bluuebunny/crossref_metadata_2025_split huggingface dataset:
DCL4 Targets
Cucumber Mosaic Virus
Satellite RNA at Novel Secondary Structures
Authors: Du Quan-Sheng , Duan Cheng-Guo , Zhang Zhong-Hui , Fang Yuan-Yuan , Fang Rong-Xiang , Xie Qi , Guo Hui-Shan 
Published: July 2007

ABSTRACT

It has been reported that plant virus-derived small interfering RNAs (vsiRNAs) originated predominantly from structured single-stranded viral RNA of a positive single-stranded RNA virus replicating in the cytoplasm and from the nuclear stem-loop 35S leader RNA of a double-stranded DNA (dsDNA) virus. Increasing lines of evidence have also shown that hierarchical actions of plant Dicer-like (DCL) proteins are required in the biogenesis process of small RNAs, and DCL4 is the primary producer of vsiRNAs. However, the structures of such single-stranded viral RNA that can be recognized by DCLs remain unknown. In an attempt to determine these structures, we have cloned siRNAs derived from the satellite RNA (satRNA) of
Cucumber mosaic virus
(CMV-satRNA) and studied the relationship between satRNA-derived siRNAs (satsiRNAs) and satRNA secondary structure. satsiRNAs were confirmed to be derived from single-stranded satRNA and are primarily 21 (64.7%) or 22 (22%) nucleotides (nt) in length. The most frequently cloned positive-strand satsiRNAs were found to derive from novel hairpins that differ from the structure of known DCL substrates, miRNA and siRNA precursors, which are prevalent stem-loop-shaped or dsRNAs. DCL4 was shown to be the primary producer of satsiRNAs. In the absence of DCL4, only 22-nt satsiRNAs were detected. Our results suggest that DCL4 is capable of accessing flexibly structured single-stranded RNA substrates (preferably T-shaped hairpins) to produce satsiRNAs. This result reveals that viral RNA of diverse structures may stimulate antiviral DCL activities in plant cells.
HIF-1 regulates heritable variation and allele expression phenotypes of the macrophage immune response gene SLC11A1 from a Z-DNA–forming microsatellite
Authors: Bayele Henry K. , Peyssonnaux Carole , Giatromanolaki Alexandra , Arrais-Silva Wagner W. , Mohamed Hiba S. , Collins Helen , Giorgio Selma , Koukourakis Michael , Johnson Randall S. , Blackwell Jenefer M. , Nizet Victor , Srai Surjit Kaila S. 
Published: July 2007

AbstractThe Ity/Lsh/Bcg locus encodes the macrophage protein Slc11a1/Nramp1, which protects inbred mice against infection by diverse intracellular pathogens including Leishmania, Mycobacterium, and Salmonella. Human susceptibility to infectious and inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and tuberculosis, shows allelic association with a highly polymorphic regulatory, Z-DNA–forming microsatellite of (GT/AC)n dinucleotides within the proximal SLC11A1 promoter. We surmised that cis-acting allelic polymorphisms may underlie heritable differences in SLC11A1 expression and phenotypic variation in disease risk. However, it is unclear what may underlie such variation in SLC11A1 allele expression. Here we show that hypoxia-inducible Factor 1 (HIF-1) regulates allelic variation in SLC11A1 expression by binding directly to the microsatellite during macrophage activation by infection or inflammation. Targeted Hif-1α ablation in murine macrophages attenuated Slc11a11 expression and responsiveness to S typhimurium infection. Our data also showed that HIF-1 may be functionally linked to complex prototypical inflammatory diseases associated with certain SLC11A1 alleles. As these alleles are highly polymorphic, our finding suggests that HIF-1 may influence heritable variation in SLC11A1-dependent innate resistance to infection and inflammation within and between populations. This report also suggests that microsatellites may play critical roles in the directional evolution of complex heritable traits by regulating gene expression phenotypes.
Expression profiling of Dexamethasone-treated primary chondrocytes identifies targets of glucocorticoid signalling in endochondral bone development
Authors: James Claudine G , Ulici Veronica , Tuckermann Jan , Underhill T Michael , Beier Frank 
Published: July 2007

Abstract

Background
Glucocorticoids (GCs) are widely used anti-inflammatory drugs. While useful in clinical practice, patients taking GCs often suffer from skeletal side effects including growth retardation in children and adolescents, and decreased bone quality in adults. On a physiological level, GCs have been implicated in the regulation of chondrogenesis and osteoblast differentiation, as well as maintaining homeostasis in cartilage and bone. We identified the glucocorticoid receptor (GR) as a potential regulator of chondrocyte hypertrophy in a microarray screen of primary limb bud mesenchyme micromass cultures. Some targets of GC regulation in chondrogenesis are known, but the global effects of pharmacological GC doses on chondrocyte gene expression have not been comprehensively evaluated.

Results
This study systematically identifies a spectrum of GC target genes in embryonic growth plate chondrocytes treated with a synthetic GR agonist, dexamethasone (DEX), at 6 and 24 hrs. Conventional analysis of this data set and gene set enrichment analysis (GSEA) was performed. Transcripts associated with metabolism were enriched in the DEX condition along with extracellular matrix genes. In contrast, a subset of growth factors and cytokines were negatively correlated with DEX treatment. Comparing DEX-induced gene expression data to developmental changes in gene expression in micromass cultures revealed an additional layer of complexity in which DEX maintains the expression of certain chondrocyte marker genes while inhibiting factors that promote vascularization and ultimately ossification of the cartilaginous template.

Conclusion
Together, these results provide insight into the mechanisms and major molecular classes functioning downstream of DEX in primary chondrocytes. In addition, comparison of our data with microarray studies of DEX treatment in other cell types demonstrated that the majority of DEX effects are tissue-specific. This study provides novel insights into the effects of pharmacological GC on chondrocyte gene transcription and establishes the foundation for subsequent functional studies.
Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource
Authors: Adzhubei Alexei A , Vlasova Anna V , Hagen-Larsen Heidi , Ruden Torgeir A , Laerdahl Jon K , Høyheim Bjørn 
Published: July 2007

Abstract

Background
To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service.

Description
Twenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component.

Conclusion
We describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches.
Health inequalities in Germany: do regional-level variables explain differentials in cardiovascular risk?
Authors: Breckenkamp Juergen , Mielck Andreas , Razum Oliver 
Published: July 2007

Abstract

Background
Socioeconomic status is a predictor not only of mortality, but also of cardiovascular risk and morbidity. An ongoing debate in the field of social inequalities and health focuses on two questions: 1) Is individual health status associated with individual income as well as with income inequality at the aggregate (e. g. regional) level? 2) If there is such an association, does it operate via a psychosocial pathway (e.g. stress) or via a "neo-materialistic" pathway (e.g. systematic under-investment in societal infrastructures)? For the first time in Germany, we here investigate the association between cardiovascular health status and income inequality at the area level, controlling for individual socio-economic status.

Methods
Individual-level explanatory variables (age, socio-economic status) and outcome data (body mass index, blood pressure, cholesterol level) as well as the regional-level variable (proportion of relative poverty) were taken from the baseline survey of the German Cardiovascular Prevention Study, a cross-sectional, community-based, multi-center intervention study, comprising six socio-economically diverse intervention regions, each with about 1800 participants aged 25–69 years. Multilevel modeling was used to examine the effects of individual and regional level variables.

Results
Regional effects are small compared to individual effects for all risk factors analyzed. Most of the total variance is explained at the individual level. Only for diastolic blood pressure in men and for cholesterol in both men and women is a statistically significant effect visible at the regional level.

Conclusion
Our analysis does not support the assumption that in Germany cardiovascular risk factors were to a large extent associated with income inequality at regional level.
Prescribing cycle training intensity from the six-minute walk test for patients with COPD
Authors: Zainuldin Muhammad R , Knoke Danielle , Mackey Martin G , Luxton Nia , Alison Jennifer A 
Published: July 2007

Abstract

Background
Cycle training intensity for patients with chronic obstructive pulmonary disease (COPD) is normally based on an incremental cycle test. Such tests are expensive and not readily available to clinicians. The six-minute walk test (6MWT) has been proposed as an alternative to an incremental cycle test for this purpose, based on the findings of previous research that the peak oxygen consumption (VO2peak) for the incremental cycle test and the 6MWT was equivalent in participants with COPD. A regression equation relating distance walked on the 6MWT and peak work rate (Wpeak) on the incremental cycle test has been described. The aim of this study is to measure the physiological responses to constant load cycle exercise performed at an intensity of 60% Wpeak determined from the 6MWT in participants with stable COPD.

Methods/Design
This study is a prospective, repeated measures design. Thirty-five participants with stable COPD and mild to severe lung disease will be recruited from referrals to pulmonary rehabilitation. Subjects with co-morbidities limiting exercise performance will be excluded. Two 6MWTs will be performed. The better 6MWT will be used to calculate Wpeak for cycle exercise from a regression equation. After 30 minutes rest, subjects will perform ten minutes of constant-load cycle exercise at 60% of the calculated Wpeak. During all exercise, cardiorespiratory and metabolic data (Cosmed K4b2), dyspnoea and rate of perceived exertion (RPE) will be recorded. The VO2 measured at the end of cycle exercise will be compared to VO2peak of the 6MWT (VO2bike/VO2walk). Pearson's correlation coefficient will be calculated for the relationship between VO2bike and VO2walk. A one-way analysis of variance (ANOVA), with Bonferroni correction, will be performed to determine whether the ratio of VO2bike/VO2walk is affected by disease severity.

Discussion
This novel study will measure the physiological responses to cycle exercise, in terms of VO2peak, performed at an intensity determined from the 6MWT in participants with COPD. Positive findings will enable clinicians to more precisely prescribe cycle training intensity by utilising a simple, reliable and inexpensive 6MWT, thus providing a better standard of care for patients with COPD referred to pulmonary rehabilitation.

Trial Registration
ACTRNO12606000496516
Acute and delayed neuroinflammatory response following experimental penetrating ballistic brain injury in the rat
Authors: Williams Anthony J , Wei Hans H , Dave Jitendra R , Tortella Frank C 
Published: July 2007

Abstract

Background
Neuroinflammation following acute brain trauma is considered to play a prominent role in both the pathological and reconstructive response of the brain to injury. Here we characterize and contrast both an acute and delayed phase of inflammation following experimental penetrating ballistic brain injury (PBBI) in rats out to 7 days post-injury.

Methods
Quantitative real time PCR (QRT-PCR) was used to evaluate changes in inflammatory gene expression from the brain tissue of rats exposed to a unilateral frontal PBBI. Brain histopathology was assessed using hematoxylin and eosin (H&E), silver staining, and immunoreactivity for astrocytes (GFAP), microglia (OX-18) and the inflammatory proteins IL-1β and ICAM-1.

Results
Time course analysis of gene expression levels using QRT-PCR indicated a peak increase during the acute phase of the injury between 3–6 h for the cytokines TNF-α (8–11 fold), IL-1β (11–13 fold), and IL-6 (40–74 fold) as well as the cellular adhesion molecules VCAM (2–3 fold), ICAM-1 (7–15 fold), and E-selectin (11–13 fold). Consistent with the upregulation of pro-inflammatory genes, peripheral blood cell infiltration was a prominent post-injury event with peak levels of infiltrating neutrophils (24 h) and macrophages (72 h) observed throughout the core lesion. In regions of the forebrain immediately surrounding the lesion, strong immunoreactivity for activated astrocytes (GFAP) was observed as early as 6 h post-injury followed by prominent microglial reactivity (OX-18) at 72 h and resolution of both cell types in cortical brain regions by day 7. Delayed thalamic inflammation (remote from the primary lesion) was also observed as indicated by both microglial and astrocyte reactivity (72 h to 7 days) concomitant with the presence of fiber degeneration (silver staining).

Conclusion
In summary, PBBI induces both an acute and delayed neuroinflammatory response occurring in distinct brain regions, which may provide useful diagnostic information for the treatment of this type of brain injury.
Renal-hepatic-pancreatic dysplasia syndrome (ivemark's syndrome)
Authors: Vankalakunti Mahesha , Gupta Kirti , Kakkar Nandita , Das Ashim 
Published: July 2007

Abstract

Background
Renal-Hepatic-Pancreatic dysplasia syndrome described by Ivemark in 1959 constitutes a triad pancreatic fibrosis, renal dysplasia and hepatic dysgenesis.

Case presentation
We describe two unrelated cases of Renal-Hepatic-Pancreatic dysplasia syndrome in stillborn babies. The characteristic microscopic features were present in both the cases. The second case illustrates the unique association lymphangiectasia with Renal-Hepatic-Pancreatic dysplasia syndrome. Both cases are unrelated and there is no history of any consanguineous marriage.

Conclusion
These two cases are unrelated and are rare. In the developmental research, the perinatal autopsy needs to be utilized as a major tool and an Ad hoc committee formation is required to formulate the approach towards syndromic diseases.
Metabolic network visualization eliminating node redundance and preserving metabolic pathways
Authors: Bourqui Romain , Cottret Ludovic , Lacroix Vincent , Auber David , Mary Patrick , Sagot Marie-France , Jourdan Fabien 
Published: July 2007

AbstractBackgroundThe tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.ResultsWe propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster.ConclusionThe method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.
Dexamethasone to prevent postextubation airway obstruction in adults: a prospective, randomized, double-blind, placebo-controlled study
Authors: Lee Chao-Hsien , Peng Ming-Jen , Wu Chien-Liang 
Published: July 2007

Abstract
Introduction
Prophylactic steroid therapy to reduce the occurrence of postextubation laryngeal edema is controversial. Only a limited number of prospective trials involve adults in an intensive care unit. The purpose of this study was to ascertain whether administration of multiple doses of dexamethasone to critically ill, intubated patients reduces or prevents the occurrence of postextubation airway obstruction. Another specific objective of our study was to investigate whether an after-effect (that is, a transient lingering benefit) exists 24 hours after the discontinuation of dexamethasone.

Methods
A randomized, placebo-controlled, double-blind trial was conducted in an adult medical intensive care unit of a tertiary care hospital. Eighty-six patients who had been intubated for more than 48 hours with a cuff leak volume (CLV) of less than 110 ml and who met weaning criteria were randomly assigned to receive either dexamethasone (5 mg; n = 43) or placebo (normal saline; n = 43) every six hours for a total of four doses on the day preceding extubation. CLV was measured before the first injection, one hour after each injection, and 24 hours after the fourth injection. Extubation was carried out 24 hours after the last injection. Postextubation obstruction (defined as the presence of stridor) was recorded within 48 hours of extubation.

Results
Administration of dexamethasone during the 24-hour period preceding extubation resulted in a statistically significant increase in the CLV (p < 0.05). The significant increase of CLV and change of CLV relative to baseline tidal volume (percentage) occurred not only throughout the treatment period, but also 24 hours after the last dexamethasone injection. The incidence of postextubation stridor was significantly lower in the dexamethasone group than in the placebo group (10% [4/40] versus 27.5% [11/40]; p = 0.037), whereas there was no significant difference in reintubation rate between the two groups (2.5% [1/40] versus 5% [2/40]; p = 0.561).

Conclusion
Prophylactic administration of multiple-dose dexamethasone is effective in reducing the incidence of postextubation stridor in adult patients at high risk for postextubation laryngeal edema. The after-effect of dexamethasone may validate the reduced incidence of postextubation stridor after multiple doses of dexamethasone.

Trial registration
NCT00452062.
Two Cycles of Doxorubicin, Bleomycin, Vinblastine, and Dacarbazine Plus Extended-Field Radiotherapy Is Superior to Radiotherapy Alone in Early Favorable Hodgkin's Lymphoma: Final Results of the GHSG HD7 Trial
Authors: Engert Andreas , Franklin Jeremy , Eich Hans Theodor , Brillant Corinne , Sehlen Susanne , Cartoni Claudio , Herrmann Richard , Pfreundschuh Michael , Sieber Markus , Tesch Hans , Franke Astrid , Koch Peter , de Wit Maike , Paulus Ursula , Hasenclever Dirk , Loeffler Markus , Müller Rolf-Peter , Müller-Hermelink Hans Konrad , Dühmke Eckhart , Diehl Volker 
Published: July 2007

Purpose To investigate whether combined-modality treatment (CMT) with two cycles of doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) followed by extended-field radiotherapy (EF-RT) is superior to EF-RT alone in patients with early favorable Hodgkin's lymphoma (HL). Patients and Methods Between 1993 and 1998, 650 patients with newly diagnosed, histology-proven HL in clinical stages IA to IIB without risk factors were enrolled onto this multicenter study and randomly assigned to receive 30 Gy EF-RT plus 10 Gy to the involved field (arm A) or two cycles of ABVD followed by the same radiotherapy (arm B). Results At a median observation time of 87 months, there was no difference between treatment arms in terms of complete response rate (arm A, 95%; arm B, 94%) and overall survival (at 7 years: arm A, 92%; arm B, 94%; P = .43). However, freedom from treatment failure was significantly different, with 7-year rates of 67% in arm A (95% CI, 61% to 73%) and 88% in arm B (95% CI, 84% to 92%; P ≤ .0001). This was due mainly to significantly more relapses after EF-RT only (arm A, 22%; arm B, 3%). No patient treated with CMT experienced relapse before year 3. Relapses were treated mainly with bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone, or with the combination cyclophosphamide, vincristine, procarbazine, and prednisone/ABVD; treatment of relapse was significantly more successful in arm A than in arm B (P = .017). In total, there were 39 second malignancies, with 21 in arm A and 18 in arm B, respectively. The incidence was approximately 0.8% per year during years 2 to 9 and was highest in older patients (P < .0001) and those with “B” symptoms (P = .012). Conclusion CMT consisting of two cycles of ABVD plus EF-RT is more effective than EF-RT alone.
Bending of normally loaded simply supported rectangular plates in the large-deflection range
Authors: Scholes A , Bernstein E L 
Published: July 2007

Means of solving the non-linear differential equations of plate bending are revieweed and a method based on minimizing the corresponding energy integral is selected as offering most advantages. The energy intergral can be approximated either by using finite-difference approximatons or by assuming a form of displacement variation. Two sets of non-linear algebraic equations (in the in-plane and out-of-plane deflections) are thus formed and, by substitution alternately in each set, the resulting linear equations are solved. Results for simply supported rectangular plates have been worked out in some detail; these are compared with tests made on plates of various aspect ratios. Good agreement on maximum values of stress and deflection was obtained.