bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tyrosine kinase inhibitor–induced platelet dysfunction in patients with chronic myeloid leukemia
Authors: Quintás-Cardama Alfonso , Han Xin , Kantarjian Hagop , Cortes Jorge 
Published: May 2009

Abstract
Dasatinib is associated with increased risk of bleeding among patients with chronic myeloid leukemia, even in the absence of thrombocytopenia, suggesting the presence of a hemostatic defect. We tested platelet aggregation in 91 patients with chronic myeloid leukemia in chronic phase either off-therapy (n = 4) or receiving dasatinib (n = 27), bosutinib (n = 32), imatinib (n = 19), or nilotinib (n = 9). All but 3 patients simultaneously receiving imatinib and warfarin had normal coagulation studies. All 4 patients off therapy had normal platelet aggregation. Impaired platelet aggregation on stimulation with arachidonic acid, epinephrine, or both was observed in 70%, 85%, and 59% of patients on dasatinib, respectively. Eighty-five percent of patients on bosutinib, 100% on nilotinib, and 33% on imatinib had normal platelet aggregation. Dasatinib 400 nM induced rapid and marked prolongation of closure time to collagen/epinephrine in normal whole blood on the PFA-100 system. In conclusion, dasatinib and, to some extent, imatinib produce abnormalities in platelet aggregometry testing.
Genetic variation in caspase genes and risk of non-Hodgkin lymphoma: a pooled analysis of 3 population-based case-control studies
Authors: Lan Qing , Morton Lindsay M. , Armstrong Bruce , Hartge Patricia , Menashe Idan , Zheng Tongzhang , Purdue Mark P. , Cerhan James R. , Zhang Yawei , Grulich Andrew , Cozen Wendy , Yeager Meredith , Holford Theodore R. , Vajdic Claire M. , Davis Scott , Leaderer Brian , Kricker Anne , Schenk Maryjean , Zahm Shelia H. , Chatterjee Nilanjan , Chanock Stephen J. , Rothman Nathaniel , Wang Sophia S. 
Published: May 2009

AbstractCaspases play a critical role in regulation of apoptosis, cell differentiation, inflammation, and innate immunity, and several are mutated or have altered expression in non-Hodgkin lymphoma (NHL). To study the impact of genetic variation in caspases on NHL risk, we analyzed tag single nucleotide polymorphisms (SNPs) in 12 caspase and related genes in 3 population-based case-control studies (1946 cases and 1808 controls). Gene-based analysis, adjusting for the number of tagSNPs genotyped in each gene, showed significant associations for CASP8, CASP9, and CASP1. SNP-based analysis showed that CASP8 rs6736233 (odds ratio (OR) CG = 1.21; ORCC = 2.13; P trend = .011); CASP9 rs4661636 (ORCT = 0.89; ORTT = 0.77; P trend = .011); and CASP1 rs1785882 (ORAT = 1.12; ORAA = 1.30; P trend = .0054) were significantly associated with NHL risk and consistent across studies. It is noteworthy that genetic variants in CASP8 were associated with risk of all major NHL subtypes. Our findings suggest that genetic variation in caspases may play an important role in lymphomagenesis.
Weak preservation of local neutral substitution rates across mammalian genomes
Authors: Imamura Hideo , Karro John E , Chuang Jeffrey H 
Published: May 2009

Abstract

Background
The rate at which neutral (non-functional) bases undergo substitution is highly dependent on their location within a genome. However, it is not clear how fast these location-dependent rates change, or to what extent the substitution rate patterns are conserved between lineages. To address this question, which is critical not only for understanding the substitution process but also for evaluating phylogenetic footprinting algorithms, we examine ancestral repeats: a predominantly neutral dataset with a significantly higher genomic density than other datasets commonly used to study substitution rate variation. Using this repeat data, we measure the extent to which orthologous ancestral repeat sequences exhibit similar substitution patterns in separate mammalian lineages, allowing us to ascertain how well local substitution rates have been preserved across species.

Results
We calculated substitution rates for each ancestral repeat in each of three independent mammalian lineages (primate – from human/macaque alignments, rodent – from mouse/rat alignments, and laurasiatheria – from dog/cow alignments). We then measured the correlation of local substitution rates among these lineages. Overall we found the correlations between lineages to be statistically significant, but too weak to have much predictive power (r
2 <5%). These correlations were found to be primarily driven by regional effects at the scale of several hundred kb or larger. A few repeat classes (e.g. 7SK, Charlie8, and MER121) also exhibited stronger conservation of rate patterns, likely due to the effect of repeat-specific purifying selection. These classes should be excluded when estimating local neutral substitution rates.

Conclusion
Although local neutral substitution rates have some correlations among mammalian species, these correlations have little predictive power on the scale of individual repeats. This indicates that local substitution rates have changed significantly among the lineages we have studied, and are likely to have changed even more for more diverged lineages. The correlations that do persist are too weak to be responsible for many of the highly conserved elements found by phylogenetic footprinting algorithms, leading us to conclude that such elements must be conserved due to selective forces.
Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants
Authors: Li Wenyan , Liu Bing , Yu Lujun , Feng Dongru , Wang Hongbin , Wang Jinfa 
Published: May 2009

Abstract

Background
The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes that catalyze the reduction of double-bonds in α, β-unsaturated aldehydes or ketones and are part of the octadecanoid pathway that converts linolenic acid to jasmonic acid. In plants, OPRs belong to the old yellow enzyme family and form multigene families. Although discoveries about this family in Arabidopsis and other species have been reported in some studies, the evolution and function of multiple OPRs in plants are not clearly understood.

Results
A comparative genomic analysis was performed to investigate the phylogenetic relationship, structural evolution and functional divergence among OPR paralogues in plants. In total, 74 OPR genes were identified from 11 species representing the 6 major green plant lineages: green algae, mosses, lycophytes, gymnosperms, monocots and dicots. Phylogenetic analysis showed that seven well-conserved subfamilies exist in plants. All OPR genes from green algae were clustered into a single subfamily, while those from land plants fell into six other subfamilies, suggesting that the events leading to the expansion of the OPR family occurred in land plants. Further analysis revealed that lineage-specific expansion, especially by tandem duplication, contributed to the current OPR subfamilies in land plants after divergence from aquatic plants. Interestingly, exon/intron structure analysis showed that the gene structures of OPR paralogues exhibits diversity in intron number and length, while the intron positions and phase were highly conserved across different lineage species. These observations together with the phylogenetic tree revealed that successive single intron loss, as well as indels within introns, occurred during the process of structural evolution of OPR paralogues. Functional divergence analysis revealed that altered functional constraints have occurred at specific amino acid positions after diversification of the paralogues. Most notably, significant functional divergence was also found in all pairs, except for the II/IV, II/V and V/VI pairs. Strikingly, analysis of the site-specific profiles established by posterior probability revealed that the positive-selection sites and/or critical amino acid residues for functional divergence are mainly distributed in α-helices and substrate binding loop (SBL), indicating the functional importance of these regions for this protein family.

Conclusion
This study highlights the molecular evolution of the OPR gene family in all plant lineages and indicates critical amino acid residues likely relevant for the distinct functional properties of the paralogues. Further experimental verification of these findings may provide valuable information on the OPRs' biochemical and physiological functions.
Association of IL-10 and IL-10Rβ gene polymorphisms with graft-versus-host disease after haematopoietic stem cell transplantation from an HLA-identical sibling donor
Authors: Sivula Jyrki , Turpeinen Hannu , Volin Liisa , Partanen Jukka 
Published: May 2009

Abstract

Background
Extensive allelic matching in the human leukocyte antigen (HLA) genes is regarded as a prerequisite for good clinical success of allogeneic haematopoietic stem cell transplantation (HSCT). Also other genetic factors can be assumed to play a role in preventing and controlling the complications associated with allogeneic HSCT, in particular graft-versus-host disease (GvHD). Interleukin-10 (IL-10) and its receptor (IL-10R), key regulators of the immune response, are among these candidates. We studied the association of IL-10 and IL-10Rβ gene polymorphisms with the occurrence of GvHD in 309 HLA-identical sibling donor and recipient pairs.

Results
The difference in genotypic IL-10 production between patient and donor in combination with patient IL-10Rβ A/A genotype predisposed strongly to acute GvHD (OR = 7.15, p = 0.000023). On the other hand, a combination of same genotypic IL-10 production with patient IL-10Rβ A/A genotype protected from chronic GvHD (OR = 0.407, p = 0.0097).

Conclusion
Our results suggest that IL-10 and IL-10Rβ genes have a synergistic effect on the risk of GvHD.
Human sex hormone-binding globulin gene expression- multiple promoters and complex alternative splicing
Authors: Nakhla Atif M , Hryb Daniel J , Rosner William , Romas Nicholas A , Xiang Zhaoying , Kahn Scott M 
Published: May 2009

Abstract

Background
Human sex hormone-binding globulin (SHBG) regulates free sex steroid concentrations in plasma and modulates rapid, membrane based steroid signaling. SHBG is encoded by an eight exon-long transcript whose expression is regulated by a downstream promoter (PL). The SHBG gene was previously shown to express a second major transcript of unknown function, derived from an upstream promoter (PT), and two minor transcripts.

Results
We report that transcriptional expression of the human SHBG gene is far more complex than previously described. PL and PT direct the expression of at least six independent transcripts each, resulting from alternative splicing of exons 4, 5, 6, and/or 7. We mapped two transcriptional start sites downstream of PL and PT, and present evidence for a third SHBG gene promoter (PN) within the neighboring FXR2 gene; PN regulates the expression of at least seven independent SHBG gene transcripts, each possessing a novel, 164-nt first exon (1N). Transcriptional expression patterns were generated for human prostate, breast, testis, liver, and brain, and the LNCaP, MCF-7, and HepG2 cell lines. Each expresses the SHBG transcript, albeit in varying abundance. Alternative splicing was more pronounced in the cancer cell lines. PL- PT- and PN-derived transcripts were most abundant in liver, testis, and prostate, respectively. Initial findings reveal the existence of a smaller immunoreactive SHBG species in LNCaP, MCF-7, and HepG2 cells.

Conclusion
These results extend our understanding of human SHBG gene transcription, and raise new and important questions regarding the role of novel alternatively spliced transcripts, their function in hormonally responsive tissues including the breast and prostate, and the role that aberrant SHBG gene expression may play in cancer.
Application of biomedical informatics to chronic pediatric diseases: a systematic review
Authors: Moeinedin Fatemeh , Moineddin Rahim , Jadad Alejandro R , Hamid Jemila S , To Teresa , Beyene Joseph 
Published: May 2009

AbstractBackgroundChronic diseases affect millions of children worldwide leading to substantial disease burden to the children and their families as well as escalating health care costs. The increasing trend in the prevalence of complex pediatric chronic diseases requires innovative and optimal delivery of care. Biomedical informatics applications play an important role in improving health outcomes while being cost-effective. However, their utility in pediatric chronic diseases has not been studied in a comprehensive and systematic way. The objective of this study was to conduct a systematic review of the effects of biomedical informatics applications in pediatric chronic diseases.MethodsA comprehensive literature search was conducted using MEDLINE, the Cochrane Library and EMBASE databases from inception of each database to September 2008. We included studies of any methodological type and any language that applied biomedical informatics to chronic conditions in children and adolescents 18 years of age or younger. Two independent reviewers carried out study selection and data extraction. Quality assessment was performed using a study design evaluation instrument to appraise the strength of the studies and their methodological adequacy. Because of heterogeneity in the conditions and outcomes we studied, a formal meta-analysis was not performed.ResultsBased on our search strategy, 655 titles and abstracts were reviewed. From this set we identified 27 relevant articles that met our inclusion criteria. The results from these studies indicated that biomedical informatics applications have favourable clinical and patient outcomes including, but not limited to, reduced number of emergency room visits, improved knowledge on disease management, and enhanced satisfaction. Seventy percent of reviewed papers were published after year 2000, 89% of users were patients and 11% were either providers or caregivers. The majority (96%) of the selected studies reported improved outcomes.ConclusionPublished studies suggested positive impacts of informatics predominantly in pediatric asthma. As electronic tools become more widely adopted, there will be opportunities to improve patient care in a wide range of chronic illnesses through informatics solutions.
Test characteristics of two rapid antigen detection tests (SD FK50 and SD FK60) for the diagnosis of malaria in returned travellers
Authors: Van der Palen Mirna , Gillet Philippe , Bottieau Emmanuel , Cnops Lieselotte , Van Esbroeck Marjan , Jacobs Jan 
Published: May 2009

Abstract

Background
Two malaria rapid diagnostic tests were evaluated in a travel clinic setting: the SD FK50 Malaria Ag Plasmodium falciparum test (a two-band test) and the SD FK60 Malaria Ag P. falciparum/Pan test (a three-band test).

Methods
A panel of stored whole blood samples (n = 452 and n = 614 for FK50 and FK60, respectively) from returned travellers was used. The reference method was microscopy with PCR in case of discordant results.

Results
For both tests, overall sensitivity for the detection of P. falciparum was 93.5%, reaching 97.6% and 100% at parasite densities above 100 and 1,000/μl respectively. Overall sensitivities for Plasmodium vivax, Plasmodium ovale and Plasmodium malariae for the FK60 test were 87.5%, 76.3% and 45.2%, but they reached 92.6% and 90.5% for P. vivax and P. ovale at parasite densities above 500/μl. Specificities were above 95% for all species and both tests when corrected by PCR, with visible histidine-rich protein-2 lines for P. malariae (n = 3) and P. vivax and P. ovale (1 sample each). Line intensities were reproducible and correlated to parasite densities. The FK60 tests provided clues to estimate parasite densities for P. falciparum below or above 1,000/μl.

Conclusion
Both the FK50 and FK60 performed well for the diagnosis of P. falciparum in the present setting, and the FK60 for the diagnosis of P. vivax and P. ovale at parasite densities > 500/μl. The potential use of the FK60 as a semi-quantitative estimation of parasite density needs to be further explored.
Rate of red blood cell destruction varies in different strains of mice infected with Plasmodium berghei-ANKA after chronic exposure
Authors: Helegbe Gideon Kofi , Huy Nguyen T , Yanagi Tetsuo , Shuaibu Mohammed N , Yamazaki Akiko , Kikuchi Mihoko , Yasunami Michio , Hirayama Kenji 
Published: May 2009

AbstractBackgroundSevere malaria anaemia in the semi-immune individuals in the holo-endemic area has been observed to occur at low parasite density with individual variation in the responses. Thus the following has been thought to be involved: auto-immune-mediated mechanisms of uninfected red blood cell destruction, and host genetic factors to explain the differences in individual responses under the same malaria transmission. In this study, the extent of red blood cell (RBC) destruction in different strains of semi-immune mice model at relatively low parasitaemia was studied.MethodologyTo generate semi-immunity, four strains of mice were taken through several cycles of infection and treatment. By means of immunofluorescent assay and ELISA, sera were screened for anti-erythrocyte auto-antibodies, and their relationship with haematological parameters and parasitaemia in the strains of semi-immune mice was investigated.ResultsUpon challenge withPlasmodium bergheiANKA after generating semi-immune status, different mean percentage haemoglobin (Hb) drop was observed in the mice strains (Balb/c = 47.1%; NZW = 30.05%; C57BL/6 = 28.44%; CBA = 25.1%), which occurred on different days for each strain (for Balb/c, mean period = 13.6 days; for C57BL/6, NZW, and CBA mean period = 10.6, 10.8, 10.9 days respectively). Binding of antibody to white ghost RBCs was observed in sera of the four strains of semi-immune mice by immunofluorescence. Mean percentage Hb drop per parasitaemia was highest in Balb/c (73.6), followed by C57BL/6 (8.6), CBA (6.9) and NZW (4.0), p = 0.0005. Consequently, auto-antibodies level to ghost RBC were correlated with degree of anaemia and were highest in Balb/c, when compared with the other strains, p < 0.001.ConclusionThe results presented in this study seem to indicate that anti-RBC auto-antibodies may be involved in the destruction of uninfected RBC in semi-immune mice at relatively low parasite burden. Host genetic factors may also influence the outcome of auto-immune mediated destruction of RBC due to the variation in Hb loss per % parasitaemia and differences in antibody titer for each semi-immune mice strain. However, further studies at the molecular level ought to be carried out to confirm this.
Luteinizing hormone induces expression of 11beta-hydroxysteroid dehydrogenase type 2 in rat Leydig cells
Authors: Wang Qian , Zhang Ping , Gao Hui-Bao 
Published: May 2009

AbstractBackgroundLeydig cells are the primary source of testosterone in male vertebrates. The biosynthesis of testosterone in Leydig cells is strictly dependent on luteinizing hormone (LH). On the other hand, it can be directly inhibited by excessive glucocorticoid (Corticosterone, CORT, in rats) which is beyond the protective capability of 11beta-Hydroxysteroid dehydrogenase type 1 (11beta-HSD1) and type 2 (11beta-HSD2; encoded by gene Hsd11b2 in rats) in Leydig cells. Our previous study found that LH increases 11beta-HSD1 expression in rat Leydig cells, but the effect of LH on the expression and activity of 11beta-HSD2 is not investigated yet.MethodsThe Leydig cells were isolated from male Sprague-Dawley rats (90 days of age). After Leydig cells were incubated either for 24 h with various concentrations of LH (2.5, 5, 10 and 20 ng/mL) or for different time periods (2, 8, 12 and 24 h) with 20 ng/mL LH, the mRNA expression of 11beta-HSD2 was measured by real-time PCR. 11beta-HSD2 protein levels in Leydig cells were assayed by Western Blot and 11beta-HSD2 enzyme activity was determined by calculating the ratio of conversion of [3H]CORT to [3H]11-dehydrocorticosterone by 24 h after stimulation with 20 ng/ml LH. Four reporter gene plasmids containing various lengths of Hsd11b2 promoter region were constructed and transfected into mouse Leydig tumor cells to investigate the effect of LH on Hsd11b2 transcription. A glucocorticoid-responsive reporter gene plasmid, GRE-Luc, was constructed. To evaluate influence of LH on intracellular glucocorticoid level, rat Leydig cells were transfected with GRE-Luc, and luciferase activities were measured after incubation with CORT alone or CORT plus LH.ResultsWe observed dose- and temporal-dependent induction of rat 11beta-HSD2 mRNA expression in Leydig cells subject to LH stimulation. The protein and enzyme activity of 11beta-HSD2 and the luciferase activity of reporter gene driven by promoter regions of Hsd11b2 were increased by LH treatment. LH decreased the glucocorticoid-induced luciferase activity of GRE-Luc reporter gene.ConclusionThe results of the present study suggest that LH increases the expression and enzyme activity of 11beta-HSD2, and therefore enhances capacity for oxidative inactivation of glucocorticoid in rat Leydig cells in vitro.
Conservation of Nef function across highly diverse lineages of SIVsmm
Authors: Schmökel Jan , Li Hui , Bailes Elizabeth , Schindler Michael , Silvestri Guido , Hahn Beatrice H , Apetrei Cristian , Kirchhoff Frank 
Published: May 2009

AbstractBackgroundSIVsmm is a simian immunodeficiency virus that persists efficiently without causing disease in naturally infected sooty mangabeys (SMs) but induces AIDS upon cross-species transmission to humans and macaques. Current phylogenetic data indicate that SIVsmm strains comprise a highly diverse group of viruses that can be subdivided into different lineages. Since only certain SIVsmm strains have successfully crossed the species barrier to humans and macaques, the question has been raised whether there are lineage specific differences in SIVsmm biology. In the present study we examined whether representatives of five different SIVsmm lineages show differences in the function of the accessory Nef protein, which plays an important role in viral persistence, transmission and pathogenesis.ResultsWe found thatnefalleles from all SIVsmm lineages down-modulated CD4, MHC-I, CD28 and CD3 and up-regulated the invariant chain (Ii) associated with immature MHC-II molecules in human-derived cells. Moreover, they generally suppressed the responsiveness of virally infected T cells to activation, enhanced virion infectivity and promoted virus replication in human peripheral blood mononuclear cells. The functional activity of thesenefalleles in the various assays varied substantially between different strains of SIVsmm but quantitative analyses did not reveal any significant lineage-specific differences in Nef function.ConclusionNefalleles from different lineages of SIVsmm do not require adaptive changes to be functionally active in human cells. Strain rather than lineage-specific differences in Nef function may impact the virological and immunological feature of SIVsmm in SMs and possibly affected viral fitness and pathogenicity in human and macaque hosts.