Surgical scientific publication and the 1991-1995 war in Croatia

The aim of this study was to evaluate surgical scientific publication in relation to the 1991-1995 war in Croatia, based on the articles indexed in Medline database that were published in 1980-2005 period. The number of articles was extracted from PubMed and analysed with trend analysis, which is preferred analytic approach over calculation of crude publication rates. The results indicate sporadic pre-war output, which was almost completely reduced by the onset of war. During wartime, a significant increasing trend in the number of published surgical articles that were related to warfare was detected (p = 0.003). During the post-war period a gradual shift towards surgical articles that were not related to warfare was detected, also marked by the significant increasing trend (p = 0.027). Both trends were significantly steeper than the overall Croatian biomedical output, suggesting that surgical scientific articles were being published more dynamically than in other biomedical areas in Croatia. The results suggest that war in Croatia has had a strong modifying effect on the surgical scientific output.     

Optimal search strategies for detecting health services research studies in MEDLINE

Background

Evidence from health services research (HSR) is currently thinly spread through many journals, making it difficult for health services researchers, managers and policy-makers to find research on clinical practice guidelines and the appropriateness, process, outcomes, cost and economics of health care services. We undertook to develop and test search terms to retrieve from the MEDLINE database HSR articles meeting minimum quality standards.

Methods

The retrieval performance of 7445 methodologic search terms and phrases in MEDLINE (the test) were compared with a hand search of the literature (the gold standard) for each issue of 68 journal titles for the year 2000 (a total of 25 936 articles). We determined sensitivity, specificity and precision (the positive predictive value) of the MEDLINE search strategies.

Results

A majority of the articles that were classified as outcome assessment, but fewer than half of those in the other categories, were considered methodologically acceptable (no methodologic criteria were applied for cost studies). Combining individual search terms to maximize sensitivity, while keeping specificity at 50% or more, led to sensitivities in the range of 88.1% to 100% for several categories (specificities ranged from 52.9% to 97.4%). When terms were combined to maximize specificity while keeping sensitivity at 50% or more, specificities of 88.8% to 99.8% were achieved. When terms were combined to maximize sensitivity and specificity while minimizing the differences between the 2 measurements, most strategies for HSR categories achieved sensitivity and specificity of at least 80%.

Interpretation

Sensitive and specific search strategies were validated for retrieval of HSR literature from MEDLINE. These strategies have been made available for public use by the US National Library of Medicine at www.nlm.nih.gov/nichsr/hedges/search.html.With the increasing emphasis on “using evidence” and “value for money” in health services, it is essential that researchers, clinicians, health system managers and public policy-makers be able to retrieve relevant, high-quality reports of health services research (HSR). Efficiently retrieved research evidence can aid in decision-making about which services to provide and in the resource allocation decisions to support those services, reducing the need for arbitrary decisions and aiding collaboration with clinicians and consumers.¹ MEDLINE is a huge and expanding bibliographic resource that is freely available to all with Internet access. Yet the volume of the literature often overwhelms both clinicians and health system decision-makers.^2,3 End-users of MEDLINE and other large bibliographic databases have difficulty executing precise searches^2,3 and are often unaware of what kind of information to seek, where to find it^3,4 and how to judge its quality.³HSR has been defined as the scientific study of the effect of health care delivery; the organization and management of health care access, quality, cost and financing; and the evaluation of the impact of health services and technology (Allmang NA, Koonce TY. Health services research topic searches. Bethesda [MD]: National Library of Medicine; 2000. Unpublished report). More recently, HSR has been defined as the multidisciplinary field of scientific investigation that studies how social factors, financing systems, organizational structures and processes, health technologies and personal behaviours affect access to health care, the quality and cost of health care and, ultimately, health and well-being.⁵ HSR articles constitute only a tiny fraction of the MEDLINE database and are spread through a large number of journals; hence, MEDLINE searching is challenging. Conversely, journal browsing is impractical as a means of retrieving all relevant studies for a given question or staying abreast of the literature. Our aim was to develop methodologic search filters for MEDLINE to enable end-users to efficiently retrieve articles of relevance to clinical practice guidelines (CPGs) and the appropriateness, process, outcomes, cost and economics of health services.     

Our "Collegium Antropologicum" officially the most improved social science journal in the world for mid-2002

Thomson ISI's bimonthly web-product ISI Essential Science Indicators (ESI) is an in-depth analytical tool that regularly reports quantitative analyses of research performance and science trends, covering about 8,500 scientific journals from the entire world. In each issue ESI lists the scientists, institutions, countries and journals that are most improved from one update to the next, i.e. that show the largest percentage increase in total citations. In its edition of January 2003, it reported that our "Collegium Antropologicum" was the most improved journal in the field of Social Sciences during the period from July 2002 to September 2002. The field of Social Sciences is one of 22 categories of science regularly analyzed by ESI. It includes anthropology, public health, sociology, social work and policy, political science, law, education, communication, library and information sciences, environmental studies and rehabilitation. Due to journal's success, which is based on publications of predominantly Croatian scientists within the past seven post-war years, Croatia was also officially the most improved among more than 200 countries, and University of Zagreb was the most improved in the field of Social Science among thousands of other institutions. We hope that this is an early sign of revival of the scientific activity in our country after the War in Croatia (1991-1995).     

Croatian national reference Y-STR haplotype database

A reference Y-chromosome short tandem repeat (STR) haplotype database is needed for Y-STR match interpretation as well as for national and regional characterization of populations. The aim of this study was to create a comprehensive Y-STR haplotype database of the Croatian contemporary population and to analyze substructure between the five Croatian regions. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vu?eti?". A total of 1,100 unrelated men from eastern, western, northern, southern and central Croatia were selected for the purpose of this study. Y-STRs were typed using the AmpFISTR Yfiler PCR amplification kit. Analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool included 16 population samples with 20,247 haplotypes. A total of 947 haplotypes were recorded, 848 of which were unique (89.5%). Haplotype diversity was 0.998, with the most frequent haplotype found in 9 of 1,100 men (0.82%). Locus diversity varied from 0.266 for DYS392 to 0.868 for DYS385. Discrimination capacity was 86.1%. Our results suggested high level of similarity among regional subpopulations within Croatia, except for mildly different southern Croatia. Relative resemblance was found with Bosnia and Herzegovina and Serbia. Whit Atheys' Haplogroup Predictor was used to estimate the frequencies of Y-chromosome haplogroups. I2a, R1a, E1b1b and R1b haplogroups were most frequent in all Croatian regions. These results are important in forensics and contribute to the population genetics and genetic background of the contemporary Croatian population.     

A modified statistically optimal null filter method for recognizing protein-coding regions

Computer-aided protein-coding gene prediction in uncharacterized genomic DNA sequences is one of the most important issues of biological signal processing.A modified filter method based on a statistically optimal null filter(SONF) theory is proposed for recognizing protein-coding regions.The square deviation gain(SDG) between the input and output of the model is used to identify the coding regions.The effective SDG amplification model with Class I and Class II enhancement is designed to suppress the non-coding regions.Also,an evaluation algorithm has been used to compare the modified model with most gene prediction methods currently available in terms of sensitivity,specificity and precision.The performance for identification of protein-coding regions has been evaluated at the nucleotide level using benchmark datasets and 91.4%,96%,93.7% were obtained for sensitivity,specificity and precision,respectively.These results suggest that the proposed model is potentially useful in gene finding field,which can help recognize protein-coding regions with higher precision and speed than present algorithms.     

Fitness level of adult economically active population in the Republic of Croatia estimated by EUROFIT system

The study presents the results of the EUROFIT CROATIA project that was conducted according to the instructions of Council of Europe. The aim of the study was evaluation of fitness level of the employed Croatian population. The measurements comprised EUROFIT battery of tests as well as Baecke's questionnaire for evaluation of habitual physical activity. The sample was comprised of 1628 active inhabitants, 18-60 years of age, all of who were employed and living in Croatia. The obtained results of functional, motor and morphological characteristics were presented according to the sex and age. The results shower poor aerobic capacity, high obesity indicators and low motor performance in both sexes, which pointed to the increased risk for developing many cardiovascular or musculo-skeletal diseases. The overall fitness level of Croatian population showed to be unsatisfactory and it should be improved by engagement in sports-recreational activities.     

Causal Bayesian network for tagging syntactical structure of Croatian sentences

Paper describes tagging syntactical structure of Croatian language sentences using causal Bayesian network. In the first part of the paper we describe Bayesian model for tagging sentences. Base on this idea, we will test our model on Croatian language sentences on Database of grammatical sentences of Croatian language (http://infoz.ffzg.hr / tepes /). This paper is result of our new research connected with the paper hidden Markov model for tagging of Croatian language texts for project Linguistic Analysis of The European languages and the paper Probability distribution on the parse trees for the project Annotated database and syntactic structure of Croatian languages.     

Identification of phosphopeptides with unknown cleavage specificity by a de novo sequencing assisted database search strategy

In theory, proteases with broad cleavage specificity could be applied to digest protein samples to improve the phosphoproteomic analysis coverage. However, in practice this approach is seldom employed. This is because the identification of phosphopeptides without enzyme specificity by conventional database search strategy is extremely difficult due to the huge search space. In this study, we investigated the performance of a de novo sequencing assisted database search strategy for the identification of such phosphopeptides. Firstly, we compared the performance of conventional database search strategy and the de novo sequencing assisted database search strategy for the identification of peptides and phosphopeptides without stetting enzyme specificity. It was found that the identification sensitivity dropped significantly for the conventional one while it was only slightly decreased for the new approach. Then, this new search strategy was applied to identify phosphopeptides generated by Proteinase K digestion, which resulted in the identification of 717 phosphopeptides. Finally, this strategy was utilized for the identification of serum endogenous phosphopeptides, which were generated in vivo by different kinds of proteases and kinases, and the identification of 68 unique serum endogenous phosphopepitdes was successfully achieved.     

Designing filters for fast-known NcRNA identification

Detecting members of known noncoding RNA (ncRNA) families in genomic DNA is an important part of sequence annotation. However, the most widely used tool for modeling ncRNA families, the covariance model (CM), incurs a high-computational cost when used for genome-wide search. This cost can be reduced by using a filter to exclude sequences that are unlikely to contain the ncRNA of interest, applying the CM only where it is likely to match strongly. Despite recent advances, designing an efficient filter that can detect ncRNA instances lacking strong conservation while excluding most irrelevant sequences remains challenging. In this work, we design three types of filters based on multiple secondary structure profiles (SSPs). An SSP augments a regular profile (i.e., a position weight matrix) with secondary structure information but can still be efficiently scanned against long sequences. Multi-SSPbased filters combine evidence from multiple SSP matches and can achieve high sensitivity and specificity. Our SSP-based filters are extensively tested in BRAliBase III data set, Rfam 9.0, and a published soil metagenomic data set. In addition, we compare the SSPbased filters with several other ncRNA search tools including Infernal (with profile HMMs as filters), ERPIN, and tRNAscan-SE. Our experiments demonstrate that carefully designed SSP filters can achieve significant speedup over unfiltered CM search while maintaining high sensitivity for various ncRNA families. The designed filters and filter-scanning programs are available at our website: www.cse.msu.edu/~yannisun/ssp/.     

Students online: learning medical genetics.

It is possible to focus medical genetics education by using a model that integrates the skills of end-user searching of the medical literature into the traditional course content. Since 1988, 313 first-year medical students were studied as they accessed MEDLINE to retrieve information about biochemical genetic disorders. Their search behavior was studied by analyzing data from the National Library of Medicine's traffic files. The skills that they initially learned were reinforced as they searched clinical genetics problem cases in the second-year pathology course, and these skills were consolidated in the third year when the students addressed specific patient-care questions in pediatrics. The students' perception of the value of this model was studied by analyzing questionnaires completed during the exercise. It was demonstrated that when students were taught the skills of accessing MEDLINE by computer, they could formulate a question, retrieve current information, critically review relevant articles, communicate effectively, and use these skills to contribute to patient care.     

Current status of iodine intake in Croatia--the results of 2009 survey

In 1996, due to persistence of mild to moderate iodine deficiency, new law on obligatory salt iodination with 25 mg of potassium iodide (KI) per kg of salt was implemented in Croatia. Along with a new law, a new program for monitoring of iodine prophylaxis was implemented. Investigations of goiter and iodine intake performed in 2002, demonstrated sufficient iodine intake in Croatia with overall median of urinary iodine concentration (UIC) for schoolchildren in Croatia of 140 microg/L. In 2002, thyroid volumes (TV) measured by ultrasound in schoolchildren from all four geographic regions of Croatia were for the first time within the normal range according to ICCIDD reference values. Nowadays, Croatia is internationally recognized as iodine sufficient country. The aim of the present study was to assess current status of iodine intake in Croatia. The investigation was carried out in 2009. A total of 386 schoolchildren aged 7-10 years from all four major geographic regions of Croatia, 103 euthyroid pregnant women and 36 women of child-bearing age from Zagreb, the capital, were included in the survey. Urinary iodine concentration (UIC) was measured in all participants. Thyroid volumes were measured by ultrasound in schoolchildren from the capital of Zagreb (N = 101) and the village of Rude (N = 56). In the time period 2002-2009, the content of KI was analyzed in 384 salt samples from Croatian salt plants and samples of imported salt. An overall median UIC for schoolchildren in Croatia was 248 microg/L. Median UIC in pregnant women was 159 microg/L, with 50% of samples below and under 150 microg/L. Median UIC in women of child-bearing age was 136 microg/L. Thyroid volumes in schoolchildren were within the normal range according to the new reference values. Mean value of KI/kg of salt in samples from Croatian salt plants was 25.5 mg/kg and 24.9 mg/kg in samples of imported salt. A total of 72/384 (18.8%) of salt samples didn't corresponded to the Croatian law on obligatory salt iodination. Presented data indicate sufficient iodine intake of the Croatian population. Current medians of UIC in schoolchildren in Croatia are significantly higher than medians measured in 2002. This indicates that other potential sources of iodine are present in Croatian diet that may contribute to overall iodine intake. Due to rising medians of UIC in schoolchildren in Croatia, it is important to conduct nutrition studies to identify potential sources of "silent prophylaxis" in order to avoid iodine excess.     

Search filters for finding prognostic and diagnostic prediction studies in Medline to enhance systematic reviews

Background

The interest in prognostic reviews is increasing, but to properly review existing evidence an accurate search filer for finding prediction research is needed. The aim of this paper was to validate and update two previously introduced search filters for finding prediction research in Medline: the Ingui filter and the Haynes Broad filter.

Methodology/Principal Findings

Based on a hand search of 6 general journals in 2008 we constructed two sets of papers. Set 1 consisted of prediction research papers (n = 71), and set 2 consisted of the remaining papers (n = 1133). Both search filters were validated in two ways, using diagnostic accuracy measures as performance measures. First, we compared studies in set 1 (reference) with studies retrieved by the search strategies as applied in Medline. Second, we compared studies from 4 published systematic reviews (reference) with studies retrieved by the search filter as applied in Medline. Next – using word frequency methods – we constructed an additional search string for finding prediction research. Both search filters were good in identifying clinical prediction models: sensitivity ranged from 0.94 to 1.0 using our hand search as reference, and 0.78 to 0.89 using the systematic reviews as reference. This latter performance measure even increased to around 0.95 (range 0.90 to 0.97) when either search filter was combined with the additional string that we developed. Retrieval rate of explorative prediction research was poor, both using our hand search or our systematic review as reference, and even combined with our additional search string: sensitivity ranged from 0.44 to 0.85.

Conclusions/Significance

Explorative prediction research is difficult to find in Medline, using any of the currently available search filters. Yet, application of either the Ingui filter or the Haynes broad filter results in a very low number missed clinical prediction model studies.     

HIV-infected children in Croatia--medical care versus ethical and social issues

The era of pediatric HIV-infection in Croatia began in 1987 when the first child from an HIV-infected mother was born. The authors present some medical data of children diagnosed as HIV-infected or observed because of maternal HIV-infection in Croatia until the end of 2005. Although the number of HN-infected children in Croatia is still relatively small, in the last two decades the Croatian society was confronted with many ethical and social issues regarding HIV-infection and discrimination. There were many obstacles in providing proper care and integrating HIV-infected children in the Croatian society. Stigmatisation, fear and lack of knowledge were major contributors. For the first time, the integration of an HIV-infected child with revealed HIV-status into school was described. Changes in attitudes towards HIV-infected people can only be achieved through planned permanent educational programs.     

Nutritional studies in Croatia--a century of research

This paper is dedicated to the pioneers of nutritional research in Croatia: to Professor Edvin Ferber, Professor Hubert Maver and Professor Ratko Buzina, to whom we owe exceptional contribution in the development of science of nutrition, as well as for many scientific publications from the fifties to the eighties in the 20th century, leaving us great information about nutritional state in Croatian population. The paper brings a review of nuitritional research in Croatia with an emphasis on history of research and papers published in Collegium Antropologicum. Since first publications on the subject, a number of institutions and scholars participated in numerous research projects which resulted in a vast number of published papers, depicting a multidisciplinary approach to the subject. In addition, the results of 44 analyses that have been a part of doctoral (18) and master's research (26) are discussed.     

Online coverage of the literature on thermal physiology

Online searches for research topics in thermal physiology usually do not retrieve more than 40% of the existing publications. In order to determine whether this low retrieval rate is due to deficient coverage of the literature or to problems in storage and retrieval of information, a list of 25 major papers, 25 minor papers and 15 obscure papers on thermal physiology was compiled. The 65 documents were searched online in the MEDLINE database. Retrieval rate was more than 60% for obscure papers, 80% for minor papers, and 90% for major papers. It is concluded that MEDLINE has an appropriate coverage of the literature on thermal physiology and that the low retrieval rate in online searches is due mostly to problems in information processing.     

Impact of PubMed search filters on the retrieval of evidence by physicians

Background:

Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians.

Methods:

We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries “therapy”) and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles.

Results:

The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were nonrelevant (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p < 0.003) with no substantive change in comprehensiveness (44% of relevant articles found; p = 0.55).

Interpretation:

The use of PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.Retrieving health literature is a cornerstone of evidence-based practice. With the rapid increase in available evidence, physicians can no longer rely on one or two key journals to stay current. Increasingly, physicians search bibliographic databases, such as PubMed, for research evidence, which is dispersed across hundreds of journals. Each year, physicians perform over 200 million searches in PubMed.^1,2 Physicians face challenges while searching PubMed and often miss relevant articles while retrieving too many nonrelevant articles.^3–6 Clinical decision-making based on evidence from a search may be impaired if relevant articles are missed. Retrieving many nonrelevant articles impedes the efficiency of searching. Improved search strategies are therefore necessary to retrieve a manageable amount of information. The use of PubMed search filters may help solve this problem. Filters are objectively derived, pretested strategies optimized to help users efficiently retrieve articles for a specific purpose.^7,8PubMed provides two types of clinical search filters: methods-based and topic-based. Methods-based filters (known as clinical queries) were designed to retrieve articles on therapy, diagnosis, prognosis and etiology.^9–13 For example, the clinical queries “therapy” filter is optimized to retrieve publications of randomized controlled trials. Methods-based filters can be used for any clinical discipline and are available for general use in PubMed (www.ncbi.nlm.nih.gov/pubmed/clinical). Topic-based filters, in contrast, are designed to retrieve articles within a specific discipline or topic. For example, the recently developed nephrology filters were optimized to retrieve articles with renal content.¹Physicians can use methods- and topic-based filters alone or in combination. For example, Figure 1A shows a search without search filters for studies about the effectiveness of hepatitis B vaccination in patients with chronic kidney disease. Alternatively, this search could be performed with search filters (Figure 1B). Using filters removes the task of generating and including method-specific or topic-specific terms in a search strategy because the filters act as optimized substitutes. For example, applying the nephrology filter eliminates the need to enter renal terms and synonyms in a search query (e.g., chronic kidney disease, end-stage renal disease, chronic renal failure). The nephrology filter, instead, maximizes the retrieval of all renal content (see the nephrology filter strategy in Figure 1B).Open in a separate windowFigure 1:PubMed searches without (A) and with (B) filters. This figure was created from the PubMed clinical queries Web interface; this page currently does not feature a “clinical category” section. When we performed searches with the nephrology filter (B), we removed the term “chronic kidney disease” because the filter acts as an optimized substitute for clinical content terms.In theory, filters should make searching more efficient; however, empiric evidence of this among physicians is lacking. We conducted this study to determine whether the use of methods-based filters and topic-based filters (alone and in combination) improve the efficiency of physician searches in PubMed. The area of renal medicine is an excellent test model because the literature in this field is dispersed across 400 multidisciplinary journals, and many nephrologists search PubMed for information to guide patient care.^14,15     

Ranking the whole MEDLINE database according to a large training set using text indexing

Background  

The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine.     

Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold

It is a major challenge to develop effective sequence database search algorithms to translate molecular weight and fragment mass information obtained from tandem mass spectrometry into high quality peptide and protein assignments. We investigated the peptide identification performance of Mascot and X!Tandem for mass tolerance settings common for low and high accuracy mass spectrometry. We demonstrated that sensitivity and specificity of peptide identification can vary substantially for different mass tolerance settings, but this effect was more significant for Mascot. We present an adjusted Mascot threshold, which allows the user to freely select the best trade-off between sensitivity and specificity. The adjusted Mascot threshold was compared with the default Mascot and X!Tandem scoring thresholds and shown to be more sensitive at the same false discovery rates for both low and high accuracy mass spectrometry data.     

A search filter for increasing the retrieval of animal studies in Embase

Collecting and analysing all available literature before starting a new animal experiment is important and it is indispensable when writing systematic reviews of animal research. In practice, finding all animal studies relevant to a specific research question turns out to be anything but simple. In order to facilitate this search process, we previously developed a search filter for retrieving animal studies in the most often used biomedical database, PubMed. It is a general requirement for systematic reviews, however, that at least two databases are searched. In this report, we therefore present a similar search filter for a second important database, namely Embase. We show that our filter retrieves more animal studies than (a combination of) the options currently available in Embase. Our search filters for PubMed and Embase therefore represent valuable tools for improving the quality of (systematic) reviews and thereby of new animal experiments.