bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of Epidermal Growth Factor Receptor Expression by Epstein-Barr Virus Latent Membrane Protein 1 C-Terminal-Activating Region 1 Is Mediated by NF-κB p50 Homodimer/Bcl-3 Complexes
Authors: Thornburg Natalie J. , Raab-Traub Nancy 
Published: September 2007

ABSTRACT

The Epstein-Barr virus (EBV) is associated with the development of numerous malignancies, including the epithelial malignancy nasopharyngeal carcinoma (NPC). The viral oncoprotein latent membrane protein 1 (LMP1) is expressed in almost all EBV-associated malignancies and has profound effects on gene expression. LMP1 acts as a constitutively active tumor necrosis factor receptor and activates multiple forms of the NF-κB family of transcription factors. LMP1 has two domains that both activate NF-κB. In epithelial cells, LMP1 C-terminal activating region 1 (CTAR1) uniquely activates p50/p50-, p50/p52-, and p65-containing complexes while CTAR2 activates canonical p50/p65 complexes. CTAR1 also uniquely upregulates the epidermal growth factor receptor (EGFR). In NPC, NF-κB p50/p50 homodimers and the transactivator Bcl-3 were detected on the EGFR promoter. In this study, the role of NF-κB p50 and Bcl-3 in LMP1-mediated upregulation of EGFR was analyzed. In LMP1-CTAR1-expressing cells, chromatin immunoprecipitation detected p50 and Bcl-3 on the NF-κB consensus sites within the
egfr
promoter. Transient overexpression of p50 and Bcl-3 increased EGFR expression, confirming the regulation of EGFR by these factors. Treatment with p105/p50 siRNA effectively reduced p105/p50 levels but unexpectedly increased Bcl-3 expression and levels of p50/Bcl-3 complexes, resulting in increased EGFR expression. These data suggest that induction of p50/p50/Bcl-3 complexes by LMP1 CTAR1 mediates LMP1-induced EGFR upregulation and that formation of the p50/p50/Bcl-3 complex is negatively regulated by the p105 precursor. The distinct forms of NF-κB that are induced by LMP1 CTAR1 likely activate distinct cellular genes.
Characterization of a Second Vaccinia Virus mRNA-Decapping Enzyme Conserved in Poxviruses
Authors: Parrish Susan , Moss Bernard 
Published: September 2007

ABSTRACT

Vaccinia virus (VACV) encodes enzymes that cap the 5′ end of viral mRNAs, which enhances their stability and translation. Nevertheless, recent studies demonstrated that the VACV D10 protein (VACV-WR_115) decaps mRNA, an enzymatic activity not previously shown to be encoded by a virus. The decapping activity of D10 is dependent on a Nudix hydrolase motif that is also present in the VACV D9 protein (VACV-WR_114), which shares 25% sequence identity with D10. Here, we showed that a purified recombinant VACV D9 fusion protein also decaps mRNA and that this activity was abolished by point mutations in the Nudix hydrolase motif. Decapping was specific for a methylated cap attached to RNA and resulted in the liberation of m
7
GDP. D9 differed from D10 in requiring a longer capped RNA substrate for optimal activity, having greater sensitivity to inhibition by uncapped RNA, and having lower sensitivity to inhibition by nucleotide cap analogs unattached to RNA. Since D9 is expressed early in infection and D10 late, we suggest that the two proteins enhance mRNA turnover and manipulate gene expression in a complementary and overlapping manner.
Kaposi's Sarcoma-Associated Herpesvirus Encodes an Ortholog of miR-155
Authors: Skalsky Rebecca L. , Samols Mark A. , Plaisance Karlie B. , Boss Isaac W. , Riva Alberto , Lopez M. Cecilia , Baker Henry V. , Renne Rolf 
Published: September 2007

ABSTRACT
MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate gene expression by binding to 3′-untranslated regions (3′UTRs) of target mRNAs. Kaposi's sarcoma-associated herpesvirus (KSHV), a virus linked to malignancies including primary effusion lymphoma (PEL), encodes 12 miRNA genes, but only a few regulatory targets are known. We found that KSHV-miR-K12-11 shares 100% seed sequence homology with hsa-miR-155, an miRNA frequently found to be up-regulated in lymphomas and critically important for B-cell development. Based on this seed sequence homology, we hypothesized that both miRNAs regulate a common set of target genes and, as a result, could have similar biological activities. Examination of five PEL lines showed that PELs do not express miR-155 but do express high levels of miR-K12-11. Bioinformatic tools predicted the transcriptional repressor BACH-1 to be targeted by both miRNAs, and ectopic expression of either miR-155 or miR-K12-11 inhibited a BACH-1 3′UTR-containing reporter. Furthermore, BACH-1 protein levels are low in cells expressing either miRNA. Gene expression profiling of miRNA-expressing stable cell lines revealed 66 genes that were commonly down-regulated. For select genes, miRNA targeting was confirmed by reporter assays. Thus, based on our in silico predictions, reporter assays, and expression profiling data, miR-K12-11 and miR-155 regulate a common set of cellular targets. Given the role of miR-155 during B-cell maturation, we speculate that miR-K12-11 may contribute to the distinct developmental phenotype of PEL cells, which are blocked in a late stage of B-cell development. Together, these findings indicate that KSHV miR-K12-11 is an ortholog of miR-155.
Factors associated with long-term sick leave in sick-listed employees: a systematic review
Authors: Dekkers-Sánchez P M , Hoving J L , Sluiter J K , Frings-Dresen M H W 
Published: September 2007

Objective:The objective of this systematic review was to investigate which factors are associated with continued sick leave among workers on sick leave for at least 6 weeks.Methods:A systematic literature search was performed in Medline, EMBASE and PsycINFO, based on combinations of MeSH terms and free text words. Only cohort studies of workers on sick leave for more than 6 weeks at baseline were included. Outcome was measured in terms of factors related to long-term sick leave. The factors were classified first as predisposing, precipitating or perpetuating factors, and then as individual or work-related factors. Methodological quality was assessed for all studies and the strength of the evidence for each factor was assessed using the levels of evidence rating system.Results:Five cohort studies fulfilled all inclusion criteria and 77 factors were investigated. Of these, 16 different significant factors associated with long-term sick leave were identified and were all classified as predisposing factors. Evidence was found for 14 individual factors and two work-related factors. The level of evidence was found to be insufficient for all factors except older age and history of sick leave, which were found to have weak evidence.Conclusions:Based on this review, there is weak evidence that older age and history of sickness absence are factors associated with long-term sick leave in sick-listed employees. There is insufficient evidence for an effect of other individual or work-related factors on long-term sick leave. There are no published studies on perpetuating factors related to long-term sick leave.
Change In Total Angular Momentum Within The Z3F0 Titanium Excited StateInduced By Collisions With Hydrogen And Nitrogen Molecules
Authors: Quichaud V. , Dézert D. , Aubreton J. , Degout D. , Catherinot A. 
Published: September 2007

Collisions that produce a change in the total angular‐momentum and quenching processes involving the
triplet Z3F0 titanium excited level and diatomic molecules have been studied by laser perturbation and
time‐resolved spectroscopy. The thermally averaged total angular‐momentum changing cross sections
in units of

urn:x-wiley:02786273:media:lc030758:lc030758-math-0002

, respectively, for nitrogen and hydrogen colliding partners.Large quenching cross sections are obtained, as , and in units of 10-16 cm2.
These results are discussed in relation with previous measurements dealing with titanium‐noble‐gas
collisions, and with available published results.
Spectroscopic Study of Hydrogen Bonded7‐Azaindole Clusters
Authors: Nakajima A. , Ono F. , Kihara Y. , Ogawa A. , Matsubara K. , Ishikawa K. , Baba M. , kaya k. 
Published: September 2007

The geometric structures of 7‐azaindole (7‐AzI) and its dimer were investigated by laser‐induced fluorescence (LIF). The rotationally resolved LIF spectrum (resolution: ∼0.00003 cm-1 of 7‐AzI monomer shows that (i) rotational constants are A′′ 0.13082(5), B′′ = 0.05677(2), C′′ = 0.03970(1), A′ = 0.12468(5), B′ = 0.056752(2), and C′ = 0.03911(1), and (ii) the transition dipole moment direction is tilted at an angle of ± 21(5) degrees with respect to a axis. The LIF spectrum (resolution: ∼0.06 cm-1) of the nonreactive 7‐AzI dimer suggests there are three possibilities for the geometric structure, having “single bonded”, “T‐shaped”, and “non‐planar” structures.The ionization energy of 7‐AzI was determined to be 8.1171(5) eV by using pulsed‐field ionization photoelectron spectroscopy (PFI‐PES). Several vibronic bands of 7‐AzI cation were observed and compared with those of neutral 7‐AzI in the S0 and S1 states. The electron binding energies of 7‐AzI cluster anions (2 ≤ n ≤ 5) were determined by photoelectron spectroscopy.
Time‐Resolved Resonance RamanSpectroscopy of Excited‐StatePorphyrins
Authors: Bell S. E. J. , Rice J. H. , McGarvey J. J. , Hester R. E. , Moore J. N. , Perutz R. N. , Ye T.-Q. , Mizutani Y. , Kitagawa T. 
Published: September 2007

Time‐resolved resonance Raman (TR3) and absorbance difference studies of the excited
states of Cu(TPP) (TPP=5,10,15,20‐tetraphenylporphyrin) have been carried out with
< 10 ps times resolution in THF and pyridine solvents. In THF the distinctive transient
Raman bands in the ν2 and ν4 regions, previously observed with ns laser pulses, grow in
the first 55 ps before decaying in 100′s of ps. The ∆A spectra also show biphasic decay.
This behaviour is associated with attack by solvent on the 4‐coordinate excited state to
form the longer lived species observed in TR3 experiments.In pyridine two component decay is also observed but it is the shorter‐lived species
which gives the transient Raman bands seen previously with ns laser excitation. This
state is different from that seen in THF. At 5 ps delay ν4 is broader than in the ground
state and, more importantly, there is a significant shift in the two pyridine bands at ca.
1000 cm-1. This implies a significant involvement of the pyridine‐based orbitals in the
excited state.
Structural and functional implications of positive selection at the primate angiogenin gene
Authors: Osorio Daniel S , Antunes Agostinho , Ramos Maria J 
Published: September 2007

Abstract

Background
Angiogenesis, the formation of new blood vessels, is a primordial process in development and its dysregulation has a central role in the pathogenesis of many diseases. Angiogenin (ANG), a peculiar member of the RNase A superfamily, is a potent inducer of angiogenesis involved in many different types of cancer, amyotrophic lateral sclerosis and also with a possible role in the innate immune defense. The evolutionary path of this family has been a highly dynamic one, where positive selection has played a strong role. In this work we used a combined gene and protein level approach to determine the main sites under diversifying selection on the primate ANG gene and analyze its structural and functional implications.

Results
We obtained evidence for positive selection in the primate ANG gene. Site specific analysis pointed out 15 sites under positive selection, most of which also exhibited drastic changes in amino acid properties. The mapping of these sites in the ANG 3D-structure described five clusters, four of which were located in functional regions: two in the active site region, one in the nucleolar location signal and one in the cell-binding site. Eight of the 15 sites under selection in the primate ANG gene were highly or moderately conserved in the RNase A family, suggesting a directed event and not a simple consequence of local structural or functional permissiveness. Moreover, 11 sites were exposed to the surface of the protein indicating that they may influence the interactions performed by ANG.

Conclusion
Using a maximum likelihood gene level analysis we identified 15 sites under positive selection in the primate ANG genes, that were further corroborated through a protein level analysis of radical changes in amino acid properties. These sites mapped onto the main functional regions of the ANG protein. The fact that evidence for positive selection is present in all ANG regions required for angiogenesis may be a good indication that angiogenesis is the process under selection. However, other possibilities to be considered arise from the possible involvement of ANG in innate immunity and the potential influence or co-evolution with its interacting proteins and ligands.
Quantitative measurement of pathogen specific human memory T cell repertoire diversity using a CDR3β-specific microarray
Authors: Wang Xujing , Jia Shuang , Meyer Lisa , Yassai Maryam B , Naumov Yuri N , Gorski Jack , Hessner Martin J 
Published: September 2007

AbstractBackgroundProviding quantitative microarray data that is sensitive to very small differences in target sequence would be a useful tool in any number of venues where a sample can consist of a multiple related sequences present in various abundances. Examples of such applications would include measurement of pseudo species in viral infections and the measurement of species of antibodies or T cell receptors that constitute immune repertoires. Difficulties that must be overcome in such a method would be to account for cross-hybridization and for differences in hybridization efficiencies between the arrayed probes and their corresponding targets. We have used the memory T cell repertoire to an influenza-derived peptide as a test case for developing such a method.ResultsThe arrayed probes were corresponded to a 17 nucleotide TCR-specific region that distinguished sequences differing by as little as a single nucleotide. Hybridization efficiency between highly related Cy5-labeled subject sequences was normalized by including an equimolar mixture of Cy3-labeled synthetic targets representing all 108 arrayed probes. The same synthetic targets were used to measure the degree of cross hybridization between probes. Reconstitution studies found the system sensitive to input ratios as low as 0.5% and accurate in measuring known input percentages (R2= 0.81, R = 0.90, p < 0.0001). A data handling protocol was developed to incorporate the differences in hybridization efficiency. To validate the array in T cell repertoire analysis, it was used to analyze human recall responses to influenza in three human subjects and compared to traditional cloning and sequencing. When evaluating the rank order of clonotype abundance determined by each method, the approaches were not found significantly different (Wilcoxon rank-sum test, p > 0.05).ConclusionThis novel strategy appears to be robust and can be adapted to any situation where complex mixtures of highly similar sequences need to be quantitatively resolved.
Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing
Authors: Schlueter Jessica A , Lin Jer-Young , Schlueter Shannon D , Vasylenko-Sanders Iryna F , Deshpande Shweta , Yi Jing , O'Bleness Majesta , Roe Bruce A , Nelson Rex T , Scheffler Brian E , Jackson Scott A , Shoemaker Randy C 
Published: September 2007

Abstract

Background
Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.

Results
Seventeen BACs representing ~2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.

Conclusion
This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.
Multidisciplinary outpatient care program for patients with chronic low back pain: design of a randomized controlled trial and cost-effectiveness study [ISRCTN28478651]
Authors: Lambeek Ludeke C , Anema Johannes R , van Royen Barend J , Buijs Peter C , Wuisman Paul I , van Tulder Maurits W , van Mechelen Willem 
Published: September 2007

AbstractBackgroundChronic low back pain (LBP) is a major public and occupational health problem, which is associated with very high costs. Although medical costs for chronic LBP are high, most costs are related to productivity losses due to sick leave. In general, the prognosis for return to work (RTW) is good but a minority of patients will be absent long-term from work. Research shows that work related problems are associated with an increase in seeking medical care and sick leave. Usual medical care of patients is however, not specifically aimed at RTW.The objective is to present the design of a randomized controlled trial, i.e. the BRIDGE-study, evaluating the effectiveness in improving RTW and cost-effectiveness of a multidisciplinary outpatient care program situated in both primary and outpatient care setting compared with usual clinical medical care for patients with chronic LBP.Methods/DesignThe design is a randomized controlled trial with an economic evaluation alongside. The study population consists of patients with chronic LBP who are completely or partially sick listed and visit an outpatient clinic of one of the participating hospitals in Amsterdam (the Netherlands). Two interventions will be compared. 1. a multidisciplinary outpatient care program consisting of a workplace intervention based on participatory ergonomics, and a graded activity program using cognitive behavioural principles. 2. usual care provided by the medical specialist, the occupational physician, the patient's general practitioner and allied health professionals. The primary outcome measure is sick leave duration until full RTW. Sick leave duration is measured monthly by self-report during one year. Data on sick leave during one-year follow-up are also requested form the employers. Secondary outcome measures are pain intensity, functional status, pain coping, patient satisfaction and quality of life. Outcome measures are assessed before randomization and 3, 6, and 12 months later. All statistical analysis will be performed according to the intension-to-treat principle.DiscussionUsual care of primary and outpatient health services isn't directly aimed at RTW, therefor it is desirable to look for care which is aimed at RTW. Research shows that several occupational interventions in primary care are aimed at RTW. They have shown a significant reduction of sick leave for employee with LBP. If a comparable reduction of sick leave duration of patients with chronic LBP of who attend an outpatient clinic can be achieved, such reductions will be obviously substantial for the Netherlands and will have a considerable impact.Trial registrationISRCTN28478651
Collecting data for sexually transmitted infections (STI) surveillance: what do patients prefer in Flanders?
Authors: Verhoeven Veronique , Colliers Annelies , Verster Ann , Avonts Dirk , Peremans Lieve , Van Royen Paul 
Published: September 2007

Abstract
Background
STI surveillance systems are subject to qualitative and quantitative underreporting. General practitioners (GPs), who are key subjects in case reporting, explain their underreporting partly by their observation that taking a sexual history is embarrassing for patients, and that patients are reluctant to disclose information on their sexual practices. In this study we examine patients' willingness to provide data for STI surveillance.

Methods
A questionnaire-based survey in a stratified population sample of 300 patients aged 18–60 years.

Results
The large majority of respondents stated to be willing to give information on their sexual practices for the purpose of STI surveillance. They preferred to answer sexual history questions to their GP; filling in a form on the internet was the second best option.

Conclusion
Based on these results, it is unlikely that the cooperation of patients would be a weak link in STI surveillance strategies. This observation, together with the fact that the majority of patients at risk for STIs have regular access to general practice services, justify renewed efforts to enliven primary care-based STI surveillance strategies.
Trends in hyperlipidemia and hypertension management in type 2 diabetes patients from 1998–2004: a longitudinal observational study
Authors: Greving Jacoba P , Denig Petra , de Zeeuw Dick , Bilo Henk JG , Haaijer-Ruskamp Flora M 
Published: September 2007

Abstract

Background
Lack of treatment initiation or intensification might explain why some patients with type 2 diabetes do not reach target goals. The objective is to assess trends in risk factor treatment, and identify determinants for medication adjustments in patients with uncontrolled hypertension and/or hyperlipidemia.

Methods
We conducted a cohort study using data from the Zwolle Outpatient Diabetes project Integrated Available Care (ZODIAC)-study in The Netherlands. Management of hypertension and hyperlipidemia was assessed yearly from 1998–2004 by measuring the percentage of patients receiving a treatment initiation or intensification among all patients with elevated risk factor levels. Generalized estimating equation analyses were performed.

Results
During the study period, the percentage of patients with an elevated total cholesterol/high-density lipoproteins ratio (>6) decreased considerably (from 29% to 4%) whereas the percentage of hypertensive patients decreased only slightly (≥ 150/85 mmHg; from 58% to 51%). Initiation of lipid-lowering therapy and intensification of antihypertensive therapy was higher in more recent years. However, still two-third of patients with insufficiently controlled blood pressure in 2003 did not receive an initiation or intensification of antihypertensive treatment in the following year. Treatment changes were mainly determined by elevated levels of the corresponding risk factor. We did not observe increased initiation rates for lipid-lowering therapy in patients with both hypertension and hyperlipidemia.

Conclusion
Hypertension and hyperlipidemia management in type 2 diabetes patients has improved in the past decade but further improvement is possible. Greater effort is needed to stimulate medication adjustments in patients with insufficiently controlled hypertension and combined risk factors.