Full Text Clustering and Relationship Network Analysis of Biomedical Publications

Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers.     

Trial Publication after Registration in ClinicalTrials.Gov: A Cross-Sectional Analysis

Background

ClinicalTrials.gov is a publicly accessible, Internet-based registry of clinical trials managed by the US National Library of Medicine that has the potential to address selective trial publication. Our objectives were to examine completeness of registration within ClinicalTrials.gov and to determine the extent and correlates of selective publication.

Methods and Findings

We examined reporting of registration information among a cross-section of trials that had been registered at ClinicalTrials.gov after December 31, 1999 and updated as having been completed by June 8, 2007, excluding phase I trials. We then determined publication status among a random 10% subsample by searching MEDLINE using a systematic protocol, after excluding trials completed after December 31, 2005 to allow at least 2 y for publication following completion. Among the full sample of completed trials (n = 7,515), nearly 100% reported all data elements mandated by ClinicalTrials.gov, such as intervention and sponsorship. Optional data element reporting varied, with 53% reporting trial end date, 66% reporting primary outcome, and 87% reporting trial start date. Among the 10% subsample, less than half (311 of 677, 46%) of trials were published, among which 96 (31%) provided a citation within ClinicalTrials.gov of a publication describing trial results. Trials primarily sponsored by industry (40%, 144 of 357) were less likely to be published when compared with nonindustry/nongovernment sponsored trials (56%, 110 of 198; p<0.001), but there was no significant difference when compared with government sponsored trials (47%, 57 of 122; p = 0.22). Among trials that reported an end date, 75 of 123 (61%) completed prior to 2004, 50 of 96 (52%) completed during 2004, and 62 of 149 (42%) completed during 2005 were published (p = 0.006).

Conclusions

Reporting of optional data elements varied and publication rates among completed trials registered within ClinicalTrials.gov were low. Without greater attention to reporting of all data elements, the potential for ClinicalTrials.gov to address selective publication of clinical trials will be limited. Please see later in the article for the Editors'' Summary     

Circulating Irisin Levels Are Not Affected by Coffee Intake: A Randomized Controlled Trial

Irisin, secreted by skeletal muscle and possibly fat, is hypothesized to play an important role in modulating energy expenditure, obesity and metabolism. Coffee consumption also increases energy expenditure and leads to positive metabolic effects, but whether these effects are mediated by irisin remains unknown. The objective of this study was to determine the association between baseline irisin levels and the metabolic profile in humans and to investigate whether consumption of caffeinated coffee alters irisin levels. To this end, a secondary analysis was performed investigating irisin levels at baseline and after eight weeks in 32 healthy, overweight coffee drinkers who were randomized to consumption of 5 cups per day of instant caffeinated coffee, decaffeinated coffee, or water. Spearman correlation and analysis of covariance analyses were performed to identify possible associations. Irisin levels were positively correlated with waist circumference (r = 0.41, p = 0.02), fat mass (r = 0.44, p = 0.01) and CRP (r = 0.47, p = 0.007). Though there was a trend towards increased levels of irisin over time in the caffeinated coffee group (+1.8%) when compared to the placebo group (−4%) this did not reach statistical significance (p = 0.75 for the trend). This first randomized trial failed to reveal any effects of coffee consumption on irisin levels, but a larger trial, appropriately sized on the basis of data provided by this study, is needed to conclusively investigate such a relationship.

Trial Registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00305097","term_id":"NCT00305097"}}NCT00305097     

纳米线在生物医学工程中的应用

纳米线由于其直径大小接近生物大分子,并且纳米线可以作为电子电路物理组成中的一部分,所以在一定范围通过纳米线将生物细胞分子和电子电路进行对接变得可行。该文主要介绍了生物组件通过纳米线实现对生物分子的传感,通过纳米线对细胞的信号检测,以及在生物分子的输送中的应用等的最新发展。     

Registration methods in radiotherapy

PurposeThe aim of this study is to present a short and comprehensive review of the methods of medical image registration, their conditions and applications in radiotherapy. A particular focus was placed on the methods of deformable image registration.MethodsTo structure and deepen the knowledge on medical image registration in radiotherapy, a medical literature analysis was made using the Google Scholar browser and the medical database of the PubMed library.ResultsChronological review of image registration methods in radiotherapy based on 34 selected articles. A particular attention was given to show: (i) potential regions of the application of different methods of registration, (ii) mathematical basis of the deformable methods and (iii) the methods of quality control for the registration process.ConclusionsThe primary aim of the medical image registration process is to connect the contents of images. What we want to achieve is a complementary or extended knowledge that can be used for more precise localisation of pathogenic lesions and continuous improvement of patient treatment. Therefore, the choice of imaging mode is dependent on the type of clinical study. It is impossible to visualise all anatomical details or functional changes using a single modality machine. Therefore, fusion of various modality images is of great clinical relevance. A natural problem in analysing the fusion of medical images is geographical errors related to displacement. The registered images are performed not at the same time and, very often, at different respiratory phases.     

Semantic Similarity in Biomedical Ontologies

In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization.     

Fruit Flies in Biomedical Research

Many scientists complain that the current funding situation is dire. Indeed, there has been an overall decline in support in funding for research from the National Institutes of Health and the National Science Foundation. Within the Drosophila field, some of us question how long this funding crunch will last as it demotivates principal investigators and perhaps more importantly affects the long-term career choice of many young scientists. Yet numerous very interesting biological processes and avenues remain to be investigated in Drosophila, and probing questions can be answered fast and efficiently in flies to reveal new biological phenomena. Moreover, Drosophila is an excellent model organism for studies that have translational impact for genetic disease and for other medical implications such as vector-borne illnesses. We would like to promote a better collaboration between Drosophila geneticists/biologists and human geneticists/bioinformaticians/clinicians, as it would benefit both fields and significantly impact the research on human diseases.     

Long-Term Changes in Nutrients and Mussel Stocks Are Related to Numbers of Breeding Eiders Somateria mollissima at a Large Baltic Colony

Background

The Baltic/Wadden Sea eider Somateria mollissima flyway population is decreasing, and this trend is also reflected in the large eider colony at Christiansø situated in the Baltic Sea. This colony showed a 15-fold increase from 1925 until the mid-1990''s, followed by a rapid decline in recent years, although the causes of this trend remain unknown. Most birds from the colony winter in the Wadden Sea, from which environmental data and information on the size of the main diet, the mussel Mytilus edulis stock exists. We hypothesised that changes in nutrients and water temperature in the Wadden Sea had an effect on the ecosystem affecting the size of mussel stocks, the principal food item for eiders, thereby influencing the number of breeding eider in the Christiansø colony.

Methodology/Principal Finding

A positive relationship between the amount of fertilizer used by farmers and the concentration of phosphorus in the Wadden Sea (with a time lag of one year) allowed analysis of the predictions concerning effects of nutrients for the period 1925–2010. There was (1) increasing amounts of fertilizer used in agriculture and this increased the amount of nutrients in the marine environment thereby increasing the mussel stocks in the Wadden Sea. (2) The number of eiders at Christiansø increased when the amount of fertilizer increased. Finally (3) the number of eiders in the colony at Christiansø increased with the amount of mussel stocks in the Wadden Sea.

Conclusions/Significance

The trend in the number of eiders at Christiansø is representative for the entire flyway population, and since nutrient reduction in the marine environment occurs in most parts of Northwest Europe, we hypothesize that this environmental candidate parameter is involved in the overall regulation of the Baltic/Wadden Sea eider population during recent decades.     

Exercise-Induced Changes in Visceral Adipose Tissue Mass Are Regulated by IL-6 Signaling: A Randomized Controlled Trial

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生物医学光子学的无损伤影象方法

二十一世纪将是信息和生命科学的时代 ,而生物光子学是此两大领域结合的一门新兴交叉学科 ,对推动生命科学的研究具有极其重要的意义。根据最近的研究动态 ,生物光子学领域最有希望的一个新生点就是利用光学和激光技术 ,发展生命科学研究的形态学方法 ,即 :生命过程动态信息的高灵敏度成像 ,包括从单功能分子、亚细胞、细胞到组织的多种光与生物分子作用信息的成像 ,从而实现生物学研究方法从集合到个体(单分子 ) ;从离体到活体 ;从静态到动态的变革。这些新的物理方法的引入不但能使生物学的研究手段发生革命性变革 ,同时也促进生物学基础…     

Misconduct Policies in High-Impact Biomedical Journals

Background

It is not clear which research misconduct policies are adopted by biomedical journals. This study assessed the prevalence and content policies of the most influential biomedical journals on misconduct and procedures for handling and responding to allegations of misconduct.

Methods

We conducted a cross-sectional study of misconduct policies of 399 high-impact biomedical journals in 27 biomedical categories of the Journal Citation Reports in December 2011. Journal websites were reviewed for information relevant to misconduct policies.

Results

Of 399 journals, 140 (35.1%) provided explicit definitions of misconduct. Falsification was explicitly mentioned by 113 (28.3%) journals, fabrication by 104 (26.1%), plagiarism by 224 (56.1%), duplication by 242 (60.7%) and image manipulation by 154 (38.6%). Procedures for responding to misconduct were described in 179 (44.9%) websites, including retraction, (30.8%) and expression of concern (16.3%). Plagiarism-checking services were used by 112 (28.1%) journals. The prevalences of all types of misconduct policies were higher in journals that endorsed any policy from editors’ associations, Office of Research Integrity or professional societies compared to those that did not state adherence to these policy-producing bodies. Elsevier and Wiley-Blackwell had the most journals included (22.6% and 14.8%, respectively), with Wiley journals having greater a prevalence of misconduct definition and policies on falsification, fabrication and expression of concern and Elsevier of plagiarism-checking services.

Conclusions

Only a third of top-ranking peer-reviewed journals had publicly-available definitions of misconduct and less than a half described procedures for handling allegations of misconduct. As endorsement of international policies from policy-producing bodies was positively associated with implementation of policies and procedures, journals and their publishers should standardize their policies globally in order to increase public trust in the integrity of the published record in biomedicine.