bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communisL.)
Authors: Qiu Lijun , Yang Chun , Tian Bo , Yang Jun-Bo , Liu Aizhong
Published: January 2011

Background

The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers.

Results

In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (H
e) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean.

Conclusion

Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure analysis, facilitating breeding and crop improvement of castor bean.
The Patient Health Questionnaire-9 for detection of major depressive disorder in primary care: consequences of current thresholds in a crosssectional study
Authors: Zuithoff Nicolaas PA , Vergouwe Yvonne , King Michael , Nazareth Irwin , van Wezep Manja J , Moons Karel GM , Geerlings Mirjam I
Published: January 2011

Background

There is a need for brief instruments to ascertain the diagnosis of major depressive disorder. In this study, we present the reliability, construct validity and accuracy of the PHQ-9 and PHQ-2 to detect major depressive disorder in primary care.

Methods

Cross-sectional analyses within a large prospective cohort study (PREDICT-NL). Data was collected in seven large general practices in the centre of the Netherlands. 1338 subjects were recruited in the general practice waiting room, irrespective of their presenting complaint. The diagnostic accuracy (the area under the ROC curve and sensitivities and specificities for various thresholds) was calculated against a diagnosis of major depressive disorder determined with the Composite International Diagnostic Interview (CIDI).

Results

The PHQ-9 showed a high degree of internal consistency (ICC = 0.88) and test-retest reliability (correlation = 0.94). With respect to construct validity, it showed a clear association with functional status measurements, sick days and number of consultations. The discriminative ability was good for the PHQ-9 (area under the ROC curve = 0.87, 95% CI: 0.84-0.90) and the PHQ-2 (ROC area = 0.83, 95% CI 0.80-0.87). Sensitivities at the recommended thresholds were 0.49 for the PHQ-9 at a score of 10 and 0.28 for a categorical algorithm. Adjustment of the threshold and the algorithm improved sensitivities to 0.82 and 0.84 respectively but the specificity decreased from 0.95 to 0.82 (threshold) and from 0.98 to 0.81 (algorithm). Similar results were found for the PHQ-2: the recommended threshold of 3 had a sensitivity of 0.42 and lowering the threshold resulted in an improved sensitivity of 0.81.

Conclusion

The PHQ-9 and the PHQ-2 are useful instruments to detect major depressive disorder in primary care, provided a high score is followed by an additional diagnostic work-up. However, often recommended thresholds for the PHQ-9 and the PHQ-2 resulted in many undetected major depressive disorders.
Cluster analysis for identifying sub-groups and selecting potential discriminatory variables in human encephalitis
Authors: Hamid Jemila S , Meaney Christopher , Crowcroft Natasha S , Granerod Julia , Beyene Joseph
Published: January 2011

Background

Encephalitis is an acute clinical syndrome of the central nervous system (CNS), often associated with fatal outcome or permanent damage, including cognitive and behavioural impairment, affective disorders and epileptic seizures. Infection of the central nervous system is considered to be a major cause of encephalitis and more than 100 different pathogens have been recognized as causative agents. However, a large proportion of cases have unknown disease etiology.

Methods

We perform hierarchical cluster analysis on a multicenter England encephalitis data set with the aim of identifying sub-groups in human encephalitis. We use the simple matching similarity measure which is appropriate for binary data sets and performed variable selection using cluster heatmaps. We also use heatmaps to visually assess underlying patterns in the data, identify the main clinical and laboratory features and identify potential risk factors associated with encephalitis.

Results

Our results identified fever, personality and behavioural change, headache and lethargy as the main characteristics of encephalitis. Diagnostic variables such as brain scan and measurements from cerebrospinal fluids are also identified as main indicators of encephalitis. Our analysis revealed six major clusters in the England encephalitis data set. However, marked within-cluster heterogeneity is observed in some of the big clusters indicating possible sub-groups. Overall, the results show that patients are clustered according to symptom and diagnostic variables rather than causal agents. Exposure variables such as recent infection, sick person contact and animal contact have been identified as potential risk factors.

Conclusions

It is in general assumed and is a common practice to group encephalitis cases according to disease etiology. However, our results indicate that patients are clustered with respect to mainly symptom and diagnostic variables rather than causal agents. These similarities and/or differences with respect to symptom and diagnostic measurements might be attributed to host factors. The idea that characteristics of the host may be more important than the pathogen is also consistent with the observation that for some causes, such as herpes simplex virus (HSV), encephalitis is a rare outcome of a common infection.
Increased incidence of glucose disorders during pregnancy is not explained by pre-pregnancy obesity in London, Canada
Authors: Davenport Margie H , Campbell M Karen , Mottola Michelle F
Published: January 2011

Background

The increasing incidence of impaired glucose tolerance (IGT), gestational diabetes (GDM) and type 2 diabetes (T2D) during pregnancy was hypothesized to be associated with increases in pre-pregnancy body mass index (BMI). The aims were to 1) determine the prevalence of IGT/GDM/T2 D over a 10 year period; 2) examine the relationship between maternal overweight/obesity and IGT/GDM/T2D; and 3) examine the extent to which maternal metabolic complications impact maternal and fetal pregnancy outcomes.

Methods

Data arose from a perinatal database which contains maternal characteristics and perinatal outcome for all singleton infants born in London, Canada between January 1, 2000 and December 31, 2009. Univariable and multivariable odds ratios (OR) were estimated using logistic regression with IGT/GDM/T2 D being the outcome of interest.

Results

A total of 36,597 women were included in the analyses. Population incidence of IGT, GDM and T2 D rose from 0.7%, 2.9% and 0.5% in 2000 to 1.2%, 4.2% and 0.9% in 2009. The univariable OR for IGT, GDM and T2 D were 1.65, 1.52 and 2.06, respectively, over the ten year period. After controlling for maternal age, parity and pre-pregnancy BMI the OR did not decrease. Although there was a positive relationship between pre-pregnancy BMI and prevalence of IGT/GDM/T2 D, this did not explain the time trends in the latter. Diagnosis of IGT/GDM/T2 D increased the risk of having an Apgar score <7 at 5 minutes, which was partially explained by gestational hypertension, high placental ratio, gestational age and large for gestational age babies.

Conclusions

We found a significant increase in the incidence of IGT/GDM/T2 D for the decade between 2000-2009 which was not explained by rising prevalence of maternal overweight/obesity.
Potential drug interactions and duplicate prescriptions among ambulatory cancer patients: a prevalence study using an advanced screening method
Authors: van Leeuwen Roelof WF , Swart Eleonora L , Boom Frits A , Schuitenmaker Martin S , Hugtenburg Jacqueline G
Published: January 2011

Background

The pharmacotherapeutic treatment of patients with cancer is generally associated with multiple side-effects. Drug interactions and duplicate prescriptions between anti-cancer drugs or interactions with medication to treat comorbidity can reinforce or intensify side-effects.

The aim of the present study is to gain more insight into the prevalence of drug interactions and duplicate prescriptions among patients being treated in the outpatient day care departments for oncology and hematological illnesses. For the first time the prevalence of drug interactions with OTC-drugs in cancer patients will be studied. Possible risk factors for the occurrence of these drug-related problems will also be studied.

Methods/Design

A multicenter cross-sectional observational study of the epidemiology of drug interactions and duplicate prescriptions is performed among all oncology and hemato-oncology patients treated with systemic anti-cancer drugs at the oncology and hematology outpatient day care department of the VU University medical center and the Zaans Medical Center.

Discussion

In this article the prevalence of potential drug interactions in outpatient day-care patients treated with anti-cancer agents is studied using a novel more extensive screening method. If this study shows a high prevalence of drug interactions clinical pharmacists and oncologists must collaborate to develop a pharmaceutical screening programme, including an automated electronic warning system, to support drug prescribing for ambulatory cancer patient. This programme could minimize the occurrence of drug related problems such as drug interactions and duplicate prescriptions, thereby increasing quality of life.

Trial registration

This study is registered, number NTR2238.
The Colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information
Authors: Allen Wendy L , Jithesh Puthen V , Oliver Gavin R , Proutski Irina , Longley Daniel B , Lenz Heinz-Josef , Proutski Vitali , Harkin Paul , Johnston Patrick G
Published: January 2011

Background

To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome.

Methods

DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information.

Results

The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance.

Conclusions

Analysis from our in vitro and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including IGF2BP2, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.
In search of quality evidence for lifestyle management and glycemic control in children and adolescents with type 2 diabetes: A systematic review
Authors: Johnson Steven T , Newton Amanda S , Chopra Meera , Buckingham Jeanette , Huang Terry TK , Franks Paul W , Jetha Mary M , Ball Geoff DC
Published: January 2011

Background

Our purpose was to evaluate the impact of lifestyle behavior modification on glycemic control among children and youth with clinically defined Type 2 Diabetes (T2D).

Methods

We conducted a systematic review of studies (randomized trials, quasi-experimental studies) evaluating lifestyle (diet and/or physical activity) modification and glycemic control (HbA1c). Our data sources included bibliographic databases (EMBASE, CINAHL®, Cochrane Library, Medline®, PASCAL, PsycINFO®, and Sociological Abstracts), manual reference search, and contact with study authors. Two reviewers independently selected studies that included any intervention targeting diet and/or physical activity alone or in combination as a means to reduce HbA1c in children and youth under the age of 18 with T2D.

Results

Our search strategy generated 4,572 citations. The majority of citations were not relevant to the study objective. One study met inclusion criteria. In this retrospective study, morbidly obese youth with T2D were treated with a very low carbohydrate diet. This single study received a quality index score of < 11, indicating poor study quality and thus limiting confidence in the study's conclusions.

Conclusions

There is no high quality evidence to suggest lifestyle modification improves either short- or long-term glycemic control in children and youth with T2D. Additional research is clearly warranted to define optimal lifestyle behaviour strategies for young people with T2D.
Validation of the Arabic version of the Cohen perceived stress scale (PSS-10) among pregnant and postpartum women
Authors: Chaaya Monique , Osman Hibah , Naassan Georges , Mahfoud Ziyad
Published: January 2011

Background

This study was conducted to evaluate the validity of the Arabic translation of the Cohen Perceived Stress Scale (PSS-10) in pregnant and postpartum women.

Methods

A sample of 268 women participated. These included 113 women in their third trimester of pregnancy, 97 in the postpartum period and 58 healthy female university students. GHQ-12 and EPDS were also administered to the participants. Internal consistency reliability, assessed using Cronbach's α, was 0.74.

Results

PSS-10 significantly correlated with both EPDS and GHQ12 (ρ = 0.58 and ρ = 0.48 respectively), and significantly increased with higher scores on stressful life events. PSS-10 scores were higher among university students who also recorded higher stressful life events scores.

Conclusion

The Arabic translated version of the PSS-10 showed reasonably adequate psychometric properties.
Systematic review of mass media interventions designed to improve public recognition of stroke symptoms, emergency response and early treatment
Authors: Lecouturier Jan , Rodgers Helen , Murtagh Madeleine J , White Martin , Ford Gary A , Thomson Richard G
Published: January 2011

Background

Mass media interventions have been implemented to improve emergency response to stroke given the emergence of effective acute treatments, but their impact is unclear.

Methods

Systematic review of mass media interventions aimed at improving emergency response to stroke, with narrative synthesis and review of intervention development.

Results

Ten studies were included (six targeted the public, four both public and professionals) published between 1992 and 2010. Only three were controlled before and after studies, and only one had reported how the intervention was developed. Campaigns aimed only at the public reported significant increase in awareness of symptoms/signs, but little impact on awareness of need for emergency response. Of the two controlled before and after studies, one reported no impact on those over 65 years, the age group at increased risk of stroke and most likely to witness a stroke, and the other found a significant increase in awareness of two or more warning signs of stroke in the same group post-intervention. One campaign targeted at public and professionals did not reduce time to presentation at hospital to within two hours, but increased and sustained thrombolysis rates. This suggests the campaign had a primary impact on professionals and improved the way that services for stroke were organised.

Conclusions

Campaigns aimed at the public may raise awareness of symptoms/signs of stroke, but have limited impact on behaviour. Campaigns aimed at both public and professionals may have more impact on professionals than the public. New campaigns should follow the principles of good design and be robustly evaluated.
Selective decontamination of the gastrointestinal tract in patients undergoing esophageal resection
Authors: Näf Franziska , Warschkow René , Kolb Walter , Zünd Michael , Lange Jochen , Steffen Thomas
Published: January 2011

Background

Selective decontamination of the digestive tract (SDD) to eliminate gram-negative bacteria is still not widely accepted, although it reduces the incidence of nosocomial infections. In a previous retrospective study, a clear benefit to perioperative morbidity, and a reduction in nosocomial infections were found in patients who underwent an esophageal anastomosis. Thus, SDD was applied routinely for esophageal anastomoses. We report the outcome of a cohort of 81 patients who underwent this treatment.

Methods

From 2002, patients who underwent an esophageal anastomosis (esophagojejunostomy) were prospectively recorded. Perioperatively, patients received polymyxin, tobramycin, vancomycin and nystatin by mouth four times a day. Outcome was compared to a control group that was treated before 2002 (68 patients without SDD and 53 patients with SDD). Postoperative morbidity and mortality were assessed.

Results

Between 2002 and 2007, 81 patients who underwent an esophageal anastomosis received SDD. Compared to a retrospective control group, patients with SDD had significantly less pneumonia (OR 0.06 (0.01-0.46), p < 0.001) and lower morbidity (OR 0.16 (0.05-0.49), p < 0.001). Furthermore, fewer anastomotic insufficiencies and complications were found. Similar results were found in the analysis of the patients treated before 2002.

Conclusions

SDD significantly reduces perioperative morbidity and mortality in patients who undergo a distal esophageal anastomosis compared to a historical control group. In patients with an anastomotic leakage, there was a strong tendency of SDD to reduce postoperative mortality.
Effect of smoking on subgingival microflora of patients with periodontitis in Japan
Authors: Kubota Michiya , Tanno-Nakanishi Mariko , Yamada Satoru , Okuda Katsuji , Ishihara Kazuyuki
Published: January 2011

Background

Smoking is a risk factor for periodontitis. To clarify the contribution of smoking to periodontitis, it is essential to assess the relationship between smoking and the subgingival microflora. The aim of this study was to gain an insight into the influence of smoking on the microflora of Japanese patients with periodontitis.

Methods

Sixty-seven Japanese patients with chronic periodontitis (19 to 83 years old, 23 women and 44 men) were enrolled in the present study. They consisted of 30 smokers and 37 non-smokers. Periodontal parameters including probing pocket depth (PPD) and bleeding on probing (BOP) and oral hygiene status were recorded. Detection of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, Fusobacterium nucleatum/periodonticum, Treponema denticola and Campylobacter rectus in subgingival plaque samples was performed by polymerase chain reaction. Association between the detection of periodontopathic bacteria and smoking status was analyzed by multiple logistic regression analysis and chi-square test.

Results

A statistically significant association was found between having a PPD ≥ 4 mm and detection of T. denticola, P. intermedia, T. forsythia, or C. rectus, with odds ratios ranging from 2.17 to 3.54. A significant association was noted between BOP and the detection of C. rectus or P. intermedia, and smoking, with odds ratios ranging from 1.99 to 5.62. Prevalence of C. rectus was higher in smokers than non-smokers, whereas that of A. actinomycetemcomitans was lower in smokers.

Conclusions

Within limits, the analysis of the subgingival microbial flora in smokers and non-smokers with chronic periodontitis suggests a relevant association between smoking and colonization by the specific periodontal pathogens including C. rectus.
The effects of tualang honey on female reproductive organs, tibia bone and hormonal profile in ovariectomised rats - animal model for menopause
Authors: Zaid Siti SM , Sulaiman Siti A , Sirajudeen Kuttulebbai NM , Othman Nor H
Published: January 2011

Background

Honey is a highly nutritional natural product that has been widely used in folk medicine for a number of therapeutic purposes. We evaluated whether Malaysian Tualang honey (AgroMas, Malaysia) was effective in reducing menopausal syndrome in ovariectomised female rats; an animal model for menopause.

Methods

The rats were divided into two control groups and three test groups. The control groups were sham-operated (SH) and ovariectomised (OVX) rats. The SH and OVX control rats were fed on 0.5 ml of distill water. The rats in the test groups were fed with low dose 0.2 g/kg (THL), medium dose, 1.0 g/kg (THM) and high dose 2.0 g/kg (THH) of Tualang honey in 0.5 ml of distill water. The administration was given by oral gavage once daily for 2 weeks. The reproductive organs (uterus and vagina), tibia bone and aorta were taken for histopathological examination while serum for hormonal assays.

Results

Administration of Tualang honey for 2 weeks to ovariectomised rats significantly increased the weight of the uterus and the thickness of vaginal epithelium, restored the morphology of the tibia bones and reduced the body weight compared to rats in the ovariectomised group. The levels of estradiol and progesterone, in honey treated groups were markedly lower than that in the OVX group. At low doses (0.2 g/kg; THL group) of Tualang honey there was an increased in serum free testosterone levels compared to OVX group (P < 0.01). Progesterone concentrations was significantly decreased in the OVX group as compared to SHAM group (P < 0.05).

Conclusions

Tualang honey was shown to have beneficial effects on menopausal (ovariectomised) rats by preventing uterine atrophy, increased bone density and suppression of increased body weight. Honey could be an alternative to HRT.
Type 2 diabetes genetic association database manually curated for the study design and odds ratio
Authors: Lim Ji Eun , Hong Kyung-Won , Jin Hyun-Seok , Kim Yang Seok , Park Hun Kuk , Oh Bermseok
Published: January 2011

Background

The prevalence of type 2 diabetes has reached epidemic proportions worldwide, and the incidence of life-threatening complications of diabetes through continued exposure of tissues to high glucose levels is increasing. Advances in genotyping technology have increased the scale and accuracy of the genotype data so that an association genetic study has expanded enormously. Consequently, it is difficult to search the published association data efficiently, and several databases on the association results have been constructed, but these databases have their limitations to researchers: some providing only genome-wide association data, some not focused on the association but more on the integrative data, and some are not user-friendly. In this study, a user-friend database of type 2 diabetes genetic association of manually curated information was constructed.

Description

The list of publications used in this study was collected from the HuGE Navigator, which is an online database of published genome epidemiology literature. Because type 2 diabetes genetic association database (T2DGADB) aims to provide specialized information on the genetic risk factors involved in the development of type 2 diabetes, 701 of the 1,771 publications in the type 2 Diabetes case-control study for the development of the disease were extracted.

Conclusions

In the database, the association results were grouped as either positive or negative. The gene and SNP names were replaced with gene symbols and rsSNP numbers, the association p-values were determined manually, and the results are displayed by graphs and tables. In addition, the study design in publications, such as the population type and size are described. This database can be used for research purposes, such as an association and functional study of type 2 diabetes related genes, and as a primary genetic resource to construct a diabetes risk test in the preparation of personalized medicine in the future.
Cost-effectiveness of six strategies for Helicobacter pyloridiagnosis and management in uninvestigated dyspepsia assuming a high resource intensity practice pattern
Authors: Holmes Kyland P , Fang John C , Jackson Brian R
Published: January 2011

Background

Initial assessment of dyspepsia often includes noninvasive testing for Helicobacter pylori infection. Commercially available tests vary widely in cost and accuracy. Although there is extensive literature on the cost-effectiveness of H. pylori treatment, there is little information comparing the cost-effectiveness of various currently used, noninvasive testing strategies.

Methods

A Markov simulation was used to calculate cost per symptom-free year and cost per correct diagnosis. Uncertainty in outcomes was estimated using probabilistic sensitivity analysis.

Results

Under the baseline assumptions, cost per symptom-free year was $122 for empiric proton pump inhibitor (PPI) trial, and costs for the noninvasive test strategies ranged from $123 (stool antigen) to $129 (IgG/IgA combined serology). Confidence intervals had significant overlap.

Conclusions

Under our assumptions for how testing for H. pylori infection is employed in United States medical practice, the available noninvasive tests all have similar cost-effectiveness between one another as well as with empiric PPI trial.
The road to commercialization in Africa: lessons from developing the sickle-cell drug Niprisan
Authors: Perampaladas Kumar , Masum Hassan , Kapoor Andrew , Shah Ronak , Daar Abdallah S , Singer Peter A
Published: January 2011

Background

Developing novel drugs from traditional medicinal knowledge can serve as a means to improve public health. Yet countries in sub-Saharan Africa face barriers in translating traditional medicinal knowledge into commercially viable health products. Barriers in moving along the road towards making a new drug available include insufficient manufacturing capacity; knowledge sharing between scientists and medical healers; regulatory hurdles; quality control issues; pricing and distribution; and lack of financing. The case study method was used to illustrate efforts to overcome these barriers during the development in Nigeria of Niprisan – a novel drug for the treatment of sickle cell anemia, a chronic blood disorder with few effective therapies.

Discussion

Building on the knowledge of a traditional medicine practitioner, Nigeria’s National Institute for Pharmaceutical Research and Development (NIPRD) developed the traditional herbal medicine Niprisan. The commercialization of Niprisan reached a number of commercial milestones, including regulatory approval in Nigeria; securing US-based commercial partner XeChem; demonstrating clinical efficacy and safety; being awarded orphan drug status by the US Food and Drug Administration; and striking important relationships with domestic and international groups. Despite these successes, however, XeChem did not achieve mainstream success for Niprisan in Nigeria or in the United States. A number of reasons, including inconsistent funding and manufacturing and management challenges, have been put forth to explain Niprisan’s commercial demise. As of this writing, NIPRD is considering options for another commercial partner to take the drug forward.

Evidence from the Niprisan experience suggests that establishing benefit-sharing agreements, fostering partnerships with established research institutions, improving standardization and quality control, ensuring financial and managerial due diligence, and recruiting entrepreneurial leaders capable of holding dual scientific and business responsibilities should be incorporated into future drug development initiatives based on traditional medicines. Country-level supporting policies and conditions are also important. With more experience and support, and an improved environment for innovation, developing new drugs from traditional medicines may be an attractive approach to addressing diseases in sub-Saharan Africa and other regions.
Automated estimation of parasitaemia of Plasmodium yoelii-infected mice by digital image analysis of Giemsa-stained thin blood smears
Authors: Ma Charles , Harrison Paul , Wang Lina , Coppel Ross L
Published: January 2011

Background

Parasitaemia, the percentage of infected erythrocytes, is used to measure progress of experimental Plasmodium infection in infected hosts. The most widely used technique for parasitaemia determination is manual microscopic enumeration of Giemsa-stained blood films. This process is onerous, time consuming and relies on the expertise of the experimenter giving rise to person-to-person variability. Here the development of image-analysis software, named Plasmodium AutoCount, which can automatically generate parasitaemia values from Plasmodium-infected blood smears, is reported.

Methods

Giemsa-stained blood smear images were captured with a camera attached to a microscope and analysed using a programme written in the Python programming language. The programme design involved foreground detection, cell and infection detection, and spurious hit filtering. A number of parameters were adjusted by a calibration process using a set of representative images. Another programme, Counting Aid, written in Visual Basic, was developed to aid manual counting when the quality of blood smear preparation is too poor for use with the automated programme.

Results

This programme has been validated for use in estimation of parasitemia in mouse infection by Plasmodium yoelii and used to monitor parasitaemia on a daily basis for an entire challenge infection. The parasitaemia values determined by Plasmodium AutoCount were shown to be highly correlated with the results obtained by manual counting, and the discrepancy between automated and manual counting results were comparable to those found among manual counts of different experimenters.

Conclusions

Plasmodium AutoCount has proven to be a useful tool for rapid and accurate determination of parasitaemia from infected mouse blood. For greater accuracy when smear quality is poor, Plasmodium AutoCount, can be used in conjunction with Counting Aid.
MicroRNA-148b is frequently down-regulated in gastric cancer and acts as a tumor suppressor by inhibiting cell proliferation
Authors: Song Yong-Xi , Yue Zhen-Yu , Wang Zhen-Ning , Xu Ying-Ying , Luo Yang , Xu Hui-Mian , Zhang Xue , Jiang Li , Xing Cheng-Zhong , Zhang Yong
Published: January 2011

Background

MicroRNAs (miRNAs) are involved in cancer development and progression, acting as tumor suppressors or oncogenes. Our previous studies have revealed that miR-148a and miR-152 are significantly down-regulated in gastrointestinal cancers. Interestingly, miR-148b has the same "seed sequences" as miR-148a and miR-152. Although aberrant expression of miR-148b has been observed in several types of cancer, its pathophysiologic role and relevance to tumorigenesis are still largely unknown. The purpose of this study was to elucidate the molecular mechanisms by which miR-148b acts as a tumor suppressor in gastric cancer.

Results

We showed significant down-regulation of miR-148b in 106 gastric cancer tissues and four gastric cancer cell lines, compared with their non-tumor counterparts by real-time RT-PCR.In situhybridization of ten cases confirmed an overt decrease in the level of miR-148b in gastric cancer tissues. Moreover, the expression of miR-148b was demonstrated to be associated with tumor size (P = 0.027) by a Mann-Whitney U test. We also found that miR-148b could inhibit cell proliferationin vitroby MTT assay, growth curves and an anchorage-independent growth assay in MGC-803, SGC-7901, BGC-823 and AGS cells. An experiment in nude mice revealed that miR-148b could suppress tumorigenicityin vivo. Using a luciferase activity assay and western blot, CCKBR was identified as a target of miR-148b in cells. Moreover, an obvious inverse correlation was observed between the expression of CCKBR protein and miR-148b in 49 pairs of tissues (P = 0.002, Spearman's correlation).

Conclusions

These findings provide important evidence that miR-148b targets CCKBR and is significant in suppressing gastric cancer cell growth. Maybe miR-148b would become a potential biomarker and therapeutic target against gastric cancer.
Overexpression of proto-oncogene FBI-1 activates membrane type 1-matrix metalloproteinase in association with adverse outcome in ovarian cancers
Authors: Jiang LiLi , Siu Michelle KY , Wong Oscar GW , Tam Kar Fai , Lam Eric W-F , Ngan Hextan YS , Le Xiao-Feng , Wong Esther SY , Chan Hoi Yan , Cheung Annie NY
Published: January 2011

Background

FBI-1 (f actor that b inds to the i nducer of short transcripts of human immunodeficiency virus-1) is a member of the POK (POZ and Kruppel) family of transcription factors and play important roles in cellular differentiation and oncogenesis. Recent evidence suggests that FBI-1 is expressed at high levels in a subset of human lymphomas and some epithelial solid tumors. However, the function of FBI-1 in human ovarian cancers remains elusive.

Results

In this study, we investigated the role of FBI-1 in human ovarian cancers, in particularly, its function in cancer cell invasion via modulating membrane type 1-matrix metalloproteinase (MT1-MMP). Significantly higher FBI-1 protein and mRNA expression levels were demonstrated in ovarian cancers samples and cell lines compared with borderline tumors and benign cystadenomas. Increased FBI-1 mRNA expression was correlated significantly with gene amplification (P = 0.037). Moreover, higher FBI-1 expression was found in metastatic foci (P = 0.036) and malignant ascites (P = 0.021), and was significantly associated with advanced stage (P = 0.012), shorter overall survival (P = 0.032) and disease-free survival (P = 0.016). In vitro, overexpressed FBI-1 significantly enhanced cell migration and invasion both in OVCA 420 and SKOV-3 ovarian carcinoma cells, irrespective of p53 status, accompanied with elevated expression of MT1-MMP, but not MMP-2 or TIMP-2. Moreover, knockdown of MT1-MMP abolished FBI-1-mediated cell migration and invasion. Conversely, stable knockdown of FBI-1 remarkably reduced the motility of these cells with decreased expression of MT1-MMP. Promoter assay and chromatin immunoprecipitation study indicated that FBI-1 could directly interact with the promoter spanning ~600bp of the 5'-flanking sequence of MT1-MMP and enhanced its expression in a dose-dependent manner. Furthermore, stable knockdown and ectopic expression of FBI-1 decreased and increased cell proliferation respectively in OVCA 420, but not in the p53 null SKOV-3 cells.

Conclusions

Our results suggested an important role of FBI-1 in ovarian cancer cell proliferation, cell mobility, and invasiveness, and that FBI-1 can be a potential target of chemotherapy.
VEGF121b and VEGF165b are weakly angiogenic isoforms of VEGF-A
Authors: Catena Raúl , Larzabal Leyre , Larrayoz Marta , Molina Eva , Hermida Jose , Agorreta Jackeline , Montes Ramon , Pio Ruben , Montuenga Luis M , Calvo Alfonso
Published: January 2011

Background

Different isoforms of VEGF-A (mainly VEGF121, VEGF165 and VEGF189) have been shown to display particular angiogenic properties in the generation of a functional tumor vasculature. Recently, a novel class of VEGF-A isoforms, designated as VEGFxxxb, generated through alternative splicing, have been described. Previous studies have suggested that these isoforms may inhibit angiogenesis. In the present work we have produced recombinant VEGF121/165b proteins in the yeast Pichia pastoris and constructed vectors to overexpress these isoforms and assess their angiogenic potential.

Results

Recombinant VEGF121/165b proteins generated either in yeasts or mammalian cells activated VEGFR2 and its downstream effector ERK1/2, although to a lesser extent than VEGF165. Furthermore, treatment of endothelial cells with VEGF121/165b increased cell proliferation compared to untreated cells, although such stimulation was lower than that induced by VEGF165. Moreover, in vivo angiogenesis assays confirmed angiogenesis stimulation by VEGF121/165b isoforms. A549 and PC-3 cells overexpressing VEGF121b or VEGF165b (or carrying the PCDNA3.1 empty vector, as control) and xenotransplanted into nude mice showed increased tumor volume and angiogenesis compared to controls. To assess whether the VEGFxxxb isoforms are differentially expressed in tumors compared to healthy tissues, immunohistochemical analysis was conducted on a breast cancer tissue microarray. A significant increase (p < 0.05) in both VEGFxxxb and total VEGF-A protein expression in infiltrating ductal carcinomas compared to normal breasts was observed. A positive significant correlation (r = 0.404, p = 0.033) between VEGFxxxb and total VEGF-A was found.

Conclusions

Our results demonstrate that VEGF121/165b are not anti-angiogenic, but weakly angiogenic isoforms of VEGF-A. In addition, VEGFxxxb isoforms are up-regulated in breast cancer in comparison with non malignant breast tissues. These results are to be taken into account when considering a possible use of VEGF121/165b-based therapies in patients.
The adsorption of biomolecules to multi-walled carbon nanotubes is influenced by both pulmonary surfactant lipids and surface chemistry
Authors: Gasser Michael , Rothen-Rutishauser Barbara , Krug Harald F , Gehr Peter , Nelle Mathias , Yan Bing , Wick Peter
Published: January 2011

Background

During production and processing of multi-walled carbon nanotubes (MWCNTs), they may be inhaled and may enter the pulmonary circulation. It is essential that interactions with involved body fluids like the pulmonary surfactant, the blood and others are investigated, particularly as these interactions could lead to coating of the tubes and may affect their chemical and physical characteristics. The aim of this study was to characterize the possible coatings of different functionalized MWCNTs in a cell free environment.

Results

To simulate the first contact in the lung, the tubes were coated with pulmonary surfactant and subsequently bound lipids were characterized. The further coating in the blood circulation was simulated by incubating the tubes in blood plasma. MWCNTs were amino (NH2)- and carboxyl (-COOH)-modified, in order to investigate the influence on the bound lipid and protein patterns. It was shown that surfactant lipids bind unspecifically to different functionalized MWCNTs, in contrast to the blood plasma proteins which showed characteristic binding patterns. Patterns of bound surfactant lipids were altered after a subsequent incubation in blood plasma. In addition, it was found that bound plasma protein patterns were altered when MWCNTs were previously coated with pulmonary surfactant.

Conclusions

A pulmonary surfactant coating and the functionalization of MWCNTs have both the potential to alter the MWCNTs blood plasma protein coating and to determine their properties and behaviour in biological systems.
Descriptive epidemiology of screen and non-screen sedentary time in adolescents: a cross sectional study
Authors: Olds Tim S , Maher Carol A , Ridley Kate , Kittel Daniella M
Published: January 2011

Background

Much attention has been paid to adolescents' screen time, however very few studies have examined non-screen sedentary time (NSST). This study aimed to (1) describe the magnitude and composition of screen sedentary time (SST) and NSST in Australian adolescents, (2) describe the socio-demographic correlates of SST and NSST, and (3) determine whether screen time is an adequate surrogate for total sedentary behaviour in this population.

Methods

2200 9-16 year old Australians provided detailed use of time data for four days. Non-screen sedentary time (NSST) included time spent participating in activities expected to elicit <3 METs whilst seated or lying down (other than sleeping), excluding screen-based activities (television, playing videogames or using computers). Total sedentary time was the sum of screen time and NSST.

Results

Adolescents spent a mean (SD) of 345 (105) minutes/day in NSST, which constituted 60% of total sedentary time. School activities contributed 42% of NSST, socialising 19%, self-care (mainly eating) 16%, and passive transport 15%. Screen time and NSST showed opposite patterns in relation to key socio-demographic characteristics, including sex, age, weight status, household income, parental education and day type. Because screen time was negatively correlated with NSST (r = -0.58), and exhibited a moderate correlation (r = 0.53) with total sedentary time, screen time was only a moderately effective surrogate for total sedentary time.

Conclusions

To capture a complete picture of young people's sedentary time, studies should endeavour to measure both screen time and NSST.
Mitochondrial DNA and anti-mitochondrial antibodies in serum of autistic children
Authors: Zhang Bodi , Angelidou Asimenia , Alysandratos Konstantinos-Dionysios , Vasiadi Magdalini , Francis Konstantinos , Asadi Shahrzad , Theoharides Athanasios , Sideri Kyriaki , Lykouras Lefteris , Kalogeromitros Dimitrios , Theoharides Theoharis C
Published: January 2011

Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by difficulties in communication, cognitive and learning deficits, as well as stereotypic behaviors. For the majority of cases there are no reliable biomarkers or distinct pathogenesis. However, increasing evidence indicates ASD may be associated with some immune dysregulation, and may have a neuroimmune component. We recently showed that the peptide neurotensin (NT) is increased in autistic children. We now show that NT induces release of extracellular mitochondrial DNA (mtDNA) that could act as "autoimmune" trigger. We further show that serum from young autistic patients contains mtDNA (n = 20; cytochrome B, p = 0.0002 and 7S, p = 0.006), and anti-mitochondrial antibody Type 2 (n = 14; p = 0.001) as compared to normally developing, unrelated controls (n = 12). Extracellular blood mtDNA and other components may characterize an autistic endophenotype and may contribute to its pathogenesis by activating autoimmune responses.
Angiogenesis is present in experimental autoimmune encephalomyelitis and pro-angiogenic factors are increased in multiple sclerosis lesions
Authors: Seabrook Timothy J , Littlewood-Evans Amanda , Brinkmann Volker , Pöllinger Bernadette , Schnell Christian , Hiestand Peter C
Published: January 2011

Background

Angiogenesis is a common finding in chronic inflammatory diseases; however, its role in multiple sclerosis (MS) is unclear. Central nervous system lesions from both MS and experimental autoimmune encephalomyelitis (EAE), the animal model of MS, contain T cells, macrophages and activated glia, which can produce pro-angiogenic factors. Previous EAE studies have demonstrated an increase in blood vessels, but differences between the different phases of disease have not been reported. Therefore we examined angiogenic promoting factors in MS and EAE lesions to determine if there were changes in blood vessel density at different stages of EAE.

Methods

In this series of experiments we used a combination of vascular casting, VEGF ELISA and immunohistochemistry to examine angiogenesis in experimental autoimmune encephalomyelitis (EAE). Using immunohistochemistry we also examined chronic active MS lesions for angiogenic factors.

Results

Vascular casting and histological examination of the spinal cord and brain of rats with EAE demonstrated that the density of patent blood vessels increased in the lumbar spinal cord during the relapse phase of the disease (p < 0.05). We found an increased expression of VEGF by inflammatory cells and a decrease in the recently described angiogenesis inhibitor meteorin. Examination of chronic active human MS tissues demonstrated glial expression of VEGF and glial and blood vessel expression of the pro-angiogenic receptor VEGFR2. There was a decreased expression of VEGFR1 in the lesions compared to normal white matter.

Conclusions

These findings reveal that angiogenesis is intimately involved in the progression of EAE and may have a role in MS.
Alzheimer's disease gene signature says: beware of brain viral infections
Authors: Porcellini Elisa , Carbone Ilaria , Ianni Manuela , Licastro Federico
Published: January 2011

Background

Recent findings from a genome wide association investigation in a large cohort of patients with Alzheimer's disease (AD) and non demented controls (CTR) showed that a limited set of genes was in a strong association (p > l0-5) with the disease.

Presentation of the hypothesis

In this report we suggest that the polymorphism association in 8 of these genes is consistent with a non conventional interpretation of AD etiology.

Nectin-2 (NC-2), apolipoprotein E (APOE), glycoprotein carcinoembryonic antigen related cell adhesion molecule- 16 (CEACAM-16), B-cell lymphoma-3 (Bcl-3), translocase of outer mitochondrial membrane 40 homolog (T0MM-40), complement receptor-1 (CR-l), APOJ or clusterin and C-type lectin domain A family-16 member (CLEC-16A) result in a genetic signature that might affect individual brain susceptibility to infection by herpes virus family during aging, leading to neuronal loss, inflammation and amyloid deposition.

Implications of the hypothesis

We hypothesized that such genetic trait may predispose to AD via complex and diverse mechanisms each contributing to an increase of individual susceptibility to brain viral infections