bluuebunny/crossref_metadata_2025_split huggingface dataset:
The supernatant of apoptotic cells causes transcriptional activation of hypoxia-inducible factor–1α in macrophages via sphingosine-1-phosphate and transforming growth factor-β
Authors: Herr Barbara , Zhou Jie , Werno Christian , Menrad Heidi , Namgaladze Dmitry , Weigert Andreas , Dehne Nathalie , Brüne Bernhard 
Published: June 2009

AbstractMacrophages infiltrating solid tumors exhibit a tumor-supporting phenotype and are critical for tumor development. Little is known which tumor-derived signal provokes this phenotype shift and how these signals are interpreted in macrophages to support tumor growth. We used the supernatant of apoptotic cells and noticed transcriptional, nuclear factor of activated T cells-dependent up-regulation of hypoxia-inducible factor (HIF)–1α mRNA, subsequent protein expression, and HIF-1 activity. Blocking calcineurin with cyclosporine A attenuated nuclear factor of activated T cells binding during electrophoretic mobility shift assay analysis and circumvented the HIF-1α mRNA increase. Knockdown experiments, receptor analysis, and antibody neutralization pointed to sphingosine-1-phosphate and transforming growth factor-β as the initiators of the HIF-1 response. The use of macrophages from conditional HIF-1α knockout mice revealed that macrophages, under the impact of apoptotic cell supernatants, use HIF-1 to produce factors that induce CD31 expression in murine embryonic stem cells. Our study supports the notion that soluble factors produced from apoptotic tumor cells activate the HIF-1 system under normoxia in macrophages to enhance their tumor-promoting capacity by, for example, releasing vascular endothelial growth factor. This shows the importance of HIF-1–elicited responses in regulatory macrophages under normoxia.
Identification of patients with poorer survival in primary myelofibrosis based on the burden of JAK2V617F mutated allele
Authors: Guglielmelli Paola , Barosi Giovanni , Specchia Giorgina , Rambaldi Alessandro , Lo Coco Francesco , Antonioli Elisabetta , Pieri Lisa , Pancrazzi Alessandro , Ponziani Vanessa , Delaini Federica , Longo Giovanni , Ammatuna Emanuele , Liso Vincenzo , Bosi Alberto , Barbui Tiziano , Vannucchi Alessandro M. 
Published: June 2009

Abstract
A total of 186 patients with primary myelofibrosis (PMF) were genotyped for JAK2V617F at diagnosis aimed at analyzing the correlation of mutational status and mutated allele burden with outcome variables, including time to anemia, leukocytosis, leukopenia, thrombocytopenia, massive splenomegaly, leukemia, and with overall survival. A total of 127 JAK2V617F-mutated patients (68% of whole series) were divided in quartiles of V617F allele burden. After a median follow-up of 17.2 months, 23 patients died, 15 because of leukemia. A JAK2V617F mutated status did not impact on the rate of leukemia transformation or overall survival. Patients in the lower quartile had shorter time to anemia and leukopenia and did not progress to large splenomegaly. Furthermore, survival was significantly reduced in the lower quartile compared with upper quartiles and JAK2 wild-type patients. In multivariate analysis, factors associated with reduced survival were age, a blast count more than 1%, and a JAK2V617F burden within first quartile. Causes of death in the lower quartile were represented mainly by systemic infections. We conclude that a low JAK2V617F allele burden at diagnosis is preferentially associated with a myelodepletive rather than myeloproliferative phenotype and represents an independent factor associated with shortened survival in patients with PMF.
Risk of arterial cardiovascular events in patients after pulmonary embolism
Authors: Klok Frederikus A. , Mos Inge C.M. , Broek Lisette , Tamsma Jouke T. , Rosendaal Frits R. , de Roos Albert , Huisman Menno V. 
Published: June 2009

AbstractStudies have reported inconsistent evidence for an association between venous thrombosis and arterial cardiovascular events. We further studied the association between both diseases by comparing the occurrence of cardiovascular events in patients diagnosed with acute pulmonary embolism (PE) contrasted to patients with comparable baseline risk characteristics (patients in whom PE was clinically suspected but ruled out). Included were 259 patients with provoked PE, 95 patients with unprovoked PE, and 334 control patients without PE. Patients diagnosed with PE were treated with vitamin K antagonists for 6 months. Median follow-up was 4.2 years. Sixty-three arterial cardiovascular events were registered (incidence, 5.1/100 patient-years). Adjusted hazard ratio was not different between patients with all-cause PE and control patients (1.39, 95% confidence interval [CI], 0.83-2.3) but increased for patients with unprovoked PE versus both patients with provoked PE and control patients without PE (2.18; 95% CI, 1.1-4.5; and 2.62; 95% CI, 1.4-4.9, respectively). This effect was confirmed after redefining the study start date to the moment the vitamin K antagonists were discontinued. Our study underlines the association between unprovoked venous thrombosis and arterial cardiovascular events; however, risk differences between patients with provoked PE and patients in whom PE was clinically suspected but ruled out could not be demonstrated.
Biochemical characterization of malate synthase G of P. aeruginosa
Authors: Roucourt Bart , Minnebo Nikki , Augustijns Patrick , Hertveldt Kirsten , Volckaert Guido , Lavigne Rob 
Published: June 2009

Abstract

Background
Malate synthase catalyzes the second step of the glyoxylate bypass, the condensation of acetyl coenzyme A and glyoxylate to form malate and coenzyme A (CoA). In several microorganisms, the glyoxylate bypass is of general importance to microbial pathogenesis. The predicted malate synthase G of Pseudomonas aeruginosa has also been implicated in virulence of this opportunistic pathogen.

Results
Here, we report the verification of the malate synthase activity of this predicted protein and its recombinant production in E. coli, purification and biochemical characterization. The malate synthase G of P. aeruginosa PAO1 has a temperature and pH optimum of 37.5°C and 8.5, respectively. Although displaying normal thermal stability, the enzyme was stable up to incubation at pH 11. The following kinetic parameters of P. aeruginosa PAO1 malate synthase G were obtained: Km glyoxylate (70 μM), Km acetyl CoA (12 μM) and Vmax (16.5 μmol/minutes/mg enzyme). In addition, deletion of the corresponding gene showed that it is a prerequisite for growth on acetate as sole carbon source.

Conclusion
The implication of the glyoxylate bypass in the pathology of various microorganisms makes malate synthase G an attractive new target for antibacterial therapy. The purification procedure and biochemical characterization assist in the development of antibacterial components directed against this target in P. aeruginosa.
Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout
Authors: Moghadam Hooman K , Ferguson Moira M , Danzmann Roy G 
Published: June 2009

Abstract

Background
Recent advances in the accumulation of genetic mapping and DNA sequence information from several salmonid species support the long standing view of an autopolyploid origin of these fishes (i.e., 4R). However, the paralogy relationships of the chromosomal segments descendent from earlier polyploidization events (i.e., 2R/3R) largely remain unknown, mainly due to an unbalanced pseudogenization of paralogous genes that were once resident on the ancient duplicated segments. Inter-specific conserved noncoding elements (CNE) might hold the key in identifying these regions, if they are associated with arrays of genes that have been highly conserved in syntenic blocks through evolution. To test this hypothesis, we investigated the chromosomal positions of subset of CNE in the rainbow trout genome using a comparative genomic framework.

Results
Through a genome wide analysis, we selected 41 pairs of adjacent CNE located on various chromosomes in zebrafish and obtained their intervening, less conserved, sequence information from rainbow trout. We identified 56 distinct fragments corresponding to about 150 Kbp of sequence data that were localized to 67 different chromosomal regions in the rainbow trout genome. The genomic positions of many duplicated CNE provided additional support for some previously suggested homeologies in this species. Additionally, we now propose 40 new potential paralogous affinities by analyzing the variation in the segregation patterns of some multi-copy CNE along with the synteny association comparison using several model vertebrates. Some of these regions appear to carry signatures of the 1R, 2R or 3R duplications. A subset of these CNE markers also demonstrated high utility in identifying homologous chromosomal segments in the genomes of Atlantic salmon and Arctic charr.

Conclusion
CNE seem to be more efficacious than coding sequences in providing insights into the ancient paralogous affinities within the vertebrate genomes. Such a feature makes these elements extremely attractive for comparative genomics studies, as they can be treated as 'anchor' markers to investigate the association of distally located candidate genes on the homologous genomic segments of closely or distantly related organisms.
Monocytes and neutrophils expressing myeloperoxidase occur in fibrous caps and thrombi in unstable coronary plaques
Authors: Tavora Fabio R , Ripple Mary , Li Ling , Burke Allen P 
Published: June 2009

Abstract

Background
Myeloperoxidase (MPO) -containing macrophages and neutrophils have been described at sites of plaque rupture. The presence of these cells in precursor lesions to acute rupture (thin cap atheroma, or vulnerable plaque) and within thrombi adjacent to ruptures has not been described, nor an association with iron-containing macrophages within unstable plaques.

Methods
We studied 61 acute ruptures, 15 organizing ruptures, 31 thin cap fibroatheromas, and 28 fibroatheromas from 72 sudden coronary death victims by immunohistochemical and histochemical techniques. Inflammatory cells were typed with anti-CD68 (macrophages), anti-BP-30 (neutrophil bactericidal glycoprotein), and anti-MPO. Iron was localized by Mallory's Prussian blue stain. In selected plaques alpha smooth muscle actin (DAKO, Carpinteria, CA, clone M0851) was performed.

Results
MPO positive cells were present in 79% of ruptured caps, 28% of thin cap fibroatheroma, and no fibroatheromas; neutrophils were present in 72% of ruptures, 8% of thin cap fibroatheromas, and no fibroatheromas. Iron containing foam cells were present in the caps of 93% of acute ruptures, of 85% of organizing ruptures, 20% of thin cap atheromas, and 10% of fibroatheromas. MPO positive cells were more frequent in occlusive than non-occlusive thrombi adjacent to ruptures (p = .006) and were more numerous in diabetics compared to non-diabetics (p = .002)

Conclusion
Unstable fibrous caps are more likely to contain MPO-positive cells, neutrophils, and iron-containing macrophages than fibrous caps of stable fibroatheromas. MPO-positive cells in thrombi adjacent to disrupted plaques are associated with occlusive thrombi and are more numerous in diabetic patients.
Expression of multidrug resistance markers ABCB1 (MDR-1/P-gp) and ABCC1 (MRP-1) in renal cell carcinoma
Authors: Walsh Naomi , Larkin Annemarie , Kennedy Susan , Connolly Lisa , Ballot Jo , Ooi Wei , Gullo Giuseppe , Crown John , Clynes Martin , O'Driscoll Lorraine 
Published: June 2009

AbstractBackgroundRenal cell carcinoma patients respond poorly to conventional chemotherapy, this unresponsiveness may be attributable to multidrug resistance (MDR). The mechanisms of MDR in renal cancer are not fully understood and the specific contribution of ABC transporter proteins which have been implicated in the chemoresistance of various cancers has not been fully defined in this disease.MethodsIn this retrospective study the expression of two of these transporter efflux pumps, namely MDR-1 P-gp (ABCB1) and MRP-1 (ABCC1) were studied by immunohistochemistry in archival material from 95 renal cell carcinoma patients.ResultsIn the first study investigating MDR-1 P-gpandMRP-1 protein expression patterns in renal cell carcinoma patients, high levels of expression of both efflux pumps are observed with 100% of tumours studied showing MDR-1 P-gpandMRP-1 positivity.ConclusionAlthough these findings do not prove a causal role, the high frequency of tumours expressing these efflux pumps suggests that they may be important contributors to the chemoresistance of this tumour type.
Palliative care for older people – exploring the views of doctors and nurses from different fields in Germany
Authors: Brueckner Torben , Schumacher Martin , Schneider Nils 
Published: June 2009

Abstract

Background
Providing appropriate palliative care for older people is a major task for health care systems worldwide, and up to now it has also been one of the most neglected. Focusing on the German health care system, we sought to explore the attitudes of health professionals regarding their understanding of palliative care for older patients and its implementation.

Methods
In a qualitative study design, focus groups were established consisting of general practitioners, geriatricians, palliative care physicians, palliative care nurses and general nurses (a total of 29 participants). The group discussions were recorded, transcribed, coded and analysed using the methodological approach of Qualitative Description.

Results
Deficiencies in teamwork and conflicting role definitions between doctors and nurses and between family practitioners and medical specialists were found to be central problems affecting the provision of appropriate palliative care for older people. It was emphasized that there are great advantages to family doctors playing a leading role, as they usually have the longest contacts to the patients. However, the professional qualifications of family doctors were to some extent criticized. The general practitioners for their part criticized the increasing specialization on the field of palliative care. All groups complained that the German compensation system gives insufficient consideration to the time-consuming care of older patients, and about excessive bureaucracy.

Conclusion
General practitioners are the central health professionals in the delivery of palliative care for older people. They should however be encouraged to involve specialized services such as palliative care teams where necessary. With the German health care reform of 2007, a legal framework has been created that allows for this. As far as its realization is concerned, it must be ensured that the spotlight remains on the needs of the patients and not on policy conflicts and rivalries between health care professionals. Older people might particularly benefit if "talking" medicine and time-consuming care were properly catered for, financially and organizationally, in the health care system.
Hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) in Italy
Authors: Campanile Floriana , Bongiorno Dafne , Borbone Sonia , Stefani Stefania 
Published: June 2009

Abstract
The aim of our study was to trace the dynamic changes of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) lineages in Italy, comparing the genotypic backgrounds of contemporary isolates over a period of 17 years, with those of a sample of early MRSA strains from 1980.
In total, 301 non-repetitive MRSA clinical isolates, recovered from 19 Italian hospitals between 1990 and 2007 were selected and analyzed for their antibiotic resistance, typed by PFGE and SCCmec, grouped into clonal-types and further characterized using Multi Locus Sequence Typing (MLST). A sample of fifteen early MRSA strains from 1980 was also used for comparison.
The most interesting feature was the recent increase of ST228-MRSA-I (formerly the Italian clone; PFGE E) over the period 2000–2007 (57%), when compared to the period 1990–1999 (29%), and its stability to date, associated with a decrease of the highly epidemic ST247-MRSA-IA (formerly the Iberian clone; PFGE A), (23% from 1990 to 1999, 6% from 2000 to 2007). ST1-MRSA-I (1 out of 2 strains carrying ccr A2B2), ST8-MRSA-I (4 strains), ST15-MRSA-I (1 out of 4 carrying ccr A2B2) and ST30-MRSA-I (2 out of 5 carrying no ccr AB-types and ccr C) were the predominant earliest STs among the MRSA strains in 1980.
A temporal shift in the susceptibility levels to glycopeptides was observed: strains with vancomycin MIC of ≥ 2 mg/L increased from 19.4% to 35.5%.
In conclusion, we describe the alternation of MRSA clones that occurred in hospitals from 1990 to 2007 and the increase of the glycopeptide MIC levels, reflecting a worldwide trend. We document the detection of ST1, ST8, ST15 and ST30 in the 1980 isolates; we hypothesize their possible latency and their appearance as the current CA-MRSA clones.
Effects of cIAP-1, cIAP-2 and XIAP triple knockdown on prostate cancer cell susceptibility to apoptosis, cell survival and proliferation
Authors: Gill Catherine , Dowling Catherine , O'Neill Amanda J , Watson R William G 
Published: June 2009

AbstractBackgroundManipulating apoptotic resistance represents an important strategy for the treatment of hormone refractory prostate cancer. We hypothesised that the Inhibitor of Apoptosis (IAP) Proteins may be mediating this resistance and knockdown of cIAP-1, cIAP-2 and XIAP would increase sensitivity to apoptosis.MethodscIAP-1, cIAP-2 and XIAP where knocked down either individually or in combination using siRNA in androgen independent prostate cancer PC-3 cells as confirmed by real-time PCR and western blotting. Cells were then treated with TRAIL, Etoposide, or Tunicamycin, and apoptosis assessed by PI DNA staining. Apoptosis was confirmed with Annexin V labelling and measurement of PARP cleavage, and was inhibited using the pan-caspase inhibitor, zVAD.fmk. Clonogenic assays and assessment of ID-1 expression by western blotting were used to measure recovery and proliferation.ResultsPC-3 are resistant to TRAIL induced apoptosis and have elevated expression of cIAP-1, cIAP-2 and XIAP. Combined knockdown sensitised PC-3 to TRAIL induced apoptosis, but not to Etoposide or Tunicmycin, with corresponding increases in caspase activity and PARP cleavage which was inhibited by ZVAD.fmk. Triple knock down decreased proliferation which was confirmed by decreased ID-1 expression.ConclusionSimultaneous knock down of the IAPs not only sensitised the PC-3 to TRAIL but also inhibited their proliferation rates and clonogenic survival. The inability to alter sensitivity to other triggers of apoptosis suggests that this effect is specific for death receptor pathways and knock down might facilitate immune-surveillance mechanisms to counter cancer progression and, in combination with therapeutic approaches using TRAIL, could represent an important treatment strategy.
Chronic crude garlic-feeding modified adult male rat testicular markers: mechanisms of action
Authors: Hammami Imen , Amara Souheila , Benahmed Mohamed , El May Michèle V , Mauduit Claire 
Published: June 2009

Abstract

Background
Garlic or Allium sativum (As) shows therapeutic effects such as reduction of blood pressure or hypercholesterolemia but side-effects on reproductive functions remain poorly investigated. Because of garlic's chemical complexity, the processing methods and yield in preparations differ in efficacy and safety. In this context, we clarify the mechanisms of action of crushed crude garlic on testicular markers.

Methods
During one month of treatment, 24 male rats were fed 5%, 10% and 15% crude garlic.

Results
We showed that crude garlic-feeding induced apoptosis in testicular germ cells (spermatocytes and spermatids). This cell death process was characterized by increased levels of active CASP3 but not CASP6. Expression of the caspase inhibitors BIRC3 and BIRC2 was increased at all doses of As while expression of XIAP and BIRC5 was unchanged. Moreover, expression of the IAP inhibitor DIABLO was increased at doses 10% and 15% of As. The germ cell death process induced by As might be related to a decrease in testosterone production because of the reduced expression of steroidogenic enzymes (Star, Cyp11a, Hsd3b5 and Hsd17b). Evaluation of Sertoli markers showed that TUBB3 and GSTA2 expression was unchanged. In contrast, AMH, RHOX5 and CDKN1B expression was decreased while GATA4 expression was increased.

Conclusion
In summary, we showed that feeding with crude garlic inhibited Leydig steroidogenic enzyme expression and Sertoli cell markers. These alterations might induce apoptosis in testicular germ cells.
Inference of gene pathways using mixture Bayesian networks
Authors: Ko Younhee , Zhai ChengXiang , Rodriguez-Zas Sandra 
Published: June 2009

AbstractBackgroundInference of gene networks typically relies on measurements across a wide range of conditions or treatments. Although one network structure is predicted, the relationship between genes could vary across conditions. A comprehensive approach to infer general and condition-dependent gene networks was evaluated. This approach integrated Bayesian network and Gaussian mixture models to describe continuous microarray gene expression measurements, and three gene networks were predicted.ResultsThe first reconstructions of a circadian rhythm pathway in honey bees and an adherens junction pathway in mouse embryos were obtained. In addition, general and condition-specific gene relationships, some unexpected, were detected in these two pathways and in a yeast cell-cycle pathway. The mixture Bayesian network approach identified all (honey bee circadian rhythm and mouse adherens junction pathways) or the vast majority (yeast cell-cycle pathway) of the gene relationships reported in empirical studies. Findings across the three pathways and data sets indicate that the mixture Bayesian network approach is well-suited to infer gene pathways based on microarray data. Furthermore, the interpretation of model estimates provided a broader understanding of the relationships between genes. The mixture models offered a comprehensive description of the relationships among genes in complex biological processes or across a wide range of conditions. The mixture parameter estimates and corresponding odds that the gene network inferred for a sample pertained to each mixture component allowed the uncovering of both general and condition-dependent gene relationships and patterns of expression.ConclusionThis study demonstrated the two main benefits of learning gene pathways using mixture Bayesian networks. First, the identification of the optimal number of mixture components supported by the data offered a robust approach to infer gene relationships and estimate gene expression profiles. Second, the classification of conditions and observations into groups that support particular mixture components helped to uncover both gene relationships that are unique or common across conditions. Results from the application of mixture Bayesian networks substantially augmented the understanding of gene networks and demonstrated the added-value of this methodology to infer gene networks.