bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of bisphosphonates on gene expression: GAPDH as a housekeeping or a new target gene?
Authors: Valenti Maria Teresa , Bertoldo Francesco , Dalle Carbonare Luca , Azzarello Giuseppe , Zenari Sonia , Zanatta Mirko , Balducci Elena , Vinante Orazio , Cascio Vincenzo Lo
Published: March 2006

Background

RT-PCR has been widely used for the analysis of gene expression in many systems, including tumor samples. GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) has been frequently considered as a constitutive housekeeping gene and used to normalize changes in specific gene expression. However, GAPDH has been shown to be up-regulated in many cancers and down-regulated by chemotherapic drugs. Bisphosphonates, potent inhibitors of bone resorption, have recently shown a direct and indirect antitumor effect in vitro and in animal models. They exert their effects mainly by inhibiting the mevalonate pathway but also by modulating the expression of many genes not only in osteoclasts but also in cancer cells.

Methods

We evaluated GAPDH gene expression by real time RT PCR in breast (MCF-7 and T47D) and prostate (PC3 and DU-145) cancer cell lines treated with amino and non-amino bisphosphonates.

Results

Our results showed that amino-bisphosphonates significantly decrease in a dose-dependent manner the expression of GAPDH gene.

Conclusion

Therefore, GAPDH is inaccurate to normalize mRNA levels in studies investigating the effect of bisphosphonates on gene expression and it should be avoided. On the other hand, this gene could be considered a potential target to observe the effects of bisphosphonates on cancer cells.
Results of radiation therapy combined with nedaplatin (cis-diammine-glycoplatinum) and 5-Fluorouracil for postoperative locoregional recurrent esophageal cancer
Authors: Jingu Keiichi , Nemoto Kenji , Matsushita Haruo , Takahashi Chiaki , Ogawa Yoshihiro , Sugawara Toshiyuki , Nakata Eiko , Takai Yoshihiro , Yamada Shogo
Published: March 2006

Background

Although the effectiveness of radiotherapy with concurrent administration of several anti-tumor drugs for postoperative recurrent esophageal cancer has been demonstrated, the results are not satisfactory. The purpose of the present study was to evaluate the effectiveness and safety of radiotherapy combined with nedaplatin and 5-FU for postoperative locoregional (excluding hematogenous metastasis) recurrent esophageal cancer.

Methods

In June 2000, we started a phase II study on treatment of postoperative locoregional recurrent esophageal cancer with radiotherapy (60 Gy/30 fr/6 weeks) combined with chemotherapy consisting of two cycles of nedaplatin (70 mg/m2/2 h) and 5-FU (500 mg/m2/24 h for 5 days).

The primary endpoint of the present study was overall survival rate, and the second endpoints were irradiated-field control rate, tumor response and toxicity.

Results

A total of 30 patients were included in this study. The 1-year and 3-year overall survival rates were 60.6% and 56.3%, respectively, with a median survival period of 39.0 months, and the 1-year and 3-year irradiated-field control rates were 86.4% and 72%, respectively. Complete response and partial response were observed in 13.3% and 60.0% of the patients, respectively. Grade 3 or higher leukocytopenia and thrombocytopenia were observed in 30% and 3.3% of the patients, respectively, but renal toxicity of grade 3 or higher was not observed. The regimen was completed in 76.7% of the patients.

In univariate analysis, the difference between survival rate in preradiotherapy performance status, recurrent pattern (worse for patients with anastomotic recurrence) and age (worse for younger patients) were statistically significant.

Conclusion

Radiotherapy combined with nedaplatin and 5-FU is a safe and effective salvage treatment for postoperative locoregional recurrent esophageal cancer.
Fibroblast-derived MT1-MMP promotes tumor progression in vitro and in vivo
Authors: Zhang Wenyue , Matrisian Lynn M , Holmbeck Kenn , Vick Catherine C , Rosenthal Eben L
Published: March 2006

Background

Identification of fibroblast derived factors in tumor progression has the potential to provide novel molecular targets for modulating tumor cell growth and metastasis. Multiple matrix metalloproteases (MMPs) are expressed by both mesenchymal and epithelial cells within head and neck squamous cell carcinomas (HNSCCs), but the relative importance of these enzymes and the cell source is the subject of controversy.

Methods

The invasive potential of HNSCC tumor cells were assessed in vitro atop type I collagen gels in coculture with wild-type (WT), MMP-2 null, MMP-9 null or MT1-MMP null fibroblasts. A floor of mouth mouse model of HNSCC was used to assess in vivo growth after co-injection of FaDu tumor cells with MMP null fibroblasts.

Results

Here we report changes in tumor phenotype when FaDu HNSCCs cells are cocultured with WT, MMP-2 null, MMP-9 null or MT1-MMP null fibroblasts in vitro and in vivo. WT, MMP-2 null and MMP-9 null fibroblasts, but not MT1-MMP null fibroblasts, spontaneously invaded into type I collagen gels. WT fibroblasts stimulated FaDu tumor cell invasion in coculture. This invasive phenotype was unaffected by combination with MMP-9 null fibroblasts, reduced with MMP-2 null fibroblasts (50%) and abrogated in MT1-MMP null fibroblasts. Co-injection of FaDu tumor cells with fibroblasts in an orthotopic oral cavity SCID mouse model demonstrated a reduction of tumor volume using MMP-9 and MMP-2 null fibroblasts (48% and 49%, respectively) compared to WT fibroblasts. Consistent with in vitro studies, MT1-MMP null fibroblasts when co-injected with FaDu cells resulted in a 90% reduction in tumor volume compared to FaDu cells injected with WT fibroblasts.

Conclusion

These data suggest a role for fibroblast-derived MMP-2 and MT1-MMP in HNSCC tumor invasion in vitro and tumor growth in vivo.
PPARγ-independent induction of growth arrest and apoptosis in prostate and bladder carcinoma
Authors: Chaffer Christine L , Thomas David M , Thompson Erik W , Williams Elizabeth D
Published: March 2006

Background

Although PPARγ antagonists have shown considerable pre-clinical efficacy, recent studies suggest PPARγ ligands induce PPARγ-independent effects. There is a need to better define such effects to permit rational utilization of these agents.

Methods

We have studied the effects of a range of endogenous and synthetic PPARγ ligands on proliferation, growth arrest (FACS analysis) and apoptosis (caspase-3/7 activation and DNA fragmentation) in multiple prostate carcinoma cell lines (DU145, PC-3 and LNCaP) and in a series of cell lines modelling metastatic transitional cell carcinoma of the bladder (TSU-Pr1, TSU-Pr1-B1 and TSU-Pr1-B2).

Results

15-deoxy-prostaglandin J2 (15dPGJ2), troglitazone (TGZ) and to a lesser extent ciglitazone exhibited inhibitory effects on cell number; the selective PPARγ antagonist GW9662 did not reverse these effects. Rosiglitazone and pioglitazone had no effect on proliferation. In addition, TGZ induced G0/G1 growth arrest whilst 15dPGJ2 induced apoptosis.

Conclusion

Troglitazone and 15dPGJ2 inhibit growth of prostate and bladder carcinoma cell lines through different mechanisms and the effects of both agents are PPARγ-independent.
Perceptions of eye health in schools in Pakistan
Authors: Ahmad Khabir , Khan Mohammad Aman , Khan Mohammad Daud , Qureshi Mohammad Babar , Chaudhry Tanveer Anjum , Gilbert Clare
Published: March 2006

Background

Research exploring children's and their teachers' perceptions of eye health is lacking. This paper reports for the first time on perceptions of primary schoolchildren and their teachers of healthy and diseased eyes, things that keep eyes healthy and damage them, and what actions to be taken in case of an eye injury.

Methods

Usingdraw and write technique, 160 boys and girls (9–12 years old) attending four primary schools in Abbottabad district, northern Pakistan, were invited to draw pictures in response to a set of semi-structured questions and then label them. Sixteen teachers who were currently teaching the selected students were interviewed one-on-one.

Results

Analysis of text accompanying 800 drawings and of the interview scripts revealed that most children and teachers perceived healthy eyes to be those which could see well, and diseased eyes to be those which have redness, watering, dirty discharge, pain, and itching; or those which have "weak eyesight" and blindness. Among things that students and teachers thought damage the eyes included sun, television, and sharp pointed objects, particularly pencils. Teachers noted that children with eye problems "have difficulty seeing the blackboard well", "screw up their eyes", and "hold their books too close".

Conclusion

We conclude that schoolchildren and their teachers had a good knowledge of eye health, but many of them had serious misconceptions e.g., use of kohl, medicines and eye drops keeps eyes healthy. Kohl is an important source of lead and can reduce children's intelligence even at low blood levels. Health education in schools must take into account children's existing knowledge of and misconceptions about various aspects of eye health. Such steps if taken could improve the relevance of eye health education to schoolchildren.
Management of neonatal hyperbilirubinemia: Pediatricians' practices and educational needs
Authors: Petrova Anna , Mehta Rajeev , Birchwood Gillian , Ostfeld Barbara , Hegyi Thomas
Published: March 2006

Background

Early detection and treatment of neonatal hyperbilirubinemia is important in the prevention of bilirubin-induced encephalopathy. In this study, we evaluated the New Jersey pediatricians' practices and beliefs regarding the management of neonatal hyperbilirubinemia and their compliance with the recommendations made by the American Academy of Pediatrics (AAP) in 1994.

Methods

A survey questionnaire was mailed to a random sample of 800 pediatricians selected from a list of 1623 New Jersey Fellows of the AAP initially in October 2003 and then in February 2004 for the non-respondents. In addition to the physicians' demographic characteristics, the questionnaire addressed various aspects of neonatal hyperbilirubinemia management including the diagnosis, treatment, and follow up as well as the pediatricians' beliefs regarding the significance of risk factors in the development of severe hyperbilirubinemia.

Results

The adjusted response rate of 49.1% (n = 356) was calculated from the 725 eligible respondents. Overall, the practicing pediatricians reported high utilization (77.9%) of the cephalocaudal progression of jaundice and low utilization (16.1%) of transcutaneous bilirubinometry for the quantification of the severity of jaundice. Most of the respondents (87.4%) identified jaundice as an indicator for serum bilirubin (TSB) testing prior to the neonate's discharge from hospital, whereas post-discharge, only 57.7% felt that a TSB was indicated (P < 0.01). If the neonate's age was under 72 hours, less than one-third of the respondents reported initiation of phototherapy at TSB levels lower than the treatment parameters recommended by the AAP in 1994, whereas if the infant was more than 72 hours old, almost 60% were initiating phototherapy at TSB lower than the 1994 AAP guidelines. Most respondents did not regard neonatal jaundice noted after discharge and gestational ages 37–38 weeks as being significant in the development of severe hyperbilirubinemia. However, the majority did recognize the importance of jaundice presenting within the first 24 hours and Rh/ABO incompatibility.

Conclusion

The pediatricians' practices regarding the low utilization of laboratory diagnosis for the quantification of jaundice after discharge and underestimation of risk factors that contribute to the development of severe hyperbilirubinemia are associated with initiation of phototherapy at lower than AAP recommended treatment parameters and recognition of neonatal hyperbilirubinemia as an important public health concern.
Individual characteristics, area social participation, and primary non-concordance with medication: a multilevel analysis
Authors: Johnell Kristina , Lindström Martin , Sundquist Jan , Eriksson Charli , Merlo Juan
Published: March 2006

Background

Non-concordance with medication remains a major public health problem that imposes a considerable financial burden on the health care system, and there is still a need for studies on correlates of non-concordance. Our first aim is to analyse whether any of the individual characteristics age, educational level, financial strain, self-rated health, social participation, and trust in the health care system are associated with primary non-concordance with medication. Our second aim is to investigate whether people living in the same area have similar probability of primary non-concordance with medication, that relates to area social participation.

Methods

We analysed cross sectional data from 9 070 women and 6 795 men aged 18 to 79 years, living in 78 areas in central Sweden, who participated in the Life & Health year 2000 survey, with multilevel logistic regression (individuals at the first level and areas at the second level).

Results

Younger age, financial strain, low self-rated health, and low trust in the health care system were associated with primary non-concordance with medication. However, area social participation was not related to primary non-concordance, and the variation in primary non-concordance between the areas was small.

Conclusion

Our results indicate that people in central Sweden with younger age, financial difficulties, low self-rated health, and low trust in the health care system may have a higher probability of primary non-concordance with medication. However, the area of residence – as defined by administrative boundaries – seems to play a minor role for primary non-concordance.
Identifying dyspepsia in the Greek population: translation and validation of a questionnaire
Authors: Anastasiou Foteini , Antonakis Nikos , Chaireti Georgia , Theodorakis Pavlos N , Lionis Christos
Published: March 2006

Background

Studies on clinical issues, including diagnostic strategies, are considered to be the core content of general practice research. The use of standardised instruments is regarded as an important component for the development of Primary Health Care research capacity. Demand for epidemiological cross-cultural comparisons in the international setting and the use of common instruments and definitions valid to each culture is bigger than ever. Dyspepsia is a common complaint in primary practice but little is known with respect to its incidence in Greece. There are some references about the Helicobacter Pylori infection in patients with functional dyspepsia or gastric ulcer in Greece but there is no specific instrument for the identification of dyspepsia. This paper reports on the validation and translation into Greek, of an English questionnaire for the identification of dyspepsia in the general population and discusses several possibilities of its use in the Greek primary care.

Methods

The selected English postal questionnaire for the identification of people with dyspepsia in the general population consists of 30 items and was developed in 1995. The translation and cultural adaptation of the questionnaire has been performed according to international standards. For the validation of the instrument the internal consistency of the items was established using the alpha coefficient of Chronbach, the reproducibility (test – retest reliability) was measured by kappa correlation coefficient and the criterion validity was calculated against the diagnosis of the patients' records using also kappa correlation coefficient.

Results

The final Greek version of the postal questionnaire for the identification of dyspepsia in the general population was reliably translated. The internal consistency of the questionnaire was good, Chronbach's alpha was found to be 0.88 (95% CI: 0.81–0.93), suggesting that all items were appropriate to measure. Kappa coefficient for reproducibility (test – retest reliability) was found 0.66 (95% CI: 0.62–0.71), whereas the kappa analysis for criterion validity was 0.63 (95% CI: 0.36–0.89).

Conclusion

This study indicates that the Greek translation is comparable with the English-language version in terms of validity and reliability, and is suitable for epidemiological research within the Greek primary health care setting.
Leading causes of certification for blindness and partial sight in England & Wales
Authors: Bunce Catey , Wormald Richard
Published: March 2006

Background

Prevention of visual impairment is an international priority agreed at the World Health Assembly of 2002- yet many countries lack contemporary data about incidence and causes from which priorities for prevention, treatment and management can be identified.

Methods

Registration as blind or partially-sighted in England and Wales is voluntary and is initiated by certification by a consultant ophthalmologist. From all certificates completed during the year April 1999 to March 2000, the main cause of visual loss was ascertained where possible and here we present information on the leading causes observed and comment on changes in the three leading causes since the last analysis conducted for 1990–1991 data.

Results

13788 people were certified as blind, 19107 were certified as partially sighted. The majority of certifications were in the older age groups. The most commonly recorded main cause of certifications for both blindness (57.2 %) and partial sight (56 %) was degeneration of the macula and posterior pole which largely comprises age-related macular degeneration. Glaucoma and diabetic retinopathy were the next most commonly recorded main causes. Overall, the age specific incidence of all three leading causes has increased since 1990–1991 – with changes in diabetic retinopathy being the most marked – particularly in the over 65's where figures have more than doubled.

Conclusion

The numbers of individuals per 100,000 population being certified blind or partially sighted due to the three leading causes – AMD, diabetic retinopathy and glaucoma have increased since 1990. This may to some extent be explained by improved ascertainment. The process of registration for severe visual impairment in England and Wales is currently undergoing review. Efforts must be made to ensure that routine collection of data on causes of severe visual impairment is continued, particularly in this age of improved technology, to allow such trends to be monitored and changes in policy to be informed.
The implications of 18F-FDG PET for the diagnosis of endoprosthetic loosening and infection in hip and knee arthroplasty: Results from a prospective, blinded study
Authors: Delank K-St , Schmidt M , Michael JW-P , Dietlein M , Schicha H , Eysel P
Published: March 2006

Background

The most frequent complications of joint arthroplasty are septic or aseptic loosening of endoprostheses. Preoperative differentiation is essential, since very different treatment methods result from the diagnoses. The aim of the current study was to evaluate the clinical value of 18F-Fluoro-deoxyglucose positron emission tomography (18F-FDG PET) as a diagnostic modality for inflammation and loosening in hip and knee joint prostheses.

Methods

18F-FDG-PET examinations and multiphase bone scan were performed on hip and knee endoprostheses in 27 patients prior to revision surgical procedures planned for prosthetic loosening. Intact prostheses were found at the opposite site in some patients so that additional 9 joints could be examined with the field of view of 18F-FDG PET. Verification and valuation of the PET and scintigraphic image findings were conducted by comparing them with information combined from intraoperative findings, histopathology, and microbiological investigations.

Results

Evidence of loosening was correctly determined in 76.4% of cases using 18F-FDG-PET, and in 75% of cases using bone scan. The detection of periprosthetic inflammation using 18F-FDG-PET had a sensitivity of 100% for septic cases and of 45.5% in cases of increased abrasion and aseptic foreign-body reactions. However, reliable differentiation between abrasion-induced and bacterial-caused inflammation was not possible using 18F-FDG-PET.

Conclusion

18F-Fluoro-deoxyglucose positron emission tomography (18F-FDG-PET) allows reliable prediction of peri-prosthetic septical inflammatory tissue reactions. Because of the high sensitivity of this method, a negative PET result in the setting of a diagnostically unclear situation eliminates the need for revision surgery. In contrast, a positive PET result gives no clear differentiation regarding the cause of inflammation.
Knee movement patterns of injured and uninjured adolescent basketball players when landing from a jump: A case-control study
Authors: Louw Quinette , Grimmer Karen , Vaughan Christopher
Published: March 2006

Background

A common knee injury mechanism sustained during basketball is landing badly from a jump. Landing is a complex task and requires good coordination, dynamic muscle control and flexibility. For adolescents whose coordination and motor control has not fully matured, landing badly from a jump can present a significant risk for injury. There is currently limited biomechanical information regarding the lower limb kinetics of adolescents when jumping, specifically regarding jump kinematics comparing injured with uninjured adolescents. This study reports on an investigation of biomechanical differences in landing patterns of uninjured and injured adolescent basketball players.

Methods

A matched case-control study design was employed. Twenty-two basketball players aged 14–16 years participated in the study: eleven previously knee-injured and eleven uninjured players matched with cases for age, gender, weight, height and years of play, and playing for the same club. Six high-speed, three-dimensional Vicon 370 cameras (120 Hz), Vicon biomechanical software and SAS Version 8 software were employed to analyse landing patterns when subjects performed a "jump shot". Linear correlations determined functional relationships between the biomechanical performance of lower limb joints, and paired t-tests determined differences between the normalised peak biomechanical parameters.

Results

The average peak vertical ground reaction forces between the cases and controls were similar. The average peak ground reaction forces between the cases and controls were moderately correlated (r = -0.47). The control (uninjured) players had significantly greater hip and knee flexion angles and significantly greater eccentric activity on landing than the uninjured cases (p< 0.01).

Conclusion

The findings of the study indicate that players with a history of knee injuries had biomechanically compromised landing techniques when compared with uninjured players matched for gender, age and club. Descriptions (norms) of expected levels of knee control, proprioceptive acuity and eccentric strength relative to landing from a jump, at different ages and physical developmental stages, would assist clinicians and coaches to identify players with inappropriate knee performance comparable to their age or developmental stage.
Testicular seminoma – unusual histology and staging with sub epithelial spread of seminoma along the vas deferans
Authors: Lockett Chris J , Nandwani Ghulam M , Stubington Simon R
Published: March 2006

Background

The route of local and metastatic spread of testicular seminoma is well recognised and accepted. The spread is via lymphatics to the paraaortic nodes.

Case Presentation

We present a case report of testicular seminoma in a 56 year old man with previously unreported histological findings. In this case seminoma tumour cells did not appear to have spread by the expected lymphatic route. There was no involvement of retro-peritoneal para-aortic lymph nodes. The tumour appeared to have spread directly along the vas deferans in the sub epithelial plane to the mesenteric lymph nodes.

Conclusion

This type of seminoma tumour spread has not previously been described and it is not a recognised route for metastasis by seminoma tumour. In this case the macroscopic clinical appearance was of a stage I tumour with normal tumour markers. However, the pathological stage of the tumour was surprisingly increased to stage III on the basis of histology and CT radiological findings. We present the unusual histological findings. In view of this unusual histological finding we reinforce the need for accurate staging and for resection of the spermatic cord close to the deep inguinal ring. Accurate staging is crucial in planning the treatment and follow up of seminoma and determines the prognosis.
Anti-thyroid peroxidase antibody and vitiligo: a controlled study
Authors: Daneshpazhooh Maryam , Mostofizadeh G Mahtab , Behjati Javad , Akhyani Maryam , Robati Reza Mahmoud
Published: March 2006

Background

Vitiligo is an acquired depigmenting disorder due to destruction of melanocytes. Although many theories have been suggested for its pathogenesis, the role of autoimmunity is the most popular one. The association of vitiligo with autoimmune thyroid diseases and the increased prevalence of autoantibodies including thyroid autoantibodies in vitiligo favor this role. Our objective was to compare the frequency of thyroid peroxidase antibody (anti-TPO) in vitiligo patients with healthy subjects in Iran.

Methods

Ninety-four cases of vitiligo (46 female and 48 male) and 96 control subjects (49 female and 47 male) were enrolled in this controlled study. Patients with known thyroid disease, history of thyroid surgery and those receiving thyroid medications were not included. The two groups were matched regarding gender and age. The demographic data, symptoms related to thyroid diseases and results of skin and thyroid examinations were recorded in a questionnaire for each subject. Thyroid function tests including free T3, free T4 and TSH-IRMA were performed. Anti-TPO levels were assessed as well. The collected data were analyzed by SPSS version-11 in vitiligo patients and subgroups according to gender, age, extent, and duration of the disease compared with the control group.

Results

Anti-TPO was detected in 17 (18.1%) of patients affected by vitiligo, while this figure was 7 (7.3%) in the control group; the difference was significant with p-value < 0.025 (Phi & Cramer's V = 0.162). When analyzing subgroups, the difference in the frequency of anti-TPO remained significant only in females (p-value < 0.044) (Phi & Cramer's V = 0.207) and in patients in the age ranges of 18–25 (p-value < 0.05) (Phi & Cramer's V = 0.28) and 26–35 year-old (p-value < 0.042) (Phi & Cramer's V = 0.304).

The difference of the frequency of anti-TPO was not significant regarding the duration and extent of vitiligo. In addition, there was no significant difference in the levels of free T3, free T4, and TSH in vitiligo patients compared with the control group.

Conclusion

According to our study, anti-TPO was shown to be significantly more common in vitiligo patients especially in young women, compared with control group. As this antibody is a relatively sensitive and specific marker of autoimmune thyroid disorders including Hashimoto thyroiditis and Graves' disease, and considering the fact that vitiligo usually precedes the onset of thyroid dysfunction, periodic follow-up of vitiligo patients for detecting thyroid diseases is further emphasized especially in young women with increased level of anti-TPO.
Modification of the Creator recombination system for proteomics applications – improved expression by addition of splice sites
Authors: Colwill Karen , Wells Clark D , Elder Kelly , Goudreault Marilyn , Hersi Kadija , Kulkarni Sarang , Hardy W Rod , Pawson Tony , Morin Gregg B
Published: March 2006

Background

Recombinational systems have been developed to rapidly shuttle Open Reading Frames (ORFs) into multiple expression vectors in order to analyze the large number of cDNAs available in the post-genomic era. In the Creator system, an ORF introduced into a donor vector can be transferred with Cre recombinase to a library of acceptor vectors optimized for different applications. Usability of the Creator system is impacted by the ability to easily manipulate DNA, the number of acceptor vectors for downstream applications, and the level of protein expression from Creator vectors.

Results

To date, we have developed over 20 novel acceptor vectors that employ a variety of promoters and epitope tags commonly employed for proteomics applications and gene function analysis. We also made several enhancements to the donor vectors including addition of different multiple cloning sites to allow shuttling from pre-existing vectors and introduction of the lacZ alpha reporter gene to allow for selection. Importantly, in order to ameliorate any effects on protein expression of the loxP site between a 5' tag and ORF, we introduced a splicing event into our expression vectors. The message produced from the resulting 'Creator Splice' vector undergoes splicing in mammalian systems to remove the loxP site. Upon analysis of our Creator Splice constructs, we discovered that protein expression levels were also significantly increased.

Conclusion

The development of new donor and acceptor vectors has increased versatility during the cloning process and made this system compatible with a wider variety of downstream applications. The modifications introduced in our Creator Splice system were designed to remove extraneous sequences due to recombination but also aided in downstream analysis by increasing protein expression levels. As a result, we can now employ epitope tags that are detected less efficiently and reduce our assay scale to allow for higher throughput. The Creator Splice system appears to be an extremely useful tool for proteomics.
RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia colistrain for Cre mediated production of minicircle DNA
Authors: Tolmachov Oleg , Palaszewski Iwona , Bigger Brian , Coutelle Charles
Published: March 2006

Background

Minicircle DNA is the non-replicating product of intramolecular site-specific recombination within a bacterial minicircle producer plasmid. Minicircle DNA can be engineered to contain predominantly human sequences which have a low content of CpG dinucleotides and thus reduced immunotoxicity for humans, whilst the immunogenic bacterial origin and antibiotic resistance marker gene sequences are entirely removed by site-specific recombination. This property makes minicircle DNA an excellent vector for non-viral gene therapy. Large-scale production of minicircle DNA requires a bacterial strain expressing tightly controlled site-specific recombinase, such asCrerecombinase. As recombinant plasmids tend to be more stable in RecA-deficient strains, we aimed to construct arecA-bacterial strain for generation of minicircle vector DNA with less chance of unwanted deletions.

Results

We describe here the construction of the RecA-deficient minicircle DNA producerEscherichia coliHB101Cre with a chromosomally locatedCrerecombinase gene under the tight control of thearaCregulon. TheCregene expression cassette was inserted into the chromosomallacZgene by creating transient homologous recombination proficiency in therecA-strain HB101 using plasmid-bornrecETgenes and homology-mediated chromosomal "pop-in, pop-out" of the plasmid pBAD75Cre containing theCregene and a temperature sensitive replication origin. Favourably for theCregene placement, at the "pop-out" step, the observed frequency of RecET-led recombination between the proximal regions of homology was 10 times higher than between the distal regions. Using the minicircle producing plasmid pFIXluc containing mutantloxP66andloxP71sites, we isolated pure minicircle DNA from the obtainedrecA-producer strain HB101Cre. The minicircle DNA preparation consisted of monomeric and, unexpectedly, also multimeric minicircle DNA forms, all containing the hybridloxP66/71site 5'-TACCGTTCGT ATAATGTATG CTATACGAAC GGTA-3', which was previously shown to be an inefficient partner in Cre-mediated recombination.

Conclusion

Using transient RecET-driven recombination we inserted a single copy of thearaCcontrolledCregene into thelacZgene on the chromosome ofE. coli recA-strain HB101. The resultantrecA-minicircle DNA producer strain HB101Cre was used to obtain pure minicircle DNA, consisting of monomeric and multimeric minicircle forms. The obtainedrecA-minicircle DNA producer strain is expected to decrease the risk of undesired deletions within minicircle producer plasmids and, therefore, to improve production of the therapeutic minicircle vectors.
Identification of similar regions of protein structures using integrated sequence and structure analysis tools
Authors: Peters Brandon , Moad Charles , Youn Eunseog , Buffington Kris , Heiland Randy , Mooney Sean
Published: March 2006

Background

Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest.

Results

Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO) ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein.

Conclusion

With structural genomics initiatives determining structures with little, if any, functional characterization, development of protein structure and function analysis tools are a necessary endeavor. We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools. These approaches are able to find statistically significant environments in a database of protein structure, and the method is able to quantify how closely associated each environment is to a predicted functional annotation.
Referral patterns and attitudes of Primary Care Physicians towards chiropractors
Authors: Greene Barry R , Smith Monica , Allareddy Veerasathpurush , Haas Mitchell
Published: March 2006

Background

Despite the increasing usage and popularity of chiropractic care, there has been limited research conducted to examine the professional relationships between conventional trained primary care physicians (PCPs) and chiropractors (DCs). The objectives of our study were to contrast the intra-professional referral patterns among PCPs with referral patterns to DCs, and to identify predictors of PCP referral to DCs.

Methods

We mailed a survey instrument to all practicing PCPs in the state of Iowa. Descriptive statistics were used to summarize their responses. Multivariable logistic regression analyses were conducted to identify demographic factors associated with inter-professional referral behaviors.

Results

A total of 517 PCPs (33%) participated in the study. PCPs enjoyed strong intra-professional referral relationships with other PCPs. Although patients exhibited a great deal of interest in chiropractic care, PCPs were unlikely themselves to make formal referral relationships with DCs. PCPs in a private practice arrangement were more likely to exhibit positive referral attitudes towards DCs (p = 0.01).

Conclusion

PCPs enjoy very good professional relationships with other PCPs. However, the lack of direct formalized referral relationships between PCPs and chiropractors has implications for efficiency, continuity, quality, and patient safety in the health care delivery system. Future research must focus on identifying facilitators and barriers for developing positive relationships between PCPs and chiropractors.
Case-based exercises fail to improve medical students' information management skills: a controlled trial
Authors: Chumley Heidi S , Dobbie Alison E , Delzell John E
Published: March 2006

Background

Tomorrow's physicians must learn to access, retrieve, integrate and apply current information into ambulatory patient encounters, yet few medical schools teach 'real time' information management.

Methods

We compared two groups of clerkship students' information management skills using a standardized patient case. The intervention group participated in case-based discussions including exercises that required them to manage new information. The control group completed the same case discussions without information management exercises.

Results

After five weeks, there was no significant difference between the control and intervention groups' scores on the standardized patient case. However, third rotation students significantly outperformed first rotation students.

Conclusion

Case-based exercises to teach information management failed to improve students' performance on a standardized patient case. Increased number of clinical rotations was associated with improved performance.
Humanities for medical students? A qualitative study of a medical humanities curriculum in a medical school program
Authors: Wachtler Caroline , Lundin Susanne , Troein Margareta
Published: March 2006

Background

Today, there is a trend towards establishing the medical humanities as a component of medical education. However, medical humanities programs that exist within the context of a medical school can be problematic. The aim of this study was to explore problems that can arise with the establishment of a medical humanities curriculum in a medical school program.

Methods

Our theoretical approach in this study is informed by derridean deconstruction and by post-structuralist analysis. We examined the ideology of the Humanities and Medicine program at Lund University, Sweden, the practical implementation of the program, and how ideology and practice corresponded. Examination of the ideology driving the humanities and medicine program was based on a critical reading of all available written material concerning the Humanities and Medicine project. The practice of the program was examined by means of a participatory observation study of one course, and by in-depth interviews with five students who participated in the course. Data was analysed using a hermeneutic editing approach.

Results

The ideological language used to describe the program calls it an interdisciplinary learning environment but at the same time shows that the conditions of the program are established by the medical faculty's agenda. In practice, the "humanities" are constructed, defined and used within a medical frame of reference. Medical students have interesting discussions, acquire concepts and enjoy the program. But they come away lacking theoretical structure to understand what they have learned. There is no place for humanities students in the program.

Conclusion

A challenge facing cross-disciplinary programs is creating an environment where the disciplines have equal standing and contribution.
Medical students' perceptions in relation to ethnicity and gender: a qualitative study
Authors: Lempp Heidi , Seale Clive
Published: March 2006

Background

The British medical student population has undergone rapid diversification over the last decades. This study focuses on medical students' views about their experiences in relation to ethnicity and gender during their undergraduate training within the context of the hidden curriculum in one British medical school as part of a wider qualitative research project into undergraduate medical education.

Method

We interviewed 36 undergraduate medical students in one British Medical School, across all five years of training using a semi-structured interview schedule. We selected them by random and quota sampling, stratified by sex and ethnicity and used the whole medical school population as a sampling frame. Data analyses involved the identification of common themes, reported by means of illustrative quotations and simple counts.

Results

The students provided information about variations patterned by gender in their motivation and influences when deciding to study medicine. Issues in relation to ethnicity were: gaining independence from parents, perceived limitations to career prospects, incompatibility of some religious beliefs with some medical practices and acquired open-mindedness towards students and patients from different ethnic backgrounds. Despite claiming no experiences of gender difference during medical training, female and male students expressed gender stereotypes, e.g. that women bring particularly caring and sympathetic attitudes to medicine, or that surgery requires the physical strength and competitiveness stereotypically associated with men that are likely to support the continuation of gender differentiation in medical careers.

Conclusion

The key themes identified in this paper in relation to ethnicity and to gender have important implications for medical educators and for those concerned with professional development. The results suggest a need to open up aspects of these relatively covert elements of student culture to scrutiny and debate and to take an explicitly wider view of the influence of what has sometimes been called the hidden curriculum upon the training of medical professionals and the practice of medicine.
Development and evaluation of an open source software tool for deidentification of pathology reports
Authors: Beckwith Bruce A , Mahaadevan Rajeshwarri , Balis Ulysses J , Kuo Frank
Published: March 2006

Background

Electronic medical records, including pathology reports, are often used for research purposes. Currently, there are few programs freely available to remove identifiers while leaving the remainder of the pathology report text intact. Our goal was to produce an open source, Health Insurance Portability and Accountability Act (HIPAA) compliant, deidentification tool tailored for pathology reports. We designed a three-step process for removing potential identifiers. The first step is to look for identifiers known to be associated with the patient, such as name, medical record number, pathology accession number, etc. Next, a series of pattern matches look for predictable patterns likely to represent identifying data; such as dates, accession numbers and addresses as well as patient, institution and physician names. Finally, individual words are compared with a database of proper names and geographic locations. Pathology reports from three institutions were used to design and test the algorithms. The software was improved iteratively on training sets until it exhibited good performance. 1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and note those that were not removed.

Results

1254 (69.7 %) of 1800 pathology reports contained identifiers in the body of the report. 3439 (98.3%) of 3499 unique identifiers in the test set were removed. Only 19 HIPAA-specified identifiers (mainly consult accession numbers and misspelled names) were missed. Of 41 non-HIPAA identifiers missed, the majority were partial institutional addresses and ages. Outside consultation case reports typically contain numerous identifiers and were the most challenging to deidentify comprehensively. There was variation in performance among reports from the three institutions, highlighting the need for site-specific customization, which is easily accomplished with our tool.

Conclusion

We have demonstrated that it is possible to create an open-source deidentification program which performs well on free-text pathology reports.
Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method
Authors: Siadaty Mir S , Knaus William A
Published: March 2006

Background

Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquisition step (which is required for subjective measures of interestingness), hence leaving a serious bottleneck. In this paper we propose a method for automatically acquiring knowledge to shorten the pattern list by locating the novel and interesting ones.

Methods

The dual-mining method is based on automatically comparing the strength of patterns mined from a database with the strength of equivalent patterns mined from a relevant knowledgebase. When these two estimates of pattern strength do not match, a high "surprise score" is assigned to the pattern, identifying the pattern as potentially interesting. The surprise score captures the degree of novelty or interestingness of the mined pattern. In addition, we show how to compute p values for each surprise score, thus filtering out noise and attaching statistical significance.

Results

We have implemented the dual-mining method using scripts written in Perl and R. We applied the method to a large patient database and a biomedical literature citation knowledgebase. The system estimated association scores for 50,000 patterns, composed of disease entities and lab results, by querying the database and the knowledgebase. It then computed the surprise scores by comparing the pairs of association scores. Finally, the system estimated statistical significance of the scores.

Conclusion

The dual-mining method eliminates more than 90% of patterns with strong associations, thus identifying them as uninteresting. We found that the pruning of patterns using the surprise score matched the biomedical evidence in the 100 cases that were examined by hand.

The method automates the acquisition of knowledge, thus reducing dependence on the knowledge elicited from human expert, which is usually a rate-limiting step.