bluuebunny/crossref_metadata_2025_split huggingface dataset:
The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa
Authors: Saban Marcia R , Hellmich Helen L , Turner Mary , Nguyen Ngoc-Bich , Vadigepalli Rajanikanth , Dyer David W , Hurst Robert E , Centola Michael , Saban Ricardo 
Published: January 2006

AbstractBackgroundAn organ such as the bladder consists of complex, interacting set of tissues and cells. Inflammation has been implicated in every major disease of the bladder, including cancer, interstitial cystitis, and infection. However, scanty is the information about individual detrusor and urothelium transcriptomes in response to inflammation. Here, we used suppression subtractive hybridizations (SSH) to determine bladder tissue- and disease-specific genes and transcriptional regulatory elements (TRE)s. Unique TREs and genes were assembled into putative networks.ResultsIt was found that the control bladder mucosa presented regulatory elements driving genes such as myosin light chain phosphatase and calponin 1 that influence the smooth muscle phenotype. In the control detrusor network the Pax-3 TRE was significantly over-represented. During development, the Pax-3 transcription factor (TF) maintains progenitor cells in an undifferentiated state whereas, during inflammation, Pax-3 was suppressed and genes involved in neuronal development (synapsin I) were up-regulated. Therefore, during inflammation, an increased maturation of neural progenitor cells in the muscle may underlie detrusor instability. NF-κB was specifically over-represented in the inflamed mucosa regulatory network. When the inflamed detrusor was compared to control, two major pathways were found, one encodingsynapsin I, a neuron-specific phosphoprotein, and the other an important apoptotic protein,siva. In response to LPS-induced inflammation, the liver X receptor was over-represented in both mucosa and detrusor regulatory networks confirming a role for this nuclear receptor in LPS-induced gene expression.ConclusionA new approach for understanding bladder muscle-urothelium interaction was developed by assembling SSH, real time PCR, and TRE analysis results into regulatory networks. Interestingly, some of the TREs and their downstream transcripts originally involved in organogenesis and oncogenesis were also activated during inflammation. The latter represents an additional link between inflammation and cancer. The regulatory networks represent key targets for development of novel drugs targeting bladder diseases.
Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium
Authors: Argiriadi Maria A , Goedken Eric R , Bruck Irina , O'Donnell Mike , Kuriyan John 
Published: January 2006

Abstract

Background
Sliding DNA clamps are processivity factors that are required for efficient DNA replication. DNA polymerases maintain proximity to nucleic acid templates by interacting with sliding clamps that encircle DNA and thereby link the polymerase enzyme to the DNA substrate. Although the structures of sliding clamps from Gram-negative bacteria (E. coli), eukaryotes, archaea, and T4-like bacteriophages are well-known, the structure of a sliding clamp from Gram-positive bacteria has not been reported previously.

Results
We have determined the crystal structure of the dimeric β subunit of the DNA polymerase III holoenzyme of Streptococcus pyogenes. The sliding clamp from this Gram-positive organism forms a ring-shaped dimeric assembly that is similar in overall structure to that of the sliding clamps from Gram-negative bacteria, bacteriophage T4, eukaryotes and archaea. The dimer has overall dimensions of ~90 Å × ~70 Å × ~25 Å with a central chamber that is large enough to accommodate duplex DNA. In comparison to the circular shape of other assemblies, the S. pyogenes clamp adopts a more elliptical structure.

Conclusion
The sequences of sliding clamps from S. pyogenes and E. coli are only 23% identical, making the generation of structural models for the S. pyogenes clamp difficult in the absence of direct experimental information. Our structure of the S. pyogenes β subunit completes the catalog of clamp structures from all the major sequence grouping of sliding clamps. The more elliptical rather than circular structure of the S. pyogenes clamp implies that the topological nature of encircling DNA, rather than a precise geometric shape, is the most conserved aspect for this family of proteins.
European active surveillance study of women taking HRT (EURAS-HRT): study protocol [NCT00214903]
Authors: Dinger Juergen C , Heinemann Lothar AJ 
Published: January 2006

Abstract

Background
The post marketing safety surveillance program for a drug containing a new chemical entity should assess both, the safety outcomes that relate specifically to the targeted population, as well as those that could potentially be related to special pharmacological characteristics of the drug. Active safety surveillance using valid epidemiological study designs has been proven to be a pertinent and reliable method to approach this endeavor.

Methods/design
The primary objective of the study is to compare incidence rates of serious adverse events in users of all types of newly prescribed oral HRT products. This active surveillance study will assess pertinent cardiovascular outcomes - in particular venous and arterial thromboembolism - and other serious adverse events (SAEs) in new HRT users over a period of several years. One product under surveillance is Angeliq®, which contains the novel progestagen drospirenone (DRSP) combined with estradiol. In addition, all other oral combined HRT products with a novel progestagen or estrogen that will be newly marketed during the study period will be studied. These new HRT products will be compared with established HRT products. The combined cohort will include at least 30,000 women recruited in several European countries. At least 90,000 years of observation are expected from the field work which started in early 2002 and will end around 2008. The participating women will complete a baseline survey using a self-administered questionnaire to describe the baseline risk. After 6 months, 12 months, and then on an annual basis, they will fill out a questionnaire in which they record complaints and events during the use of the prescribed HRTs. All adverse outcomes occurring during the observational period will be evaluated.

Discussion
A complete lifetime medical history, individually validated SAEs over time, and a low loss to follow-up rate are essential for a robust safety assessment. Therefore, the lifetime history of diseases and relevant medications will be documented. Reported SAEs will be validated and analyzed. A four level, multi-faceted follow-up process was established to ensure low loss to follow-up rates (e.g., 3–5% after three years of follow up). Multivariate methods will be used to adjust for confounding.
In vitro modulation of inflammatory cytokine and IgG levels by extracts of Perna canaliculus
Authors: Mani Sachin , Lawson John W 
Published: January 2006

AbstractBackgroundInflammation is a predominant characteristic of autoimmune diseases which is characterized by the increased expression of pro-inflammatory cytokines. Soon to be published work from our laboratory has shown that ingestion ofPerna canaliculusprevents the development of autoimmune diseases such as Systemic Lupus Erythematosus and rheumatoid arthritis in laboratory animals. The current paper attempts to illustrate how Perna can alleviate inflammation by modulating inflammatory cytokines, cyclooxygenase enzymes and Immunoglobulin-G (IgG) levels.MethodsIn the present study, hydrochloric acid [HCl] and Tween-20 were used to develop extracts of Perna. These extracts were assayed for protein content. Increasing concentrations of these extracts were then tested in cell culture for modulation of inflammatory cytokine, cyclooxygenase enzymes and IgG levels. Parallel tests were run using an available glycogen extract of Perna as a comparison to our in-house laboratory preparations.ResultsTween-20 Perna extracts were found to be more stable and less toxic in cell culture than HCl digest of Perna. They also assayed higher in protein content that HCl extracts. Although both extracts inhibited IgG production in V2E9 hybridomas, Tween-20 extracts were more consistent in IgG suppression than HCl extracts. Overall Tween-20 extracts effectively decreased levels of TNF-α, IL-1, IL-2 and IL-6 as observed using cytokine bioassays. Twenty micrograms of Tween-20 Perna extracts induced such significant decreases in inflammatory cytokine production that when tested on sensitive cell lines, they very nearly abolished the decrease in viability induced by these cytokines. Tween-20 extracts effectively inhibited both COX-1 and COX-2 cyclooxygenase activity. As a comparison, the glycogen extract also demonstrated a similar though weaker effect on COX-1 and COX-2 enzymes. The active components of both extracts (Tween-20 and glycogen) were observed to possess molecular weights above 100 kDa. Although the anti-cytokine activity of the Tween-20 extract was destroyed by Proteinase-K treatment, the anti-COX-1 and anti-COX-2 activity of both the extracts were not sensitive to protease treatment.ConclusionWe have successfully demonstrated modulation in the levels of inflammatory cytokines, cyclooxygenase enzymes and immunoglobulins by our in-house laboratory preparations ofPerna canaliculus, whereby suggesting an immunomodulatory role ofPerna canaliculusin regulating inflammation.
Inclusion of MUC1 (Ma695) in a panel of immunohistochemical markers is useful for distinguishing between endocervical and endometrial mucinous adenocarcinoma*
Authors: Khoury Thaer , Tan Dongfeng , Wang Jianmin , Intengan Marilyn , Yang Jun , Alrawi Sadir , Yan Peisha , Byrd James C 
Published: January 2006

Abstract

Background
Distinguishing endocervical adenocarcinoma (ECA) from endometrial mucinous adenocarcinoma (EMMA) is clinically significant in view of the differences in their management and prognosis. In this study, we used a panel of tumor markers to determine their ability to distinguish between primary endocervical adenocarcinoma and primary endometrial mucinous adenocarcinoma.

Methods
Immunohistochemistry using monoclonal antibodies to MUC1 (Ma695), p16, estrogen receptor (ER), progesterone receptor (PR), and vimentin, was performed to examine 32 cases, including 18 EMMAs and 14 ECAs. For MUC1, cases were scored based on the percentage of staining pattern, apical, apical and cytoplasmic (A/C), or negative. For p16, cases were scored based on the percentage of cells stained. For the rest of the antibodies, semiquantitative scoring system was carried out.

Results
For MUC1, majority of EMMA (14 of 18 cases, 78%) showed A/C staining, whereas only few ECA (2 of 14, 14%) were positive. The difference of MUC1 expression in the two groups of malignancy was statistically significant (p < 0.001). Staining for p16 was positive in 10 of 14 (71%) ECA and 4 of 18 (22%) EMMA. Estrogen receptor was positive in 3 of 14 (21%) ECA and 17 of 18 (94%) EMMA. Progesterone receptor was positive in 3 of 14 (21%) ECA and 16 of 18 (89%) EMMA. Vimentin was positive in 1 of 14 (7%) ECA, and 9 of 18 (50%) EMA, with median and range of 0 (0–6), and 1.5 (0–9) respectively.

Conclusion
A panel of immunohistochemical markers including MUC1, p16, ER, PR, and vimentin is recommended, when there is morphological and clinical doubt as to the primary site of endocervical or endometrial origin.
Real-time PCR complements immunohistochemistry in the determination of HER-2/neu status in breast cancer
Authors: Nistor Andreea , Watson Peter H , Pettigrew Norman , Tabiti Karim , Dawson Angelika , Myal Yvonne 
Published: January 2006

Abstract

Background
The clinical benefit of determining the status of HER-2/neu amplification in breast cancer patients is well accepted. Although immunohistochemistry (IHC) is the most frequently used method to assess the over-expression of HER-2 protein, fluorescent in-situ hybridization (FISH) is recognized as the "gold standard" for the determining of HER-2/neu status. The greatest discordance between the two methods occurs among breast tumors that receive an indeterminate IHC score of 2+. More recently, a real-time polymerase chain reaction (PCR) assay using the LightCycler® has been developed for quantifying HER-2/neu gene amplification. In this study, we evaluated the sensitivity and specificity of a commercially available LightCycler assay as it compares to FISH. To determine whether this assay provides an accurate alternative for the determination of HER-2/neu status, we focused primarily on tumors that were deemed indeterminate or borderline status by IHC.

Methods
Thirty-nine breast tumors receiving an IHC score of 2+ were evaluated by both FISH and LightCycler® technologies in order to determine whether quantitative real-time PCR provides an accurate alternative for the determination of HER-2/neu status.

Results
We found a high concordance (92%) between FISH and real-time PCR results. We also observed that 10% of these tumors were positive for gene amplification by both FISH and real-time PCR.

Conclusion
The data show that the results obtained for the gene amplification of HER-2/neu by real-time PCR on the LightCycler® instrument is comparable to results obtained by FISH. These results therefore suggest that real-time PCR analysis, using the LightCycler®, is a viable alternative to FISH for reassessing breast tumors which receive an IHC score of 2+, and that a combined IHC and real-time PCR approach for the determination of HER-2 status in breast cancer patients may be an effective and efficient strategy.
High sensitivity assays for docetaxel and paclitaxel in plasma using solid-phase extraction and high-performance liquid chromatography with UV detection
Authors: Andersen Anders , Warren David J , Brunsvig Paal F , Aamdal Steinar , Kristensen Gunnar B , Olsen Harald 
Published: January 2006

Abstract

Background
The taxanes paclitaxel and docetaxel have traditionally been used in high doses every third week in the treatment of cancer. Lately there has been a trend towards giving weekly low doses to improve the therapeutic index. This article describes the development of high performance liquid chromatographic (HPLC) methods suitable for monitoring taxane levels in patients, focusing on patients receiving low-dose therapy.

Methods
Paclitaxel and docetaxel were extracted from human plasma by solid phase extraction, and detected by absorbance at 227 nm after separation by reversed phase high performance liquid chromatography. The methods were validated and their performance were tested using samples from patients receiving paclitaxel or docetaxel.

Results
The limits of quantitation were 1 nM for docetaxel and 1.2 nM for paclitaxel. For both compounds linearity was confirmed from the limit of quantitation up to 1000 nM in plasma. The recoveries ranged between 92% and 118% for docetaxel and between 76% and 104% for paclitaxel. Accuracy and precision were within international acceptance criteria, that is within ± 15%, except at the limit of quantitation where values within ± 20% are acceptable. Low-dose patients included in an on going clinical trial had a median docetaxel concentration of 2.8 nM at 72 hours post infusion. Patients receiving 100 mg/m2 of paclitaxel had a mean paclitaxel concentration of 21 nM 48 hours after the end of infusion.

Conclusion
We have developed an HPLC method using UV detection capable of quantifying 1 nM of docetaxel in plasma samples. The method should be useful for pharmacokinetic determinations at all relevant doses of docetaxel. Using a similar methodology paclitaxel can be quantified down to a concentration of 1.2 nM in plasma with acceptable accuracy and precision. We further demonstrate that the previously reported negative influence of Cremophor EL on assay performance may be overcome by degradation of the detergent by incubation with lipase.
Effect of a brief intervention on evidence-based medicine skills of pediatric residents
Authors: Dinkevich Eugene , Markinson Andrea , Ahsan Sama , Lawrence Barbara 
Published: January 2006

Abstract

Background
While Evidence-Based Medicine (EBM) skills are increasingly being taught in medical schools, teaching quality has been insufficient, so that incoming pediatric residents lack adequate EBM skills required for patient care. The objective of this study was to evaluate the effectiveness of a brief teaching module developed to improve EBM skills of pediatric residents.

Methods
With-in subjects study design with pre- and post-test evaluation was performed in a large urban pediatric residency training program in Brooklyn, New York. We included PGY-1s during intern orientation, while second and third year pediatric residents were selected based on schedule availability. Sixty-nine residents were enrolled into the study, 60 (87%) completed the training. An EBM training module consisting of three or four weekly two-hour seminars was conducted. The module was designed to teach core EBM skills including (1) formulating answerable clinical questions, (2) searching the evidence, (3) critical appraisal skills including validity and applicability, and (4) understanding levels of evidence and quantitative results for therapy articles. A portion of the Fresno test of competence in EBM was used to assess EBM skills. The test presented a clinical scenario that was followed by nine short answer questions. One to three questions were used to assess EBM skills for each of the four core skills. The κ co-efficient for inter-rater reliability was 0.74 (95% CI: 0.56–0.92).

Results
Prior to the training module, the residents achieved a mean score of 17% correct overall. Post intervention, the mean score increased to 63% with improvement in each EBM category. A mean of 4.08 more questions (out of 9) were answered correctly after the training (95% CI of 3.44–4.72).

Conclusion
A brief training module was effective in improving EBM skills of pediatric residents.
Randomized controlled trial comparing four strategies for delivering e-curriculum to health care professionals [ISRCTN88148532]
Authors: Kemper Kathi J , Gardiner Paula , Gobble Jessica , Mitra Ananda , Woods Charles 
Published: January 2006

AbstractBackgroundInternet education is increasingly provided to health professionals, but little is known about the most effective strategies for delivering the content. The purpose of this study is to compare four strategies for delivering an Internet-based (e-) curriculum on clinicians' knowledge (K), confidence (CONF), and communication (COMM) about herbs and other dietary supplements (HDS).MethodsThis national randomized 2 × 2 factorial trial included physicians, pharmacists, nurses, nutritionists and trainees in these fields. Participants were randomly assigned to one of four curriculum delivery strategies for 40 brief modules about HDS: a) delivering four (4) modules weekly over ten (10) weeks by email (drip-push); b) modules accessible on web site with 4 reminders weekly for 10 weeks (drip-pull); c) 40 modules delivered within 4 days by email (bolus-push); and d) 40 modules available on the Internet with one email informing participants of availability (bolus-pull).ResultsOf the 1,267 enrollees, 25% were male; the average age was 40 years. The completion rate was 62%, without significant differences between delivery groups. There were statistically significant improvements in K, CONF and COMM scores after the course (P<0.001 for all), although the difference in COMM was small. There were no significant differences in any of the three outcomes by delivery strategy, but outcomes were better for those who paid for continuing education credit.ConclusionAll delivery strategies tested similarly improved K, CONF, COMM scores about HDS. Educators can use the strategy that is most convenient without diminishing effectiveness. Additional curricula may be necessary to make substantial changes in clinicians' communication practices.
Knowledge loss of medical students on first year basic science courses at the university of Saskatchewan
Authors: D'Eon Marcel F 
Published: January 2006

Abstract

Background
Many senior undergraduate students from the University of Saskatchewan indicated informally that they did not remember much from their first year courses and wondered why we were teaching content that did not seem relevant to later clinical work or studies. To determine the extent of the problem a course evaluation study that measured the knowledge loss of medical students on selected first year courses was conducted.
This study replicates previous memory decrement studies with three first year medicine basic science courses, something that was not found in the literature. It was expected that some courses would show more and some courses would show less knowledge loss.

Methods
In the spring of 2004 over 20 students were recruited to retake questions from three first year courses: Immunology, physiology, and neuroanatomy. Student scores on the selected questions at the time of the final examination in May 2003 (the 'test') were compared with their scores on the questions 10 or 11 months later (the 're-test') using paired samples t -tests. A repeated-measures MANOVA was used to compare the test and re-test scores among the three courses. The re-test scores were matched with the overall student ratings of the courses and the student scores on the May 2003 examinations.

Results
A statistically significant main effect of knowledge loss (F = 297.385; p < .001) and an interaction effect by course (F = 46.081; p < .001) were found. The students' scores in the Immunology course dropped 13.1%, 46.5% in Neuroanatomy, and 16.1% in physiology. Bonferroni post hoc comparisons showed a significant difference between Neuroanatomy and Physiology (mean difference of 10.7, p = .004).

Conclusion
There was considerable knowledge loss among medical students in the three basic science courses tested and this loss was not uniform across courses. Knowledge loss does not seem to be related to the marks on the final examination or the assessment of course quality by the students.
Quality research in healthcare: are researchers getting enough statistical support?
Authors: Omar Rumana Z , McNally Nick , Ambler Gareth , Pollock Allyson M 
Published: January 2006

Abstract

Background
Reviews of peer-reviewed health studies have highlighted problems with their methodological quality. As published health studies form the basis of many clinical decisions including evaluation and provisions of health services, this has scientific and ethical implications. The lack of involvement of methodologists (defined as statisticians or quantitative epidemiologists) has been suggested as one key reason for this problem and this has been linked to the lack of access to methodologists. This issue was highlighted several years ago and it was suggested that more investments were needed from health care organisations and Universities to alleviate this problem.

Methods
To assess the current level of methodological support available for health researchers in England, we surveyed the 25 National Health Services Trusts in England, that are the major recipients of the Department of Health's research and development (R&D) support funding.

Results and discussion
The survey shows that the earmarking of resources to provide appropriate methodological support to health researchers in these organisations is not widespread. Neither the level of R&D support funding received nor the volume of research undertaken by these organisations showed any association with the amount they spent in providing a central resource for methodological support for their researchers.

Conclusion
The promotion and delivery of high quality health research requires that organisations hosting health research and their academic partners put in place funding and systems to provide appropriate methodological support to ensure valid research findings. If resources are limited, health researchers may have to rely on short courses and/or a limited number of advisory sessions which may not always produce satisfactory results.