Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

Construction of ethics in clinical research - Clinical trials registration

Scientific development that has been achieved through decades finds in clinical research a great possibility of translating findings to human health application. Evidence given by clinical trials allows everyone to have access to the best health services. However, the millionaire world of pharmaceutical industries has stained clinical research with doubt and improbability. Study results (fruits of controlled clinical trials) and scientific publications (selective, manipulated and with wrong conclusions) led to an inappropriate clinical practice, favoring the involved economic aspect. In 2005, the International Committee of Medical Journal Editors (ICMJE), supported by the World Association of Medical Editors, started demanding as a requisite for publication that all clinical trials be registered at the database ClinicalTrials.gov. In 2006, the World Health Organization (WHO) created the International Clinical Trial Registry Platform (ICTRP), which gathers several registry centers from all over the world, and required that all researchers and pharmaceutical industries register clinical trials. Such obligatory registration has progressed and will extend to all scientific journals indexed in all worldwide databases. Registration of clinical trials means another step of clinical research towards transparency, ethics and impartiality, resulting in real evidence to the forthcoming changes in clinical practice as well as in the health situation.

Telomere length and its relationship with chronic diseases - New perspectives for periodontal research

Objective: The ageing process is accompanied by a variety of cellular modifications, and telomere shortening is a common finding. Large epidemiological studies have reported an association between shorter telomere length in peripheral leukocytes and several inflammatory diseases of the elderly including diabetes, atherosclerosis and, recently, periodontitis. The primary aim of this study was to critically discuss available evidence regarding the potential mechanisms relating shorter telomeres to periodontitis. Design: A narrative literature review was performed to report evidence relating shorter telomeres to the ageing process and inflammation. Then, we searched MEDLINE (1950 to May 2012) and ISI WEB OF SCIENCE (1950 to May 2012) databases for the combination of the terms 'telomere' and 'periodontitis'. Results: Although these associations suggest a possible role of telomere attrition in the onset or evolution of chronic inflammatory diseases, only two studies addressed the relationship between telomere length and periodontitis. Conclusion: We suggest that the chronic inflammatory burden observed in people with chronic periodontitis could represent the driver of telomere shortening. However, further evidence is needed to confirm whether inflammation is the cause or the consequence of the shorter leukocyte telomere length observed in people with periodontitis. © 2012 Elsevier Ltd. All rights reserved.

Qualitative methodogy: revealing a new path for research in dentistry

Currently, it is easy to find health professionals who not only attach importance to qualitative methods, but also recognize their help to better understand their patients' lives. However, its use in dentistry is still incipient, either due to ignorance or because of technical / operational difficulties in identifying possibilities for their use in research. Thus, the purpose of this study was to review the literature on the characteristics and peculiarities of the qualitative methodology, demonstrating their techniques of collecting, recording and analyzing data. For this, we performed a descriptive literature, from a survey in the "LILACS", "BBO" and "PUBMED" databases, by keywords related to the theme, selecting only the papers that mentioned the "importance" of qualitative research, the "characteristics and fundamentals," and the "techniques of collecting, recording and data analysis" involving this methodology. It was found that all studies have highlighted the importance of qualitative research to the construction of new knowledge that cannot be achieved by quantitative data. We found many different techniques to gather, record and analyze qualitative data applied to the dentistry field. It was concluded that qualitative research represents a new path to be followed by dentistry, so that we are able to plan actions in ethical and humane public health dentistry, bringing better results to the population, because of the depth of knowledge that your date can.

Clinical trial design in non-invasive brain stimulation psychiatric research

Major depressive disorder (MDD) trials - investigating either non-pharmacological or pharmacological interventions - have shown mixed results. Many reasons explain this heterogeneity, but one that stands out is the trial design due to specific challenges in the field. We aimed therefore to review the methodology of non-invasive brain stimulation (NIBS) trials and provide a framework to improve clinical trial design. We performed a systematic review for randomized, controlled MDD trials whose intervention was transcranial magnetic stimulation (rTMS) or transcranial direct current stimulation (tDCS) in MEDLINE and other databases from April 2002 to April 2008. We created an unstructured checklist based on CONSORT guidelines to extract items such as power analysis, sham method, blinding assessment, allocation concealment, operational criteria used for MDD, definition of refractory depression and primary study hypotheses. Thirty-one studies were included. We found that the main methodological issues can be divided in to three groups: (1) issues related to phase II/small trials, (2) issues related to MDD trials and, (3) specific issues of NIBS studies. Taken together, they can threaten study validity and lead to inconclusive results. Feasible solutions include: estimating the sample size a priori; measuring the degree of refractoriness of the subjects; specifying the primary hypothesis and statistical tests; controlling predictor variables through stratification randomization methods or using strict eligibility criteria; adjusting the study design to the target population; using adaptive designs and exploring NIBS efficacy employing biological markers. In conclusion, our study summarizes the main methodological issues of NIBS trials and proposes a number of alternatives to manage them. Copyright (C) 2011 John Wiley & Sons, Ltd.

QuMinS: fast and scalable querying, mining and summarizing multi-modal databases

Given a large image set, in which very few images have labels, how to guess labels for the remaining majority? How to spot images that need brand new labels different from the predefined ones? How to summarize these data to route the user’s attention to what really matters? Here we answer all these questions. Specifically, we propose QuMinS, a fast, scalable solution to two problems: (i) Low-labor labeling (LLL) – given an image set, very few images have labels, find the most appropriate labels for the rest; and (ii) Mining and attention routing – in the same setting, find clusters, the top-'N IND.O' outlier images, and the 'N IND.R' images that best represent the data. Experiments on satellite images spanning up to 2.25 GB show that, contrasting to the state-of-the-art labeling techniques, QuMinS scales linearly on the data size, being up to 40 times faster than top competitors (GCap), still achieving better or equal accuracy, it spots images that potentially require unpredicted labels, and it works even with tiny initial label sets, i.e., nearly five examples. We also report a case study of our method’s practical usage to show that QuMinS is a viable tool for automatic coffee crop detection from remote sensing images.

A REPRODUCIBLE RESEARCH TOOLKIT FOR R

We present a collection of R packages for conducting and distributing reproducible research using R, Sweave, and LaTeX. The collection consists of the cacheSweave, stashR, and SRPM packages which allow for the caching of computations in Sweave documents and the distribution of those cached computations via remotely accessible key-value databases. We describe the caching mechanism used by the cacheSweave package and tools that we have developed for authors and readers for the purposes of creating and interacting with reproducible documents.

Clinical research projects at a German medical faculty: follow-up from ethical approval to publication and citation by others

BACKGROUND: Only data of published study results are available to the scientific community for further use such as informing future research and synthesis of available evidence. If study results are reported selectively, reporting bias and distortion of summarised estimates of effect or harm of treatments can occur. The publication and citation of results of clinical research conducted in Germany was studied. METHODS: The protocols of clinical research projects submitted to the research ethics committee of the University of Freiburg (Germany) in 2000 were analysed. Published full articles in several databases were searched and investigators contacted. Data on study and publication characteristics were extracted from protocols and corresponding publications. RESULTS: 299 study protocols were included. The most frequent study design was randomised controlled trial (141; 47%), followed by uncontrolled studies (61; 20%), laboratory studies (30; 10%) and non-randomised studies (29; 10%). 182 (61%) were multicentre studies including 97 (53%) international collaborations. 152 of 299 (51%) had commercial (co-)funding and 46 (15%) non-commercial funding. 109 of the 225 completed protocols corresponded to at least one full publication (total 210 articles); the publication rate was 48%. 168 of 210 identified publications (80%) were cited in articles indexed in the ISI Web of Science. The median was 11 citations per publication (range 0-1151). CONCLUSIONS: Results of German clinical research projects conducted are largely underreported. Barriers to successful publication need to be identified and appropriate measures taken. Close monitoring of projects until publication and adequate support provided to investigators may help remedy the prevailing underreporting of research.

From Classical Terrorism to “Global” Terrorism

This article examines the history and the development of terrorism as a research subject for social sciences. It gives an impression of how the subject’s theoretical remit has changed over the last decades—explicitly taking into account the characteristics of a modern and global world and their impact on current understandings of terrorism.

Post-9/11 Terrorism Threats, News Coverage, and Public Perceptions in the United States

Terrorists, policy-makers, and terrorism scholars have long assumed that the mere threat of terrorist strikes affects societies that have experienced actual acts of terrorism. For this reason, most definitions of terrorism include the threat of violent political acts against civilians. But so far research has neither validated this conventional wisdom nor demonstrated how actual and mass-mediated threat messages by terrorists and terror alerts and threat assessments by government officials affect the public in targeted states. This paper fills the gap providing evidence that who conveys such messages matters and that mass-mediated threat messages by al Qaeda leaders and announced alerts and threat assessments by U.S. administration officials had a significant impact on the American public’s threat perceptions in the post-9/11 years.

A survey of paediatric HIV programmatic and clinical management practices in Asia and sub-Saharan Africa--the International epidemiologic Databases to Evaluate AIDS (IeDEA)

INTRODUCTION There are limited data on paediatric HIV care and treatment programmes in low-resource settings. METHODS A standardized survey was completed by International epidemiologic Databases to Evaluate AIDS paediatric cohort sites in the regions of Asia-Pacific (AP), Central Africa (CA), East Africa (EA), Southern Africa (SA) and West Africa (WA) to understand operational resource availability and paediatric management practices. Data were collected through January 2010 using a secure, web-based software program (REDCap). RESULTS A total of 64,552 children were under care at 63 clinics (AP, N=10; CA, N=4; EA, N=29; SA, N=10; WA, N=10). Most were in urban settings (N=41, 65%) and received funding from governments (N=51, 81%), PEPFAR (N=34, 54%), and/or the Global Fund (N=15, 24%). The majority were combined adult-paediatric clinics (N=36, 57%). Prevention of mother-to-child transmission was integrated at 35 (56%) sites; 89% (N=56) had access to DNA PCR for infant diagnosis. African (N=40/53) but not Asian sites recommended exclusive breastfeeding up until 4-6 months. Regular laboratory monitoring included CD4 (N=60, 95%), and viral load (N=24, 38%). Although 42 (67%) sites had the ability to conduct acid-fast bacilli (AFB) smears, 23 (37%) sites could conduct AFB cultures and 18 (29%) sites could conduct tuberculosis drug susceptibility testing. Loss to follow-up was defined as >3 months of lost contact for 25 (40%) sites, >6 months for 27 sites (43%) and >12 months for 6 sites (10%). Telephone calls (N=52, 83%) and outreach worker home visits to trace children lost to follow-up (N=45, 71%) were common. CONCLUSIONS In general, there was a high level of patient and laboratory monitoring within this multiregional paediatric cohort consortium that will facilitate detailed observational research studies. Practices will continue to be monitored as the WHO/UNAIDS Treatment 2.0 framework is implemented.

A PROCESS FOR ACHIEVING COMPARABLE DATA FROM HETEROGENEOUS DATABASES

The current state of health and biomedicine includes an enormity of heterogeneous data ‘silos’, collected for different purposes and represented differently, that are presently impossible to share or analyze in toto. The greatest challenge for large-scale and meaningful analyses of health-related data is to achieve a uniform data representation for data extracted from heterogeneous source representations. Based upon an analysis and categorization of heterogeneities, a process for achieving comparable data content by using a uniform terminological representation is developed. This process addresses the types of representational heterogeneities that commonly arise in healthcare data integration problems. Specifically, this process uses a reference terminology, and associated "maps" to transform heterogeneous data to a standard representation for comparability and secondary use. The capture of quality and precision of the “maps” between local terms and reference terminology concepts enhances the meaning of the aggregated data, empowering end users with better-informed queries for subsequent analyses. A data integration case study in the domain of pediatric asthma illustrates the development and use of a reference terminology for creating comparable data from heterogeneous source representations. The contribution of this research is a generalized process for the integration of data from heterogeneous source representations, and this process can be applied and extended to other problems where heterogeneous data needs to be merged.

The 100 Most Influential Publications in Cervical Spine Research

STUDY DESIGN Bibliometric study of current literature. OBJECTIVE To identify and analyze the 100 most cited publications in cervical spine research. SUMMARY OF BACKGROUND DATA The cervical spine is a dynamic field of research with many advances made within the last century. However, the literature has never been comprehensively analyzed to identify and compare the most influential articles as measured by the number of citations. METHODS All databases of the Thomson Reuters Web of Knowledge were utilized in a two-step approach. First, the 150 most cited cervical spine studies up to and including 2014 were identified using four keywords. Second, all keywords related to the cervical spine found in the 150 studies (n = 38) were used to conduct a second search of the database. The top 100 most cited articles were hereby selected for further analysis of current and past citations, authorship, geographic origin, article type, and level of evidence. RESULTS Total citations for the 100 studies identified ranged from 173 to 879. They were published in the time frame 1952 to 2008 in a total of 30 different journals. Most studies (n = 42) were published in the decade 1991 - 2000. Level of evidence ranged from 1 to 5 with 39 studies in the level 4 category. 13 researchers were first author more than once and 9 researchers senior author more than once. The two step approach with a secondary widening of search terms yielded an additional 27 studies, including the first ranking article. CONCLUSIONS This bibliometric study is likely to include some of the most important milestones in the field of cervical spine research of the last 100 years. LEVEL OF EVIDENCE 3.

A project to improve the information seeking skills and increase the use of evidence-based research in public health practice

The ability of public health practitioners (PHPs) to work efficiently and effectively is negatively impacted by their lack of knowledge of the broad range of evidence-based practice information resources and tools that can be utilized to guide them in their development of health policies and programs. This project, a three-hour continuing education hands-on workshop with supporting resources, was designed to increase knowledge and skills of these resources. The workshop was presented as a pre-conference continuing education program for the Texas Public Health Association (TPHA) 2008 Annual Conference. Topics included: identification of evidence-based practice resources to aid in the development of policies and programs; identification of sources of publicly available data; utilization of data for community assessments; and accessing and searching the literature through a collection of databases available to all citizens of Texas. Supplemental resources included a blog that served as a gateway to the resources explored during the presentation, a community assessment workbook that incorporates both Healthy People 2010 objectives and links to reliable sources of data, and handouts providing additional instruction on the use of the resources covered during the workshop.^ Before- and after-workshop surveys based on Kirkpatrick's 4-level model of evaluation and the Theory of Planned Behavior were administered. Of the questions related to the trainer, the workshop, and the usefulness of the workshop, participants gave "Good" to "Excellent" responses to all one question. Confidence levels overall increased a statistically significant amount; measurements of attitude, social norms, and control showed no significant differences before and after the workshop. Lastly, participants indicated they were likely to use resources shown during the workshop within a one to three month time period on average. ^ The workshop and creation of supplemental resources served as a pilot for a funded project that will be continued with the development and delivery of four 4-week long webinar-based training sessions to be completed by December 2008. ^

A systematic review of the methods used to assess race and racial disparities in uterine fibroid research

Context: Black women are reported to have a higher prevalence of uterine fibroids, and a threefold higher incidence rate and relative risk for clinical uterine fibroid development as compared to women of other races. Uterine fibroid research has reported that black women experience greater uterine fibroid morbidity and disproportionate uterine fibroid disease burden. With increased interest in understanding uterine fibroid development, and race being a critical component of uterine fibroid assessment, it is imperative that the methods used to determine the race of research participants is defined and the operational definition of the use of race as a variable is reported for methodological guidance, and to enable the research community to compare statistical data and replicate studies. ^ Objectives: To systematically review and evaluate the methods used to assess race and racial disparities in uterine fibroid research. ^ Data Sources: Databases searched for this review include: OVID Medline, NML PubMed, Ebscohost Cumulative Index to Nursing and Allied Health Plus with Full Text, and Elsevier Scopus. ^ Review Methods: Articles published in English were retrieved from data sources between January 2011 and March 2011. Broad search terms, uterine fibroids and race, were employed to retrieve a comprehensive list of citations for review screening. The initial database yield included 947 articles, after duplicate extraction 485 articles remained. In addition, 771 bibliographic citations were reviewed to identify additional articles not found through the primary database search, of which 17 new articles were included. In the first screening, 502 titles and abstracts were screened against eligibility questions to determine citations of exclusion and to retrieve full text articles for review. In the second screening, 197 full texted articles were screened against eligibility questions to determine whether or not they met full inclusion/exclusion criteria. ^ Results: 100 articles met inclusion criteria and were used in the results of this systematic review. The evidence suggested that black women have a higher prevalence of uterine fibroids when compared to white women. None of the 14 studies reporting data on prevalence reported an operational definition or conceptual framework for the use of race. There were a limited number of studies reporting on the prevalence of risk factors among racial subgroups. Of the 3 studies, 2 studies reported prevalence of risk factors lower for black women than other races, which was contrary to hypothesis. And, of the three studies reporting on prevalence of risk factors among racial subgroups, none of them reported a conceptual framework for the use of race. ^ Conclusion: In the 100 uterine fibroid studies included in this review over half, 66%, reported a specific objective to assess and recruit study participants based upon their race and/or ethnicity, but most, 51%, failed to report a method of determining the actual race of the participants, and far fewer, 4% (only four South American studies), reported a conceptual framework and/or operational definition of race as a variable. However, most, 95%, of all studies reported race-based health outcomes. The inadequate methodological guidance on the use of race in uterine fibroid studies, purporting to assess race and racial disparities, may be a primary reason that uterine fibroid research continues to report racial disparities, but fails to understand the high prevalence and increased exposures among African-American women. A standardized method of assessing race throughout uterine fibroid research would appear to be helpful in elucidating what race is actually measuring, and the risk of exposures for that measurement. ^