aggregation inhibitors on aggregate size.