bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement of tissue preparation for laser capture microdissection: application for cell type-specific miRNA expression profiling in colorectal tumors
Authors: Wang Shuyang , Wang Lei , Zhu Tengfang , Gao Xue , Li Jian , Wu Ying , Zhu Hongguang 
Published: March 2010

Abstract

Background
Laser capture microdissection (LCM) has successfully isolated pure cell populations from tissue sections and the combination of LCM with standard genomic and proteomic methods has revolutionized molecular analysis of complex tissue. However, the quantity and quality of material recovered after LCM is often still limited for analysis by using whole genomic and proteomic approaches. To procure high quality and quantity of RNA after LCM, we optimized the procedures on tissue preparations and applied the approach for cell type-specific miRNA expression profiling in colorectal tumors.

Results
We found that the ethanol fixation of tissue sections for 2 hours had the maximum improvement of RNA quality (1.8 fold, p = 0.0014) and quantity (1.5 fold, p = 0.066). Overall, the quality (RNA integrity number, RIN) for the microdissected colorectal tissues was 5.2 ± 1.5 (average ± SD) for normal (n = 43), 5.7 ± 1.1 for adenomas (n = 14) and 7.2 ± 1.2 for carcinomas (n = 44). We then compared miRNA expression profiles of 18 colorectal tissues (6 normal, 6 adenomas and 6 carcinomas) between LCM selected epithelial cells versus stromal cells using Agilent miRNA microarrays. We identified 51 differentially expressed miRNAs (p <= 0.001) between these two cell types. We found that the miRNAs in the epithelial cells could differentiate adenomas from normal and carcinomas. However, the miRNAs in the stromal and mixed cells could not separate adenomas from normal tissues. Finally, we applied quantitative RT-PCR to cross-verify the expression patterns of 7 different miRNAs using 8 LCM-selected epithelial cells and found the excellent correlation of the fold changes between the two platforms (R = 0.996).

Conclusions
Our study demonstrates the feasibility and potential power of discovering cell type-specific miRNA biomarkers in complex tissue using combination of LCM with genome-wide miRNA analysis.
Effect of MDM2 SNP309 and p53 codon 72 polymorphisms on lung cancer risk and survival among non-smoking Chinese women in Singapore
Authors: Chua Hui Wan , Ng Daniel , Choo Serena , Lum San San , Li Huihua , Soh Li Ying , Sabapathy Kanaga , Seow Adeline 
Published: March 2010

Abstract

Background
Single nucleotide polymorphism (SNP) 309 resulting in a T or G allele in the promoter of MDM2, the negative regulator of p53, has been suggested to affect cancer predisposition and age of onset, primarily in females. However, findings have been inconsistent in various cancers, and ethnicity appears to be a critical factor influencing the effects of the SNP on cancer risk. An increasing trend has been observed in the prevalence of lung cancers in non-smokers, especially females, though the underlying genetic basis is unclear.

Methods
We therefore examined the role of the SNPs in the p53 pathway (p53 codon 72 and MDM2 SNP309) on lung cancer risk and prognosis of a life-time non-smoking female Chinese population, in a hospital-based case-control study of 123 cases and 159 age-matched controls, by PCR analysis.

Results
Our findings reveal that the risk of lung cancer among individuals with the MDM2 SNP309 TT genotype was 2.1 (95% CI 1.01-4.36) relative to the GG genotype, contrary to initial expectations that the GG genotype with elevated MDM2 levels will increase cancer risk. Those who had this genotype in combination with the p53 Pro allele had a risk of 2.5 (95% CI 1.2-5.0). There was however no effect of either polymorphism on age at diagnosis of lung cancer or on overall survival.

Conclusions
The results thus demonstrate that the MDM2 SNP309 TT rather than the GG genotype is associated with increased risk of lung cancer in this population, suggesting that other mechanisms independent of increased MDM2 levels can influence cancer susceptibility.
A study of health effects of long-distance ocean voyages on seamen using a data classification approach
Authors: Lu Yunmei , Gao Yanhong , Cao Zhongbo , Cui Juan , Dong Zhennan , Tian Yaping , Xu Ying 
Published: March 2010

Abstract

Background
Long-distance ocean voyages may have substantial impacts on seamen's health, possibly causing malnutrition and other illness. Measures can possibly be taken to prevent such problems from happening through preparing special diet and making special precautions prior or during the sailing if a detailed understanding can be gained about what specific health effects such voyages may have on the seamen.

Methods
We present a computational study on 200 seamen using 41 chemistry indicators measured on their blood samples collected before and after the sailing. Our computational study is done using a data classification approach with a support vector machine-based classifier in conjunction with feature selections using a recursive feature elimination procedure.

Results
Our analysis results suggest that among the 41 blood chemistry measures, nine are most likely to be affected during the sailing, which provide important clues about the specific effects of ocean voyage on seamen's health.

Conclusions
The identification of the nine blood chemistry measures provides important clues about the effects of long-distance voyage on seamen's health. These findings will prove to be useful to guide in improving the living and working environment, as well as food preparation on ships.
Effect of HXT 1 and HXT 7 hexose transporter overexpression on wild-type and lactic acid producing Saccharomyces cerevisiae cells
Authors: Rossi Giorgia , Sauer Michael , Porro Danilo , Branduardi Paola 
Published: March 2010

Abstract

Background
Since about three decades, Saccharomyces cerevisiae can be engineered to efficiently produce proteins and metabolites. Even recognizing that in baker's yeast one determining step for the glucose consumption rate is the sugar uptake, this fact has never been conceived to improve the metabolite(s) productivity.
In this work we compared the ethanol and/or the lactic acid production from wild type and metabolically engineeredS. cerevisiae cells expressing an additional copy of one hexose transporter.

Results
Different S. cerevisiae strains (wild type and metabolically engineered for lactic acid production) were transformed with the HXT 1 or the HXT 7 gene encoding for hexose transporters.
Data obtained suggest that the overexpression of an Hxt transporter may lead to an increase in glucose uptake that could result in an increased ethanol and/or lactic acid productivities. As a consequence of the increased productivity and of the reduced process timing, a higher production was measured.

Conclusion
Metabolic pathway manipulation for improving the properties and the productivity of microorganisms is a well established concept. A high production relies on a multi-factorial system. We showed that by modulating the first step of the pathway leading to lactic acid accumulation an improvement of about 15% in lactic acid production can be obtained in a yeast strain already developed for industrial application.
Bridging the Divide between Science and Journalism
Authors: Van Eperen Laura , Marincola Francesco M , Strohm Jennifer 
Published: March 2010

Abstract
There are countless reasons nearly every scientist should learn how to communicate effectively with the media, including increased understanding of critical research findings to attract or sustain funding and build new professional partnerships that will further propel forward research. But where do scientists begin? Bridging the Divide between Science and Journalism offers practical tips for any scientist looking to work with the media.
Given the traditional and internet-based sources for medical research and healthcare-related news now available, it is imperative that scientists know how to communicate their latest findings through the appropriate channels. The credible media channels are managed by working journalists, so learning how to package vast, technical research in a form that is appetizing and "bite-sized" in order to get their attention, is an art. Reducing years of research into a headline can be extremely difficult and certainly doesn't come naturally to every scientist, so this article provides suggestions on how to work with the media to communicate your findings.
JinQi-Jiangtang tablet, a Chinese patent medicine, for pre-diabetes: a randomized controlled trial
Authors: Cao Hongbo , Ren Ming , Guo Liping , Shang Hongcai , Zhang Junhua , Song Yuzhen , Wang Hui , Wang Baohe , Li Xiantao , Hu Jing , Wang Xuemei , Wang Dehui , Chen Jianzong , Li Shuanglei , Chen Liming 
Published: March 2010

Abstract

Background
Pre-diabetes is a growing health concern where a large percentage of these patients develop full type 2 diabetes. Effective interventions on pre-diabetes can prevent or delay the occurrence or development of diabetes. Pharmaco-dynamics and pre-clinical of JinQi-Jiangtang tablets (JQJT) suggest that it could be benefit for pre-diabetes.

Methods/Design
Randomized controlled trial (RCT) is implemented in this study. The study term is 24 months (12 months for intervention and 12 months for follow up). Participants are recruited from four cities of China: Beijing, Tianjin, Xi'an and Nanning. Four hundred participants are randomized to treatment group (JQJT tablets) and control group (Placebo); two hundred participants each. People being included in this study must have been diagnosed as pre-diabetes via western medicine criteria and traditional Chinese medicine (TCM) criteria. The end-point indexes include: incidence of diabetes mellitus and reversion rate. Primary outcome indexes include: oral glucose tolerance test; insulin releasing test; glycosylated hemoglobin (HA1c). Secondary outcome indexes include: score of the Short Form 36 Health Survey Questionnaire (SF-36); score of TCM symptoms; blood lipid test. Indexes of safety include: general medical examination; blood and urine regular test; electrocardiogram (ECG), liver function (ALT) and renal function (BUN, Creatinine) test; record of adverse event, such as headache, faint, etc. Qualitative control will be implemented and a number of standard operating processes (SOPs) will be formed throughout the study: laboratory quality control measures; compliance control for researchers and participants; researcher training before study; supervision; investigational drug management and others.

Discussion
The aim of this study is to evaluate the effectiveness and safety of JinQi JiangTang (JQJT) tablets for the treatment of patients with pre-diabetes.

Trial registration
Chinese clinical trials register ChiCTR-TRC-00000401
Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster
Authors: Dewar Michael A , Kadirkamanathan Visakan , Opper Manfred , Sanguinetti Guido 
Published: March 2010

Abstract

Background
Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem.

Results
We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences.

Conclusions
The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems.
Showing Off
Authors: Ivanovitch Roman 
Published: March 2010

The article examines a group of closing gestures in Mozart's piano concertos, passages of soloistic virtuosity just before the last tuttis of the exposition and recapitulation. Serving as grand cadential clinchers and clothed in conventional figuration, these spots—sometimes called “display episodes”—appear to highlight performative prowess at the expense of compositional invention. As such, beyond an acknowledgment of the appropriateness of stock passagework at this point, analysis can have little to say: the episodes are either self-evidently simple or transparent to theoretical apparatus.I suggest, however, that by using the vantage point of variation, conceived broadly, not just as a technique but as a manner of organizing musical thoughts, new insights can emerge about these passages. This wider conception of variation is sanctioned both by historical precedent (Daube, Koch) and by contemporary usage (Sisman, Agawu); the specific invocation of it in connection with the display episodes is suggested initially by their characteristic bipartite format. Seen through the variation lens, elements such as contrapuntal ingenuity, complex modular arrangements within and between phrases, and an affinity for textural exploration come to the fore. These elements constitute a display of compositional virtuosity that is a counterpart to the more evident performative fireworks.
Tiered Polyphony and Its Determinative Role in the Piano Music of Johannes Brahms
Authors: Auerbach Brent 
Published: March 2010

Tiered polyphony describes segments of music that manifest rhythmic/metric layering (Lester 1986) in the presence of polyphony. This texture, though a hallmark of the baroque era, is capable of generating a variety of musical effects over many style periods. This article establishes three categories of the texture based on degrees of metrical dissonance: weakly, moderately, and strictly tiered polyphony. The last form is special not only for its rarity but also for the extreme independence of its lines, which create supermetrical dissonance through pitch cells and/or pitch-interval cycles.Strictly tiered polyphony figures prominently in Brahms's piano music, where it lends passages an aura of extreme drive and inexorability. Importantly, awareness of this texture can provide insights into Brahms's works unavailable through conventional approaches. The analytical portion of this article examines the Two Rhapsodies, op. 79. The unusual harmonic structure of the G-minor rhapsody is read in light of 1-cycles present within the opening tiered polyphony. In the B-minor rhapsody, the content of three concurrent cycles at the opening—a 4-cycle, 1-cycle, and 5/7-cycle—is respectively reflected in the hexatonic organization of mm. 1–67, in the A section's stormy chromatic transitions, and in the cadential gestures that permeate the B section and coda.
The Nine-Year Sustained Cost-Containment Impact of Swiss Pilot Physicians-Pharmacists Quality Circles
Authors: Niquille Anne , Ruggli Martine , Buchmann Michel , Jordan Dominique , Bugnon Olivier 
Published: March 2010

Background Six pioneer physicians-pharmacists quality circles (PPQCs) located in the Swiss canton of Fribourg (administratively corresponding to a state in the US) were under the responsibility of 6 trained community pharmacists moderating the prescribing process of 24 general practitioners (GPs). PPQCs are based on a multifaceted collaborative process mediated by community pharmacists for improving compliance with clinical guidelines within GPs’ prescribing practices. Objective To assess, over a 9-year period (1999–2007), the cost-containment impact of the PPQCs. Methods The key elements of PPQCs are a structured continuous quality improvement and education process; local networking; feedback of comparative and detailed data regarding costs, drug choice, and frequency of prescribed drugs; and structured independent literature review for interdisciplinary continuing education. The data are issued from the community pharmacy invoices to the health insurance companies. The study analyzed the cost-containment impact of the PPQCs in comparison with GPs working in similar conditions of care without particular collaboration with pharmacists, the percentage of generic prescriptions for specific cardiovascular drug classes, and the percentage of drug costs or units prescribed for specific cardiovascular drugs. Results For the 9-year period, there was a 42% decrease in the drug costs in the PPQC group as compared to the control group, representing a $225,000 (USD) savings per GP only in 2007. These results are explained by better compliance with clinical and pharmacovigilance guidelines, larger distribution of generic drugs, a more balanced attitude toward marketing strategies, and interdisciplinary continuing education on the rational use of drugs. Conclusions The PPQC work process has yielded sustainable results, such as significant cost savings, higher penetration of generics and reflection on patient safety, and the place of “new” drugs in therapy. The PPQCs may also constitute a solid basis for implementing more comprehensive collaborative programs, such as medication reviews, adherence-enhancing interventions, or disease management approaches.
Diabetes Medications Related to an Increased Risk of Falls and Fall-Related Morbidity in the Elderly
Authors: Berlie Helen D , Garwood Candice L 
Published: March 2010

Objective To review literature regarding the effect of diabetes medications as a contributing risk for falls and fall-related morbidity in elderly patients with type 2 diabetes. Data sources Primary literature was identified through PubMed MEDLINE (1966–November 2009) using the search terms elderly, aged, older adults, diabetes type 2, diabetes mellitus, falls, fractures, medication, hypoglycemia, and vitamin B12 deficiency. Each drug class and the individual agents within the classes were also included in the search. Additional references were obtained through review of references from articles obtained. Study selection and data extraction Clinical studies evaluating diabetes medications and their association with falls, as well as studies evaluating their association with the complications of falls, were considered for inclusion. Selection emphasis was placed on randomized studies evaluating diabetes medications and falls. Data synthesis There is no direct link between metformin and falls; however, an indirect association caused by neuropathy secondary to vitamin B12 deficiency may be of concern. Although hypoglycemia is a risk factor, to date, there are no trials specifically linking insulin secretagogues to falls. Insulin use has been demonstrated to increase the risk of falls in the elderly. Thiazolidinediones increase fracture risk and thus may worsen fall-related outcomes. There are no studies to date linking other agents to an increased risk of falls. Conclusions Special considerations should be made when treating elderly patients with diabetes. At this time, a patient's functional level and risk factors for falls should weigh into decision-making regarding drug selection. The risk of falls and fall-related complications associated with diabetes medications should not be ignored.
Positive (But Not Negative) Punishment Predicts Anxiety and Depression Among Prostate Cancer Patients: An Exploration of the Behaviour Analytic Model of Depression
Authors: Bitsika Vicki , Sharpley Christopher F. , Christie David R. H. 
Published: March 2010

AbstractThe relative power of Positive and Negative Punishment as predictors of anxiety and depression was investigated within the gender-specific population of Prostate Cancer patients. As well as being a more powerful predictor of total test scores, Positive Punishment was also a stronger predictor of the presence of clinical levels of anxiety and depression. Examination of the particular Positive Punishment events that were significantly associated with clinical anxiety and depression showed considerable overlap, supporting the concept of a combined anxiety-depression disorder. Suggestions for behavioural interventions with this patient group are made.
Online CBT I: Bridging the Gap Between Eliza and Modern Online CBT Treatment Packages
Authors: Helgadóttir Fjóla Dögg , Menzies Ross G. , Onslow Mark , Packman Ann , O'Brian Sue 
Published: March 2010

AbstractReviews have demonstrated large effect sizes when using computerised cognitive behaviour therapy (CBT) protocols for treating anxiety, depression and health related concerns. However, the amount of therapist contact per user seems to be the most significant prognostic indicator. Thus, in some ways current online interventions can be viewed primarily as an extension of one-on-one therapy. The present article provides guidelines for targeting this limitation of online psychological interventions. The goal is to mimic the therapeutic relationship using a computer, without having any therapist involved. Consequently, thousands of users would be able to receive treatment simultaneously, reaching a wider audience, which was the initial goal of the online model. The development of a treatment program using file audit data is suggested as an alternative to having an individual therapist for each user. This is done by allowing the ‘computer psychologist’ to tailor individualised treatments for each user based on their psychological profile. The user is provided with individualised corrective feedback based on a set of prewritten responses to common faulty thoughts. A new paradigm is proposed for online treatment delivery.
A Novel Intervention to Address Fears in Children with Asperger Syndrome: A Pilot Study of the Cognitive Behaviour Drama (CBD) Model
Authors: Karnezi Haris , Tierney Kevin 
Published: March 2010

AbstractThis article introduces a new intervention model designed to address phobic avoidances in children with Asperger syndrome, incorporating principles and techniques from cognitive and behaviour therapy into the art form of drama. This paper presents a single case study that outlines the application of the model in the treatment of a long-term fear of hand-driers in an 11-year-old boy, diagnosed with Asperger syndrome, for whom all other forms of therapy including variants of systematic desensitisation and traditional cognitive behaviour therapy had been found to be ineffective. The results of this study offer preliminary descriptive evidence of the efficacy of the model and durability of outcomes.