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PubMed2005

A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

Interest in the assignment and frequency analysis of haplotypes in samples of unrelated individuals has increased immeasurably as a result of the emphasis placed on haplotype analyses by, for example, the International HapMap Project and related initiatives. Although there are many available computer programs for haplotype analysis applicable to samples of unrelated individuals, many of these programs have limitations and/or very specific uses. In this paper, the key features of available haplotype analysis software for use with unrelated individuals, as well as pooled DNA samples from unrelated individuals, are summarised. Programs for haplotype analysis were identified through keyword searches on PUBMED and various internet search engines, a review of citations from retrieved papers and personal communications, up to June 2004. Priority was given to functioning computer programs, rather than theoretical models and methods. The available software was considered in light of a number of factors: the algorithm(s) used, algorithm accuracy, assumptions, the accommodation of genotyping error, implementation of hypothesis testing, handling of missing data, software characteristics and web-based implementations. Review papers comparing specific methods and programs are also summarised. Forty-six haplotyping programs were identified and reviewed. The programs were divided into two groups: those designed for individual genotype data (a total of 43 programs) and those designed for use with pooled DNA samples (a total of three programs). The accuracy of programs using various criteria are assessed and the programs are categorised and discussed in light of: algorithm and method, accuracy, assumptions, genotyping error, hypothesis testing, missing data, software characteristics and web implementation. Many available programs have limitations (eg some cannot accommodate missing data) and/or are designed with specific tasks in mind (eg estimating haplotype frequencies rather than assigning most likely haplotypes to individuals). It is concluded that the selection of an appropriate haplotyping program for analysis purposes should be guided by what is known about the accuracy of estimation, as well as by the limitations and assumptions built into a program.

Algorithms↗

PubMed2005

Relevance similarity: an alternative means to monitor information retrieval systems.

BACKGROUND: Relevance assessment is a major problem in the evaluation of information retrieval systems. The work presented here introduces a new parameter, "Relevance Similarity", for the measurement of the variation of relevance assessment. In a situation where individual assessment can be compared with a gold standard, this parameter is used to study the effect of such variation on the performance of a medical information retrieval system. In such a setting, Relevance Similarity is the ratio of assessors who rank a given document same as the gold standard over the total number of assessors in the group. METHODS: The study was carried out on a collection of Critically Appraised Topics (CATs). Twelve volunteers were divided into two groups of people according to their domain knowledge. They assessed the relevance of retrieved topics obtained by querying a meta-search engine with ten keywords related to medical science. Their assessments were compared to the gold standard assessment, and Relevance Similarities were calculated as the ratio of positive concordance with the gold standard for each topic. RESULTS: The similarity comparison among groups showed that a higher degree of agreements exists among evaluators with more subject knowledge. The performance of the retrieval system was not significantly different as a result of the variations in relevance assessment in this particular query set. CONCLUSION: In assessment situations where evaluators can be compared to a gold standard, Relevance Similarity provides an alternative evaluation technique to the commonly used kappa scores, which may give paradoxically low scores in highly biased situations such as document repositories containing large quantities of relevant data.

Journal Article↗

PubMed2006

Technology mediator: a new role for the reference librarian?

The Arizona Health Sciences Library has collaborated with clinical faculty to develop a federated search engine that is useful for meeting real-time clinical information needs. This article proposes a technology mediation role for the reference librarian that was inspired by the project, and describes the collaborative model used for developing technology-mediated services for targeted users.

Journal Article↗

PubMed2005

Is obesity a risk factor for low back pain? An example of using the evidence to answer a clinical question.

BACKGROUND: Obesity as a causal factor for low back pain has been controversial with no definitive answer to this date. The objective of this study was to determine whether obesity is associated with low back pain. In addition this paper aims to provide a step-by-step guide for chiropractors and osteopaths on how to ask and answer a clinical question using the literature. METHODS: A literature review using the MEDLINE search engine using the keywords "obesity", "low back pain", "body mass index" "BMI" and "osteoarthritis" from years 1990 to 2004 was utilised. The method employed is similar to that utilised by evidence-based practice advocates. RESULTS: The available data at this time is controversial with no clear-cut evidence connecting low back pain with obesity. CONCLUSION: There is a lack of a clear dose-response relationship between body mass index (BMI) and low back pain. Further, studies on the relationship between obesity and related lumbar osteoarthritis, knee pain, and disc herniation are also problematic.There is little doubt that future studies with controlled variables are needed to determine the existence of an unambiguous link, if any.

Journal Article↗

PubMed2006

Enhancing access to the Bibliome: the TREC 2004 Genomics Track.

BACKGROUND: The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their systems. The 2004 track included an ad hoc retrieval task, simulating use of a search engine to obtain documents about biomedical topics. This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed. RESULTS: A total of 27 research groups submitted 47 different runs. The most effective runs, as measured by the primary evaluation measure of mean average precision (MAP), used a combination of domain-specific and general techniques. The best MAP obtained by any run was 0.4075. Techniques that expanded queries with gene name lists as well as words from related articles had the best efficacy. However, many runs performed more poorly than a simple baseline run, indicating that careful selection of system features is essential. CONCLUSION: Various approaches to ad hoc retrieval provide a diversity of efficacy. The TREC Genomics Track and its test collection resources provide tools that allow improvement in information retrieval systems.

Journal Article↗

PubMed2025

Influence of genetic factors of humans, mosquitoes and parasites, on the evolution of Plasmodium falciparum infections, malaria transmission and genetic control methods: a review of the literature.

Despite significant progress, malaria remains a public health problem in many regions, particularly in sub-Saharan Africa. This situation is partly explained by the mosquito's resistance to insecticides and the emergence of parasite resistance to antimalarial drugs. Indeed, in spite of the various vectors' controls, insecticide resistance emerges from multi-generational selection and poses worldwide concern. In parallel, artemisinin resistance unfortunately emerged independently in multiple countries in eastern Africa. Since 2014, artemisinin resistance has been observed in 6 countries in Africa and, more concerningly, the evidence from longitudinal molecular surveys in these countries suggests that it is spreading. While phenotypic evidence of treatment failure is still limited, the increasing reports of validated artemisinin resistance mutations are alarming. Unlike the emergence of artemisinin resistance in South-East Asia, our understanding of the genetic determinants of artemisinin resistance and our ability to sequence and map the spread of resistance are significantly greater. In addition to mosquito and parasite genetics affecting malaria evolution, many human individual variants have been identified that are associated with malaria protection, but the most important of all relates to the structure or function of red blood cells, the classical polymorphisms that causes sickle cell trait, α-thalassaemia, G6PD deficiency, and the major red cell blood group variants. In that biological complex context, there is a need to characterize the various genetic factors in Plasmodium falciparum, humans and mosquitoes that are potentially associated with resistance to antimalarial drugs and insecticides, and their involvement in the evolution, severity and transmission of malaria. In this direction, A comprehensive literature review was conducted to capture the objectives highlighted above. The advances in genomic surveillance and emerging genetic control strategies, such as gene drive technology were also considered in this review. We used search engines such as PubMed and Google scholar to retrieve articles useful to the objective of this paper and information on the knowledge of genetic factors and methods that contributed to malaria control were synthesized.

Humans↗

PubMed2006

Botulinum toxin for treating spasmodic dysphonia (laryngeal dystonia): a systematic Cochrane review.

BACKGROUND: Spasmodic dysphonia is a neurological voice disorder characterized by involuntary adductor (towards midline) or abductor (away from midline) vocal fold spasms during phonation which result in phonatory breaks. Botulinum toxin is currently the gold standard of treatment. OBJECTIVE: To determine the efficacy of botulinum toxin therapy for the treatment of spasmodic dysphonia. DESIGN: Systematic Cochrane review. SEARCH STRATEGY: The search strategy for this review complied with Cochrane standards. We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE (1966 to February 2005), EMBASE (1974 to February 2005), CINAHL (through February 2005), Dissertation Abstracts International (1975 to February 2005) and PsycINFO (1975 to February 2005). The search engine FirstSearch was also used (February 2005). Reference lists for all the obtained studies and other review articles were examined for additional studies. SELECTION CRITERIA: All randomized control trials where the participants were randomly allocated prior to intervention and in which botulinum toxin was compared to an alternative treatment, placebo or non-treated control group were included. DATA COLLECTION AND ANALYSIS: Two reviewers independently evaluated all potential studies meeting the selection criteria noted above for inclusion. MAIN RESULTS: Only one study in the literature met the inclusion criteria. This was the only study identified which reported a treatment/no treatment comparison. It reported significant beneficial effects for fundamental frequency (Fo), Fo range, spectrographic analysis, independent ratings of voice severity and patient ratings of voice improvement. REVIEWER'S CONCLUSIONS: The evidence from randomized controlled trials supporting the effectiveness of botulinum toxin for management of spasmodic dysphonia is deficient. The lack of supporting evidence from randomized controlled trials results in an inability to draw unbiased generalized conclusions regarding the effectiveness of botulinum toxin for all types of spasmodic dysphonia.

Adult↗

PubMed2004

A frequency-based technique to improve the spelling suggestion rank in medical queries.

OBJECTIVE: There is an abundance of health-related information online, and millions of consumers search for such information. Spell checking is of crucial importance in returning pertinent results, so the authors propose a technique for increasing the effectiveness of spell-checking tools used for health-related information retrieval. DESIGN: A sample of incorrectly spelled medical terms was submitted to two different spell-checking tools, and the resulting suggestions, derived under two different dictionary configurations, were re-sorted according to how frequently each term appeared in log data from a medical search engine. MEASUREMENTS: Univariable analysis was carried out to assess the effect of each factor (spell-checking tool, dictionary type, re-sort, or no re-sort) on the probability of success. The factors that were statistically significant in the univariable analysis were then used in multivariable analysis to evaluate the independent effect of each of the factors. RESULTS: The re-sorted suggestions proved to be significantly more accurate than the original list returned by the spell-checking tool. The odds of finding the correct suggestion in the number one rank were increased by 63% after re-sorting using the authors' method. This effect was independent of both the dictionary and the spell-checking tools that were used. CONCLUSION: Using knowledge about the frequency of a given word's occurrence in the medical domain can significantly improve spelling correction for medical queries.

Analysis of Variance↗

PubMed2006

Prognostic value of nodal ratios in node-positive breast cancer.

PURPOSE: The American Joint Committee on Cancer staging system for breast cancer was recently updated to reflect the impact of increasing the absolute number of positive lymph nodes on prognosis. However, numerous studies suggest that nodal ratios (absolute number of involved nodes-number of nodes resected) may have greater prognostic value than absolute numbers of involved nodes. Here we examine the data supporting the use of nodal ratios in breast cancer prognosis and consider the potential advantages and disadvantages of including nodal ratios in breast cancer staging. METHODS: A systematic review of the literature was conducted using the following search engines: http://www.google.com; Thomson's ISI Web of Science; PubMed. RESULTS: In multiple reports from both prospective and retrospectively collected data sets, nodal ratios have been shown to be significant predictors of outcome, including locoregional recurrence and overall survival. These studies span all stages of breast cancer and include various treatments as well as various statistical approaches. CONCLUSION: There is considerable data supporting the use of nodal ratios in breast cancer prognosis. A thorough and methodological evaluation of the potential prognostic importance of nodal ratios in large multicenter data sets is merited and is currently being undertaken by the International Nodal Ratio Working Group.

Breast Neoplasms↗

PubMed2006

Review of interactive safer sex Web sites: practice and potential.

The Internet is increasingly being viewed as a health promotion tool with enormous potential. However, this potential cannot be realized if Web sites do not utilize the features that make the Internet a "hybrid" mass and interpersonal communication medium. The purpose of this study was to examine interactive safer sex Web sites on a number of dimensions. A comprehensive search that included Internet search engines, links from well-known sites, and previously published reviews yielded 21 Web sites that met criteria. Web sites were coded on dimensions including targeting of the Web sites, safer sex messages presented, theoretical strategies utilized, interactivity, and other characteristics. Results indicate that a moderate amount of targeting of Web sites exists, especially on age group (e.g., teenagers); the most prevalent safer sex messages were to "use condoms" and "be sexually abstinent"; raising the perceived threat of sexually transmitted diseases and HIV was the most prevalent theoretical strategy used to motivate safer sex; and finally, a moderate amount of interactivity was found on the Web sites, with most Web sites containing 4 or 5 features out of 15 features examined. Evidence that Web sites were tailoring information or messages to individuals was not found. Implications of these results for improving safer sex Web sites and developing interventions online are discussed.

Health Behavior↗

PubMed2004

Readability of cancer information on the internet.

BACKGROUND: Literacy is considered an essential component of individuals' ability to increase control over their health. However, the majority of printed cancer information is written at readability levels of high school or higher and may be difficult to comprehend by people who are searching for medical information. Since low literacy is associated with poorer health and since a growing number of people are searching the Internet for health information, our research questions were twofold: (1) What is the readability level of popular Web sites on breast, colon, and prostate cancers? and (2) Does readability level differ as a function of the Web sites' organizational origin? METHODS: Breast, colon, and prostate cancer Web sites were selected for analysis by comparing the first 100 hits of 10 popular search engines. A total of 55 Web sites on breast (n = 20), colorectal (n = 18), and prostate (n = 17) cancers were included in the final analysis and assessed for readability using SMOG, Flesch-Kincaid (F-K), and Flesch Reading Ease (FRE) measures. RESULTS: The overall mean reading level of the cancer Web sites was Grade 13.7 using the SMOG formula and Grade 10.9 according to F-K. The mean FRE score was 41.6. The majority of Web sites (63.6%) were written at college level (Grade 13+) according to SMOG, especially those with a domain of ".com" and "org." Breast cancer sites were written at easier reading grade levels than sites on prostate cancer and colorectal cancer. Breast cancer sites also showed the largest increase in reading difficulty between opening and concluding paragraphs of text. CONCLUSIONS: Readability of cancer information on the Internet is at a college level. Individuals with basic literacy skills must be considered when posting cancer information on the Internet. Otherwise this information will remain inaccessible to a segment of the population who is at risk for cancer.

Comprehension↗

PubMed2005

REVIEW: Treatment of hypothyroidism with combinations of levothyroxine plus liothyronine.

CONTEXT: Combined infusion of levothyroxine plus liothyronine, as opposed to levothyroxine alone, is the only way of restoring the concentrations of circulating TSH, T4, and T3 as well as those of both T4 and T3 in all tissues of thyroidectomized rats. Considering the substantial differences in thyroid hormone secretion, transport, and metabolism between rats and humans, whether or not combined levothyroxine plus liothyronine replacement therapy has advantages over treatment with levothyroxine alone in hypothyroid patients is still questioned. EVIDENCE ACQUISITION: We conducted a systematic review of all the published controlled studies comparing treatment with levothyroxine alone with combinations of levothyroxine plus liothyronine in hypothyroid patients, identified through the Entrez-PubMed search engine. EVIDENCE SYNTHESIS: Nine controlled clinical trials were identified that compared treatment with levothyroxine alone and treatment with combinations of levothyroxine plus liothyronine and included a sufficient number of adult hypothyroid patients to yield meaningful results. In only one study did the combined therapy appear to have beneficial effects on the mood, quality of life, and psychometric performance of the patients over levothyroxine alone. These results have not been confirmed by later studies using either T3 substitution protocols or approaches with fixed combinations of levothyroxine plus liothyronine, including those based on the physiological proportion in which T3 and T4 are secreted by the human thyroid. However, in some of these studies the patients preferred levothyroxine plus liothyronine combinations, for reasons not explained by changes in the psychological and psychometric tests employed. Yet patients' preference should be balanced against the possibility of adverse events resulting from the addition of liothyronine to levothyroxine, even in the small doses used in these studies. CONCLUSIONS: Until clear advantages of levothyroxine plus liothyronine are demonstrated, the administration of levothyroxine alone should remain the treatment of choice for replacement therapy of hypothyroidism.

Drug Therapy, Combination↗

PubMed2005

Review: aromatase inhibitors for ovulation induction.

CONTEXT: For the last 40 yr, the first line of treatment for anovulation in infertile women has been clomiphene citrate (CC). CC is a safe, effective oral agent but is known to have relatively common antiestrogenic endometrial and cervical mucous side effects that could prevent pregnancy in the face of successful ovulation. In addition, there is a significant risk of multiple pregnancy with CC, compared with natural cycles. Because of these problems, we proposed the concept of aromatase inhibition as a new method of ovulation induction that could avoid many of the adverse effects of CC. The objective of this review was to describe the different physiological mechanisms of action for CC and aromatase inhibitors (AIs) and compare studies of efficacy for both agents for ovulation induction. EVIDENCE ACQUISITION: We conducted a systematic review of all the published studies, both controlled and noncontrolled, comparing CC and AI treatment, either alone or in combination with gonadotropins, for ovulation induction or augmentation, identified through the Entrez-PubMed search engine. EVIDENCE SYNTHESIS: Because of the recent acceptance of the concept of using AIs for ovulation induction, few controlled studies were identified, and the rest of the studies were pilot or preliminary comparisons. Based on these studies, it appears that AIs are as effective as CC in inducing ovulation, are devoid of any antiestrogenic side effects, result in lower serum estrogen concentrations, and are associated with good pregnancy rates with a lower incidence of multiple pregnancy than CC. When combined with gonadotropins for assisted reproductive technologies, AIs reduce the dose of FSH required for optimal follicle recruitment and improve the response to FSH in poor responders. CONCLUSIONS: Preliminary evidence suggests that AIs may replace CC in the future because of similar efficacy with a reduced side effect profile. Although worldwide experience with AIs for ovulation induction is increasing, at present, definitive studies in the form of randomized controlled trials comparing CC with AIs are lacking.

Anovulation↗

PubMed2006

Quality of health information on the Internet in pediatric neuro-oncology.

The Internet is now the single largest source of health information and is used by many patients and their families who are affected by childhood brain tumors. To assess the quality of pediatric neuro-oncology information on the Internet, we used search engines to look for information on five common tumor types (brain stem glioma, craniopharyngioma, ependymoma, low-grade glioma, and medulloblastoma). The Web sites were evaluated for content quality by using the validated DISCERN rating instrument. Breadth of content and its accuracy were also scored by a checklist tool. Readability statistics were computed on the highest-rated sites. Of 114 evaluated Web sites, the sources were as follows: institutional, 46%; commercial, 35%; charitable, 15%; support group, 2%; and alternative medicine, 2%. Good interobserver correlation was found for both ratings instruments. The DISCERN tool rated Web sites as excellent (4%), good (7%), fair (29%), poor (39%), or very poor (21%). Only 5% of the Web sites provided one or more inaccurate pieces of information. Web sites were found deficient in topics covering etiology, late effects, prognosis, and treatment choices. Few sites offered information in languages other than English, and readability statistics showed an average required reading level of U.S. grade 12+ (the suggested level being grades 6-8 for an adult audience). The Internet is increasingly being used as a source of oncology information for patients and their families. Health care professionals should be actively involved in developing high-quality information for use in the next generation of Web sites.

Brain Neoplasms↗

PubMed2005

Unraveling the chromosomal aberrations of head and neck squamous cell carcinoma: a review.

Information from the genetic analysis of head and neck cancer has grown enormously in the last 20 years. The advent of high-resolution genetic analysis techniques such as microarray technology will further expand this field in the future. Here we review the data on chromosomal aberrations of head and neck squamous cell carcinoma, focusing on the data generated by comparative genomic hybridization analysis, and suggest how such findings will be taken forward over the next decade. With the search engine PUBMED, the key words "comparative genomic hybridisation," "head and neck," "oral," "hypopharyngeal," "laryngeal," and "squamous cell carcinoma" were used. Publications unavailable in English were excluded.

Carcinoma, Squamous Cell↗

PubMed2003

Ménière disease patient information and support: which website?

Management of Ménière's disease remains problematic. Many different therapies are available, with variable success. Ménière's patients frequently research the Internet for information about the disease and to make contact with other patients. Internet websites providing this information have grown in number vastly in the past few years. This paper aims to identify the best websites available for Ménière's patients. Using Internet search engines the top 50 websites were evaluated a Website Global Scoring and Evaluation Proforma. From the above the top ranking 15 websites were identified.

Humans↗

PubMed2005

Information on telemedicine.

Although the practice of telemedicine is still not considered part of mainstream health care, there has been a steady growth in information about telemedicine since 1999. The increasing body of literature about telemedicine, the staying power of various telemedicine societies and Websites, and the growing number of well-attended conferences about telemedicine all attest that interest in and the practice of telemedicine worldwide are very much alive and well. Searching for information has also become easier with the advent of better and faster search engines, particularly Google. Nonetheless, many Websites are out of date and the semantic confusion between 'telemedicine' and other terms such as 'telehealth' means that considerable perseverance is required to sift the wheat from the chaff. There is a wide variety of both electronic and print resources that have proven to be reliable sources of information. These include: the Internet (Web), books and reports, journals and trade magazines, telemedicine societies and conferences. While telemedicine cannot yet be considered to be part of mainstream health care, it has become a more familiar part of health terminology worldwide.

Computer Communication Networks↗

PubMed2000

Development of a pollution prevention and energy efficiency clearinghouse for biomedical research facilities.

This is the report of the National Association of Physicians for the Environment Committee on Development of a Pollution Prevention and Energy Efficiency Clearinghouse for Biomedical Research Facilities from the Leadership Conference on Biomedical Research and the Environment held at the National Institutes of Health in Bethesda, Maryland, on 1--2 November 1999. A major goal of the conference was the establishment of a World Wide Web-based clearinghouse, which would lend tremendous resources to the biomedical research community by providing access to a database of peer-reviewed articles and references dealing with a host of aspects of biomedical research relating to energy efficiency, pollution prevention, and waste reduction. A temporary website has been established with the assistance of the U.S. Environmental Protection Agency (EPA) Regions III and IV, where a pilot site provides access to the EPA's existing databases on these topics. A system of peer review for articles and promising techniques still must be developed, but a glimpse of topics and search engines is available for comment and review on the EPA Region IV-supported website (http://wrrc.p2pays.org/).

Biomedical Technology↗