Jatin Shah

Scientific Writing of Novice Researchers: What Difficulties and Encouragements Do They Encounter?

Purpose Writing scientific articles is a daunting task for novice researchers. In this qualitative study carried out in 2007, the authors evaluated the experiences of a group of novice researchers engaged in the writing process, to elucidate the main difficulties and sources of encouragement they encountered. Method Sixteen novice researchers were interviewed. Most were women (10), and most were enrolled in programs of medicine (9), followed by nursing (4) and physical therapy (3). These were drawn via convenience sampling from a randomized control trial in which 48 of them were equally assigned to either an online or a face-to-face course of instruction. On completion, interviews were conducted in focus groups of four students each. The interviews were transcribed and read independently by two of the authors, who then encoded the material based on the principles of grounded theory. Initial categories were converted to major emerging themes, which were validated when participants were asked to review the findings. Triangulation of results was carried out by discussing the emerging themes in an online forum with five specialists in college writing education. Results Classifying the diverse responses of participants led to the emergence of four major themes: cognitive burden, group support and mentoring, difficulty in distinguishing between content and structure, and backward design of manuscripts. Conclusions The themes produced by this study provide some insight into the challenges faced by novice researchers in their early attempts at scientific writing. Remedies that address these challenges are needed to substantially improve scientific writing instruction.

Electronic Data Capture for Registries and Clinical Trials in Orthopaedic Surgery Open Source versus Commercial Systems

BackgroundCollection and analysis of clinical data can help orthopaedic surgeons to practice evidence based medicine. Spreadsheets and offline relational databases are prevalent, but not flexible, secure, workflow friendly and do not support the generation of standardized and interoperable data. Additionally these data collection applications usually do not follow a structured and planned approach which may result in failure to achieve the intended goal.Questions/purposesOur purposes are (1) to provide a brief overview of EDC systems, their types, and related pros and cons as well as to describe commonly used EDC platforms and their features; and (2) describe simple steps involved in designing a registry/clinical study in DADOS P, an open source EDC system.Where are we now?Electronic data capture systems aimed at addressing these issues are widely being adopted at an institutional/national/international level but are lacking at an individual level. A wide array of features, relative pros and cons and different business models cause confusion and indecision among orthopaedic surgeons interested in implementing EDC systems.Where do we need to go?To answer clinical questions and actively participate in clinical studies, orthopaedic surgeons should collect data in parallel to their clinical activities. Adopting a simple, user-friendly, and robust EDC system can facilitate the data collection process.How do we get there?Conducting a balanced evaluation of available options and comparing them with intended goals and requirements can help orthopaedic surgeons to make an informed choice.

What Leads Indians to Participate in Clinical Trials? A Meta-Analysis of Qualitative Studies

Background With the globalization of clinical trials, large developing nations have substantially increased their participation in multi-site studies. This participation has raised ethical concerns, among them the fear that local customs, habits and culture are not respected while asking potential participants to take part in study. This knowledge gap is particularly noticeable among Indian subjects, since despite the large number of participants, little is known regarding what factors affect their willingness to participate in clinical trials. Methods We conducted a meta-analysis of all studies evaluating the factors and barriers, from the perspective of potential Indian participants, contributing to their participation in clinical trials. We searched both international as well as Indian-specific bibliographic databases, including Pubmed, Cochrane, Openjgate, MedInd, Scirus and Medknow, also performing hand searches and communicating with authors to obtain additional references. We enrolled studies dealing exclusively with the participation of Indians in clinical trials. Data extraction was conducted by three researchers, with disagreement being resolved by consensus. Results Six qualitative studies and one survey were found evaluating the main themes affecting the participation of Indian subjects. Themes included Personal health benefits, Altruism, Trust in physicians, Source of extra income, Detailed knowledge, Methods for motivating participants as factors favoring, while Mistrust on trial organizations, Concerns about efficacy and safety of trials, Psychological reasons, Trial burden, Loss of confidentiality, Dependency issues, Language as the barriers. Conclusion We identified factors that facilitated and barriers that have negative implications on trial participation decisions in Indian subjects. Due consideration and weightage should be assigned to these factors while planning future trials in India.

Application description and policy model in collaborative environment for sharing of information on epidemiological and clinical research data sets.

Background Sharing of epidemiological and clinical data sets among researchers is poor at best, in detriment of science and community at large. The purpose of this paper is therefore to (1) describe a novel Web application designed to share information on study data sets focusing on epidemiological clinical research in a collaborative environment and (2) create a policy model placing this collaborative environment into the current scientific social context. Methodology The Database of Databases application was developed based on feedback from epidemiologists and clinical researchers requiring a Web-based platform that would allow for sharing of information about epidemiological and clinical study data sets in a collaborative environment. This platform should ensure that researchers can modify the information. A Model-based predictions of number of publications and funding resulting from combinations of different policy implementation strategies (for metadata and data sharing) were generated using System Dynamics modeling. Principal Findings The application allows researchers to easily upload information about clinical study data sets, which is searchable and modifiable by other users in a wiki environment. All modifications are filtered by the database principal investigator in order to maintain quality control. The application has been extensively tested and currently contains 130 clinical study data sets from the United States, Australia, China and Singapore. Model results indicated that any policy implementation would be better than the current strategy, that metadata sharing is better than data-sharing, and that combined policies achieve the best results in terms of publications. Conclusions Based on our empirical observations and resulting model, the social network environment surrounding the application can assist epidemiologists and clinical researchers contribute and search for metadata in a collaborative environment, thus potentially facilitating collaboration efforts among research communities distributed around the globe.

Patterns of herbal combination for the treatment of insomnia commonly employed by highly experienced Chinese medicine physicians

ObjectiveTo explore the most effective herbal combinations commonly used by highly experienced Chinese medicine (CM) physicians for the treatment of insomnia.MethodsWe collected and analyzed data related to insomnia treatment from the clinics of 7 highly experienced CM physicians in Beijing. The sample included 162 patients and 460 consultations in total. Patient outcomes, such as sleep quality and sleep time per day, were manually collected from the medical records by trained CM clinicians. Three data mining methods, support vector machine (SVM), logistic regression and decision tree, and multifactor dimensionality reduction (MDR), were used to determine and confirm the herbal combinations that resulted in positive outcomes in patients suffering from insomnia.ResultsResults show that MDR is the most efficient method to predict the effective herbal combinations. Using the MDR model, we identified several combinations of herbs with 100% positive outcomes, such as stir-fried spine date seed, Szechwan lovage rhizome, and prepared thinleaf milkwort root; white peony root, golden thread, and stir-fried spine date seed; and Asiatic cornelian cherry fruit with fresh rehmannia.ConclusionsResults indicate that herbal combinations are effective treatments for patients with insomnia compared with individual herbs. It is also shown that MDR is a potent data mining method to identify the herbal combination with high rates of positive outcome.

So Different, yet So Similar: Meta-Analysis and Policy Modeling of Willingness to Participate in Clinical Trials among Brazilians and Indians

Background With the global expansion of clinical trials and the expectations of the rise of the emerging economies known as BRICs (Brazil, Russia, India and China), the understanding of factors that affect the willingness to participate in clinical trials of patients from those countries assumes a central role in the future of health research. Methods We conducted a systematic review and meta-analysis (SRMA) of willingness to participate in clinical trials among Brazilian patients and then we compared it with Indian patients (with results of another SRMA previously conducted by our group) through a system dynamics model. Results Five studies were included in the SRMA of Brazilian patients. Our main findings are 1) the major motivation for Brazilian patients to participate in clinical trials is altruism, 2) monetary reimbursement is the least important factor motivating Brazilian patients, 3) the major barrier for Brazilian patients to not participate in clinical trials is the fear of side effects, and 4) Brazilian patients are more likely willing to participate in clinical trials than Indians. Conclusion Our study provides important insights for investigators and sponsors for planning trials in Brazil (and India) in the future. Ignoring these results may lead to unnecessary fund/time spending. More studies are needed to validate our results and for better understanding of this poorly studied theme.

Good to be Bad? Distinguishing between Positive and Negative Citations in Scientific Impact

The impact of a publication is often measured by the number of citations it received, this number being taken as a proxy for the relevance of published work. However, a higher citation index does not necessarily mean that a publication necessarily had a positive feedback from citing authors, as a citation can represent a negative criticism. In order to overcome this limitation, we used sentiment analysis to rate citations as positive, neutral or negative. Adjectives are initially extracted from the citations, with the SentiWordNet lexicon being used to rate the degree of positivity and negativity for each adjective. Relevance scores were then computed to rank citations according to the sentiment expressed in the text corresponding to each citation. As expected for accurate information retrieval systems, higher precision rates were observed in the initial points of the curve. The SRC (0.6728) computed using number of raw citations is lower than the SRC (0.7397) observed by the ranking generated using sentiment scores (Table 3). Conclusion: This result indicates that child articles with higher values of relevance score were in general the ones expressing positive opinion about their parents. Therefore, the ranking generated by sentiment scores had an improved accuracy.

Workflow in Clinical Trial Sites & Its Association with Near Miss Events for Data Quality: Ethnographic, Workflow & Systems Simulation

Background With the exponential expansion of clinical trials conducted in (Brazil, Russia, India, and China) and VISTA (Vietnam, Indonesia, South Africa, Turkey, and Argentina) countries, corresponding gains in cost and enrolment efficiency quickly outpace the consonant metrics in traditional countries in North America and European Union. However, questions still remain regarding the quality of data being collected in these countries. We used ethnographic, mapping and computer simulation studies to identify/address areas of threat to near miss events for data quality in two cancer trial sites in Brazil. Methodology/Principal Findings Two sites in Sao Paolo and Rio Janeiro were evaluated using ethnographic observations of workflow during subject enrolment and data collection. Emerging themes related to threats to near miss events for data quality were derived from observations. They were then transformed into workflows using UML-AD and modeled using System Dynamics. 139 tasks were observed and mapped through the ethnographic study. The UML-AD detected four major activities in the workflow evaluation of potential research subjects prior to signature of informed consent, visit to obtain subject́s informed consent, regular data collection sessions following study protocol and closure of study protocol for a given project. Field observations pointed to three major emerging themes: (a) lack of standardized process for data registration at source document, (b) multiplicity of data repositories and (c) scarcity of decision support systems at the point of research intervention. Simulation with policy model demonstrates a reduction of the rework problem. Conclusions/Significance Patterns of threats to data quality at the two sites were similar to the threats reported in the literature for American sites. The clinical trial site managers need to reorganize staff workflow by using information technology more efficiently, establish new standard procedures and manage professionals to reduce near miss events and save time/cost. Clinical trial sponsors should improve relevant support systems.

Center of excellence in research reporting in neurosurgery--diagnostic ontology.

Motivation: Evidence-based medicine (EBM), in the field of neurosurgery, relies on diagnostic studies since Randomized Controlled Trials (RCTs) are uncommon. However, diagnostic study reporting is less standardized which increases the difficulty in reliably aggregating results. Although there have been several initiatives to standardize reporting, they have shown to be sub-optimal. Additionally, there is no central repository for storing and retrieving related articles. Results: In our approach we formulate a computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct Systematic Reviews - Meta Analysis (SR-MA) for diagnostic studies, which will assist in standardized reporting of diagnostic articles. SR-MA are studies that aggregate several studies to come to one conclusion for a particular research question. We also report high percentage of agreement among five observers as a result of the interobserver agreement test that we conducted among them to annotate 13 articles using the diagnostic ontology. Moreover, we extend our existing repository CERR-N to include diagnostic studies. Availability: The ontology is available for download as an.owl file at: http://bioportal.bioontology.org/ontologies/3013.

Surgical treatment of sleep apnea: association between surgeon/hospital volume with outcomes.

To identify the association between surgeon/hospital volume with outcomes in surgical treatment for obstructive sleep apnea (OSA) in a nationally representative sample. We hypothesized that surgeons/hospitals with lower patient volumes would have: higher mortality rates, longer hospital length of stay (LOS), and higher postoperative complication rates and hospitalization charges.