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1.  Creating an Online Dictionary of Abbreviations from MEDLINE 
Objective. The growth of the biomedical literature presents special challenges for both human readers and automatic algorithms. One such challenge derives from the common and uncontrolled use of abbreviations in the literature. Each additional abbreviation increases the effective size of the vocabulary for a field. Therefore, to create an automatically generated and maintained lexicon of abbreviations, we have developed an algorithm to match abbreviations in text with their expansions.
Design. Our method uses a statistical learning algorithm, logistic regression, to score abbreviation expansions based on their resemblance to a training set of human-annotated abbreviations. We applied it to Medstract, a corpus of MEDLINE abstracts in which abbreviations and their expansions have been manually annotated. We then ran the algorithm on all abstracts in MEDLINE, creating a dictionary of biomedical abbreviations. To test the coverage of the database, we used an independently created list of abbreviations from the China Medical Tribune.
Measurements. We measured the recall and precision of the algorithm in identifying abbreviations from the Medstract corpus. We also measured the recall when searching for abbreviations from the China Medical Tribune against the database.
Results. On the Medstract corpus, our algorithm achieves up to 83% recall at 80% precision. Applying the algorithm to all of MEDLINE yielded a database of 781,632 high-scoring abbreviations. Of all the abbreviations in the list from the China Medical Tribune, 88% were in the database.
Conclusion. We have developed an algorithm to identify abbreviations from text. We are making this available as a public abbreviation server at \url{http://abbreviation.stanford.edu/}.
doi:10.1197/jamia.M1139
PMCID: PMC349378  PMID: 12386112
2.  A study of abbreviations in the UMLS. 
Abbreviations are widely used in medicine. The understanding of abbreviations is important for medical language processing and information retrieval systems. The Unified Medical Language System (UMLS) contains a large number of abbreviations. We hypothesized that extracting and studying the UMLS abbreviations can be helpful for understanding the characteristics of abbreviations in medicine. In this paper, we describe a method for extracting abbreviations from the UMLS. We evaluated the method and studied the ambiguous nature of the abbreviations. In addition, the coverage of the UMLS abbreviations in medical reports was studied. Using our method, we extracted 163,666 unique (abbreviation, full form) pairs from the UMLS with a precision of 97.5%, and a recall of 96%. The UMLS abbreviations were highly ambiguous: 33.1% of abbreviations with six characters or less had multiple meanings; the average number of different full forms for all abbreviations with six characters or less was 2.28. The coverage of the UMLS abbreviations in medical reports was over 66%.
PMCID: PMC2243414  PMID: 11825217
3.  A Study of Abbreviations in Clinical Notes 
Various natural language processing (NLP) systems have been developed to unlock patient information from narrative clinical notes in order to support knowledge based applications such as error detection, surveillance and decision support. In many clinical notes, abbreviations are widely used without mention of their definitions, which is very different from the use of abbreviations in the biomedical literature. Thus, it is critical, but more challenging, for NLP systems to correctly interpret abbreviations in these notes. In this paper we describe a study of a two-step model for building a clinical abbreviation database: first, abbreviations in a text corpus were detected and then a sense inventory was built for those that were found. Four detection methods were developed and evaluated. Results showed that the best detection method had a precision of 91.4% and recall of 80.3%. A simple method was used to build sense inventories from two different knowledge sources: the Unified Medical Language System (UMLS) and a MEDLINE abbreviation database (ADAM). Evaluation showed the inventory from the UMLS appeared to be the more appropriate of the two for defining the sense of abbreviations, but was not ideal. It covered 35% of the senses and had an ambiguity rate of 40% for those that were covered. However, annotation by domain experts appears necessary for uncovered abbreviations and to determine the correct senses.
PMCID: PMC2655910  PMID: 18693951
4.  A randomized-controlled trial of computerized alerts to reduce unapproved medication abbreviation use 
Abbreviation use is a preventable cause of medication errors. The objective of this study was to test whether computerized alerts designed to reduce medication abbreviations and embedded within an electronic progress note program could reduce these abbreviations in the non-computer-assisted handwritten notes of physicians. Fifty-nine physicians were randomized to one of three groups: a forced correction alert group; an auto-correction alert group; or a group that received no alerts. Over time, physicians in all groups significantly reduced their use of these abbreviations in their handwritten notes. Physicians exposed to the forced correction alert showed the greatest reductions in use when compared to controls (p=0.02) and the auto-correction alert group (p=0.0005). Knowledge of unapproved abbreviations was measured before and after the intervention and did not improve (p=0.81). This work demonstrates the effects that alert systems can have on physician behavior in a non-computerized environment and in the absence of knowledge.
doi:10.1136/jamia.2010.006130
PMCID: PMC3005872  PMID: 21131606
5.  Allie: a database and a search service of abbreviations and long forms 
Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader’s expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly.
Database URL: The Allie service is available at http://allie.dbcls.jp/.
doi:10.1093/database/bar013
PMCID: PMC3077826  PMID: 21498548
6.  A study of abbreviations in MEDLINE abstracts. 
Abbreviations are widely used in writing, and the understanding of abbreviations is important for natural language processing applications. Abbreviations are not always defined in a document and they are highly ambiguous. A knowledge base that consists of abbreviations with their associated senses and a method to resolve the ambiguities are needed. In this paper, we studied the UMLS coverage, textual variants of senses, and the ambiguity of abbreviations in MEDLINE abstracts. We restricted our study to three-letter abbreviations which were defined using parenthetical expressions. When grouping similar expansions together and representing senses using groups, we found that after ignoring senses where the total number of occurrences within the corresponding group was less than 100, 82.8% of the senses matched the UMLS, covered over 93% of occurrences that were considered, and had an average of 7.74 expansions for each sense. Abbreviations are highly ambiguous: 81.2% of the abbreviations were ambiguous, and had an average of 16.6 senses. However, after ignoring senses with occurrences of less than 5, 64.6% of the abbreviations were ambiguous, and had an average of 4.91 senses.
PMCID: PMC2244212  PMID: 12463867
7.  Mapping Abbreviations to Full Forms in Biomedical Articles 
Objective: To develop methods that automatically map abbreviations to their full forms in biomedical articles.
Methods: The authors developed two methods of mapping defined and undefined abbreviations (defined abbreviations are paired with their full forms in the articles, whereas undefined ones are not). For defined abbreviations, they developed a set of pattern-matching rules to map an abbreviation to its full form and implemented the rules into a software program, AbbRE (for “abbreviation recognition and extraction”). Using the opinions of domain experts as a reference standard, they evaluated the recall and precision of AbbRE for defined abbreviations in ten biomedical articles randomly selected from the ten most frequently cited medical and biological journals. They also measured the percentage of undefined abbreviations in the same set of articles, and they investigated whether they could map undefined abbreviations to any of four public abbreviation databases (GenBank LocusLink, swissprot, LRABR of the UMLS Specialist Lexicon, and Bioabacus).
Results: AbbRE had an average 0.70 recall and 0.95 precision for the defined abbreviations. The authors found that an average of 25 percent of abbreviations were defined in biomedical articles and that of a randomly selected subset of undefined abbreviations, 68 percent could be mapped to any of four abbreviation databases. They also found that many abbreviations are ambiguous (i.e., they map to more than one full form in abbreviation databases).
Conclusion: AbbRE is efficient for mapping defined abbreviations. To couple AbbRE with abbreviation databases for the mapping of undefined abbreviations, not only exhaustive abbreviation databases but also a method to resolve the ambiguity of abbreviations in the databases are needed.
doi:10.1197/jamia.M0913
PMCID: PMC344586  PMID: 11971887
8.  Intervention to reduce the use of unsafe abbreviations in a teaching hospital 
Objectives
To determine the effectiveness of a two-phase intervention designed to reduce the use of unsafe abbreviations.
Methods
An observational prospective study was conducted at the King Khalid University Hospital in Riyadh, Saudi Arabia during May–September 2009. A list of unsafe abbreviations was formulated based on the recommendations of the Institute for Safe Medication Practices. The first 7000 medication orders written at the beginning of each period were collected. Phase one of the intervention involved educating health care professionals about the dangers of using unsafe abbreviations. In the second phase of the intervention, a policy was approved that prohibited the use of unsafe abbreviations hospital-wide. Then, another educational campaign targeted toward prescribers was organized. Descriptive statistics are used in this paper to present the results.
Results
At baseline, we identified 1980 medication abbreviations used in 7000 medication orders (28.3%). Three months after phase one of the intervention, the number of abbreviations found in 7000 medication orders had decreased to 1489 (21.3%). Six months later, after phase two of the intervention, the number of abbreviations used had decreased to 710 (10%). During this phase, the use of all abbreviations had declined relative to the baseline and phase one use levels. The decrease in the use of abbreviations was statistically significant in all three periods (P < 0.001).
Conclusion
The implementation of a complex intervention program reduced the use of unsafe abbreviations by 65%.
doi:10.1016/j.jsps.2012.10.006
PMCID: PMC3745070  PMID: 23960844
Unsafe abbreviations; Medications
9.  Avoiding Potential Medication Errors Associated with Non-intuitive Medication Abbreviations 
Background:
Pharmaceutical companies use a variety of abbreviations to denote short- and long-acting medications. Errors involving the administration of these medications are frequently reported.
Objectives:
To evaluate comprehension rates for abbreviations used to denote short- and long-acting medications and to evaluate whether changes to medication labels could reduce potential errors in the selection and administration of medications.
Methods:
In phase 1 of the study, nursing staff were asked to define 4 abbreviations and then to categorize them by release rate. In phase 2, a simulation exercise, nursing staff were asked if it would be appropriate to administer a medication illustrated in a photograph (oxycodone CR 5-mg blister pack) on the basis of information highlighted in a screen shot of an electronic medication administration record (order for oxycodone 5 mg). Three different presentations were used to identify the medication in the medication administration record and on the drug label.
Results:
In phase 1, 10 (28%) of 36 nursing staff members knew what all 4 abbreviations meant, and 14 (39%) correctly classified all 4 abbreviations as indicating a short- or a long-acting medication. In the simulation exercise (phase 2), labelling changes reduced the likelihood of a potential medication administration error.
Conclusions:
Most abbreviations used to indicate short- versus long-acting medications were not correctly understood by study participants. Of more concern was the incorrect interpretation of some abbreviations as indicating the opposite release rate (e.g., “ER” interpreted as meaning “emergency release”, rather than “extended release”, with incorrect classification as a short-acting medication). This evaluation highlighted the potential consequences of using non-intuitive abbreviations to differentiate high-risk medications having different release rates.
PMCID: PMC3161798  PMID: 22479066
medication abbreviations; release rate; medication error; human factors; abréviations des médicaments; vitesse de libération; erreurs de médication; facteurs humains
10.  Detecting Abbreviations in Discharge Summaries using Machine Learning Methods 
AMIA Annual Symposium Proceedings  2011;2011:1541-1549.
Recognition and identification of abbreviations is an important, challenging task in clinical natural language processing (NLP). A comprehensive lexical resource comprised of all common, useful clinical abbreviations would have great applicability. The authors present a corpus-based method to create a lexical resource of clinical abbreviations using machine-learning (ML) methods, and tested its ability to automatically detect abbreviations from hospital discharge summaries. Domain experts manually annotated abbreviations in seventy discharge summaries, which were randomly broken into a training set (40 documents) and a test set (30 documents). We implemented and evaluated several ML algorithms using the training set and a list of pre-defined features. The subsequent evaluation using the test set showed that the Random Forest classifier had the highest F-measure of 94.8% (precision 98.8% and recall of 91.2%). When a voting scheme was used to combine output from various ML classifiers, the system achieved the highest F-measure of 95.7%.
PMCID: PMC3243185  PMID: 22195219
11.  Communication after cancellations in orthopaedics: The patient perspective 
World Journal of Orthopedics  2014;5(1):45-50.
AIM: To examine patients’ perceptions on communication surrounding the cancellation of orthopaedic operations and to identify areas for improvement in communication.
METHODS: A prospective survey was undertaken at a university teaching hospital within the department of Trauma and Orthopaedics. Patients admitted to an acute orthopaedic unit, whose operations were cancelled, were surveyed to assess patient satisfaction and preferences for notification of cancellation of their operations. Patients with an abbreviated mental test score of < 9, patients unable to complete the survey independently, those under 16 years of age, and any patient notified of the cancellation by any of the authors were excluded from this study. Patients were surveyed the morning after their operation had been cancelled thus ensuring that every opportunity was given for the medical staff to discuss the cancellation with the patient. The survey included questions on whether or not patients were notified of the cancellation of their surgery, the qualifications of the person discussing the cancellation, and patient preferences on the process. Satisfaction was assessed via 5-point Likert scale questions.
RESULTS: Sixty-five consecutive patients had their operations cancelled on 75 occasions. Fifty-four point seven percent of the patients who had cancellations were notified by a nurse and 32% by a doctor. No formal communication occurred for 13.3% cancellations and no explanation was provided for a further 16%. Patients reported that they were dissatisfied with the explanation provided for 36 of the 75 (48%) cancellations. Of those patients who were dissatisfied, 25 (69.4%) were notified by a nurse. Twenty-three of the 24 (96%) patients notified by a doctor were satisfied with the explanation and that communication. Of those patients who were notified by a nurse 83% patients reported that they would have preferred it if a doctor had discussed the cancellation with them. There was a significant difference in satisfaction between those counselled by a nurse and those notified by a doctor (P < 0.0001).
CONCLUSION: Communication surrounding cancellations does not meet patient expectations. Patients prefer to be notified by a doctor, illustrating the importance of communication in the doctor-patient relationship.
doi:10.5312/wjo.v5.i1.45
PMCID: PMC3952693  PMID: 24649413
Communication; Patient satisfaction; Orthopaedic surgery; Cancellation
12.  Methods for Building Sense Inventories of Abbreviations in Clinical Notes 
Objective
To develop methods for building corpus-specific sense inventories of abbreviations occurring in clinical documents.
Design
A corpus of internal medicine admission notes was collected and instances of each clinical abbreviation in the corpus were clustered to different sense clusters. One instance from each cluster was manually annotated to generate a final list of senses. Two clustering-based methods (Expectation Maximization—EM and Farthest First—FF) and one random sampling method for sense detection were evaluated using a set of 12 clinical abbreviations.
Measurements
The clustering-based sense detection methods were evaluated using a set of clinical abbreviations that were manually sense annotated. “Sense Completeness” and “Annotation Cost” were used to measure the performance of different methods. Clustering error rates were also reported for different clustering algorithms.
Results
A clustering-based semi-automated method was developed to build corpus-specific sense inventories for abbreviations in hospital admission notes. Evaluation demonstrated that this method could largely reduce manual annotation cost and increase the completeness of sense inventories when compared with a manual annotation method using random samples.
Conclusion
The authors developed an effective clustering-based method for building corpus-specific sense inventories for abbreviations in a clinical corpus. To the best of the authors knowledge, this is the first time clustering technologies have been used to help building sense inventories of abbreviations in clinical text. The results demonstrated that the clustering-based method performed better than the manual annotation method using random samples for the task of building sense inventories of clinical abbreviations.
doi:10.1197/jamia.M2927
PMCID: PMC2605589  PMID: 18952935
13.  Comparison of Journal Self-Citation Rates between Some Chinese and Non-Chinese International Journals 
PLoS ONE  2012;7(11):e49001.
Background
The past 3 decades have witnessed a boost in science development in China; in parallel, more and more Chinese scientific journals are indexed by the Journal Citation Reports issued by Thomson Reuters (SCI). Evaluation of the performance of these Chinese SCI journals is necessary and helpful to improve their quality. This study aimed to evaluate these journals by calculating various journal self-citation rates, which are important parameters influencing a journal impact factor.
Methodology/Principal Findings
We defined three journal self-citation rates, and studied these rates for 99 Chinese scientific journals, almost exhausting all Chinese SCI journals currently available. Likewise, we selected 99 non-Chinese international (abbreviated as ‘world’) journals, with each being in the same JCR subject category and having similar impact factors as their Chinese counterparts. Generally, Chinese journals tended to be higher in all the three self-citation rates than world journal counterparts. Particularly, a few Chinese scientific journals had much higher self-citation rates.
Conclusions/Significance
Our results show that generally Chinese scientific journals have higher self-citation rates than those of world journals. Consequently, Chinese scientific journals tend to have lower visibility and are more isolated in the relevant fields. Considering the fact that sciences are rapidly developing in China and so are Chinese scientific journals, we expect that the differences of journal self-citation rates between Chinese and world scientific journals will gradually disappear in the future. Some suggestions to solve the problems are presented.
doi:10.1371/journal.pone.0049001
PMCID: PMC3500263  PMID: 23173041
14.  Kindergarten Predictors of Math Learning Disability 
The aim of the present study was to address how to effectively predict mathematics learning disability (MLD). Specifically, we addressed whether cognitive data obtained during kindergarten can effectively predict which children will have MLD in third grade, whether an abbreviated test battery could be as effective as a standard psychoeducational assessment at predicting MLD, and whether the abbreviated battery corresponded to the literature on MLD characteristics. Participants were 226 children who enrolled in a 4-year prospective longitudinal study during kindergarten. We administered measures of mathematics achievement, formal and informal mathematics ability, visual-spatial reasoning, and rapid automatized naming and examined which test scores and test items from kindergarten best predicted MLD at grades 2 and 3. Statistical models using standardized scores from the entire test battery correctly classified ~80–83 percent of the participants as having, or not having, MLD. Regression models using scores from only individual test items were less predictive than models containing the standard scores, except for models using a specific subset of test items that dealt with reading numerals, number constancy, magnitude judgments of one-digit numbers, or mental addition of one-digit numbers. These models were as accurate in predicting MLD as was the model including the entire set of standard scores from the battery of tests examined. Our findings indicate that it is possible to effectively predict which kindergartners are at risk for MLD, and thus the findings have implications for early screening of MLD.
doi:10.1111/j.1540-5826.2005.00129.x
PMCID: PMC2806680  PMID: 20084182
15.  Ambiguity of Human Gene Symbols in LocusLink and MEDLINE: Creating an Inventory and a Disambiguation Test Collection 
Genes are discovered almost on a daily basis and new names have to be found. Although there are guidelines for gene nomenclature, the naming process is highly creative. Human genes are often named with a gene symbol and a longer, more descriptive term; the short form is very often an abbreviation of the long form. Abbreviations in biomedical language are highly ambiguous, i.e., one gene symbol often refers to more than one gene. Using an existing abbreviation expansion algorithm, we explore MEDLINE for the use of human gene symbols derived from LocusLink. It turns out that just over 40% of these symbols occur in MEDLINE, however, many of these occurrences are not related to genes. Along the process of making an inventory, a disambiguation test collection is constructed automatically.
PMCID: PMC1480234  PMID: 14728264
16.  Thromboprophylaxis in spinal surgery: a survey 
Background
Venous Thromboembolism (VTE) is the most common complication following major joint surgery. While attention has been focused upon the incidence of thromboembolic disease following total hip or knee arthroplasty or emergency surgery for hip fracture, there exists a gap in the medical literature examining the incidence of VTE in spinal surgery. Evidence suggests that the prevalence of DVT after spinal surgery is higher than generally recognized but with a shortage of epidemiological data, guidelines for optimal prophylaxis are limited. This survey, of individuals attending the 2009 British Association of Spinal Surgeons Annual Meeting, sought to examine prevailing trends in VTE thromboprophylaxis in spinal surgery, adherence to guideline outlined by the National Institute for Health and Clinical Excellence (NICE) and to compare selections made by orthopaedic and neurosurgeons.
Methods
We developed a questionnaire with eight clinical scenarios. Participants were asked to supply details on their specialty and to select which method(s) of thromboprophylaxis they would employ for each scenario. Chi squared analysis was used for statistical comparison of the questionnaire responses.
Results
73% of neurosurgical respondents' and 31% of orthopaedic surgeons employed low molecular weight heparin (p < 0.001). Neurosurgeons also selected anti-embolism stockings more frequently (79% v 50%) while orthopaedic surgeons preferred mechanical prophylaxis (26% v 9%). There was no significant difference between trauma and non-trauma scenarios (p = 0.05).
Conclusion
There is no clear consensus in thromboprophylaxis in spinal surgery. There was a significant difference in selections across surgical disciplines with neurosurgeons more closely adhering to national guidelines. Further research examining the epidemiology of venous thromboembolism in spinal surgery and the risks-benefit relationship of thromboprophylaxis is warranted.
doi:10.1186/1749-799X-7-14
PMCID: PMC3349591  PMID: 22458927
Spinal surgery; Venous thromboembolism; Thromboprophylaxis; Orthopaedic surgery; Neurosurgery
17.  Validation of a Measure of Subjective Well-Being: An Abbreviated Version of the Day Reconstruction Method 
PLoS ONE  2012;7(8):e43887.
Background
The study of well-being is becoming a priority in social sciences. The Day Reconstruction Method (DRM) was developed to assess affective states. The aim of the present study was to validate an abbreviated version of the DRM designed for administration in population studies, and to assess its test-retest properties.
Principal Findings
1560 adults from Jodhpur (India) were interviewed using an abbreviated version of the DRM, and a week later they were re-interviewed using the original long version of the DRM, after which the abbreviated version of the DRM was compared with the original version. A regression model considering interaction terms was employed to analyse the impact of sociodemographic characteristics on net affect. Test-retest reliability was assessed, and found to be moderate. Positive affect showed more test-retest reliability than negative affect, while net affect had more temporal stability than U-index. The affect of sets A, B, and C, taken together, had a moderate predictive ability compared with the affect obtained using the full version of the DRM: AUC = 0.67 for positive affect; 0.66 for net affect; 0.61 for negative affect; and 0.60 for the U-index. Household income, gender, and setting all had a significant impact on net affect.
Conclusions
Net affect and positive affect showed moderate temporal stability, whereas negative affect and the U-index showed fair temporal stability. Evaluating the affective state using the abbreviated version of the DRM provides a profile of the population similar to that of the full version. The results provide considerable support for using the short version of the DRM as an instrument to measure subjective well-being in large population surveys.
doi:10.1371/journal.pone.0043887
PMCID: PMC3428291  PMID: 22952801
18.  Patient Perspectives with Abbreviated versus Standard Pre-Test HIV Counseling in the Prenatal Setting: A Randomized-Controlled, Non-Inferiority Trial 
PLoS ONE  2009;4(4):e5166.
Background
In the US, an unacceptably high percentage of pregnant women do not undergo prenatal HIV testing. Previous studies have found increased uptake of prenatal HIV testing with abbreviated pre-test counseling, however little is known about patient decision making, testing satisfaction and knowledge in this setting.
Methodology/Findings
A randomized-controlled, non-inferiority trial was conducted from October 2006 through February 2008 at San Francisco General Hospital (SFGH), the public teaching hospital of the City and County of San Francisco. A total of 278 English- and Spanish-speaking pregnant women were randomized to receive either abbreviated or standard nurse-performed HIV test counseling at the initial prenatal visit. Patient decision making experience was compared between abbreviated versus standard HIV counseling strategies among a sample of low-income, urban, ethnically diverse prenatal patients. The primary outcome was the decisional conflict score (DCS) using O'Connor low-literacy scale and secondary outcomes included satisfaction with test decision, basic HIV knowledge and HIV testing uptake. We conducted an intention-to-treat analysis of 278 women – 134 (48.2%) in the abbreviated arm (AA) and 144 (51.8%) in the standard arm (SA). There was no significant difference in the proportion of women with low decisional conflict (71.6% in AA vs. 76.4% in SA, p = .37), and the observed mean difference between the groups of 3.88 (95% CI: −0.65, 8.41) did not exceed the non-inferiority margin. HIV testing uptake was very high (97. 8%) and did not differ significantly between the 2 groups (99.3% in AA vs. 96.5% in SA, p = .12). Likewise, there was no difference in satisfaction with testing decision (97.8% in AA vs. 99.3% in SA, p = .36). However, women in AA had significantly lower mean HIV knowledge scores (78.4%) compared to women in SA (83.7%, p<0.01).
Conclusions/Significance
This study suggests that streamlining the pre-test counseling process, while associated with slightly lower knowledge, does not compromise patient decision making or satisfaction regarding HIV testing.
Trial Registration
ClinicalTrials.gov NCT00503308
doi:10.1371/journal.pone.0005166
PMCID: PMC2666158  PMID: 19367335
19.  Corruption in the health care sector: A barrier to access of orthopaedic care and medical devices in Uganda 
Background
Globally, injuries cause approximately as many deaths per year as HIV/AIDS, tuberculosis and malaria combined, and 90% of injury deaths occur in low- and middle- income countries. Given not all injuries kill, the disability burden, particularly from orthopaedic injuries, is much higher but is poorly measured at present. The orthopaedic services and orthopaedic medical devices needed to manage the injury burden are frequently unavailable in these countries. Corruption is known to be a major barrier to access of health care, but its effects on access to orthopaedic services is still unknown.
Methods
A qualitative case study of 45 open-ended interviews was conducted to investigate the access to orthopaedic health services and orthopaedic medical devices in Uganda. Participants included orthopaedic surgeons, related healthcare professionals, industry and government representatives, and patients. Participants’ experiences in accessing orthopaedic medical devices were explored. Thematic analysis was used to analyze and code the transcripts.
Results
Analysis of the interview data identified poor leadership in government and corruption as major barriers to access of orthopaedic care and orthopaedic medical devices. Corruption was perceived to occur at the worker, hospital and government levels in the forms of misappropriation of funds, theft of equipment, resale of drugs and medical devices, fraud and absenteeism. Other barriers elicited included insufficient health infrastructure and human resources, and high costs of orthopaedic equipment and poverty.
Conclusions
This study identified perceived corruption as a significant barrier to access of orthopaedic care and orthopaedic medical devices in Uganda. As the burden of injury continues to grow, the need to combat corruption and ensure access to orthopaedic services is imperative. Anti-corruption strategies such as transparency and accountability measures, codes of conduct, whistleblower protection, and higher wages and benefits for workers could be important and initial steps in improving access orthopaedic care and OMDs, and managing the global injury burden.
doi:10.1186/1472-698X-12-5
PMCID: PMC3492067  PMID: 22554349
20.  Machine learning with naturally labeled data for identifying abbreviation definitions 
BMC Bioinformatics  2011;12(Suppl 3):S6.
Background
The rapid growth of biomedical literature requires accurate text analysis and text processing tools. Detecting abbreviations and identifying their definitions is an important component of such tools. Most existing approaches for the abbreviation definition identification task employ rule-based methods. While achieving high precision, rule-based methods are limited to the rules defined and fail to capture many uncommon definition patterns. Supervised learning techniques, which offer more flexibility in detecting abbreviation definitions, have also been applied to the problem. However, they require manually labeled training data.
Methods
In this work, we develop a machine learning algorithm for abbreviation definition identification in text which makes use of what we term naturally labeled data. Positive training examples are naturally occurring potential abbreviation-definition pairs in text. Negative training examples are generated by randomly mixing potential abbreviations with unrelated potential definitions. The machine learner is trained to distinguish between these two sets of examples. Then, the learned feature weights are used to identify the abbreviation full form. This approach does not require manually labeled training data.
Results
We evaluate the performance of our algorithm on the Ab3P, BIOADI and Medstract corpora. Our system demonstrated results that compare favourably to the existing Ab3P and BIOADI systems. We achieve an F-measure of 91.36% on Ab3P corpus, and an F-measure of 87.13% on BIOADI corpus which are superior to the results reported by Ab3P and BIOADI systems. Moreover, we outperform these systems in terms of recall, which is one of our goals.
doi:10.1186/1471-2105-12-S3-S6
PMCID: PMC3111592  PMID: 21658293
21.  The impact of preprinted prescription forms on medication prescribing errors in an ophthalmology clinic in northeast Thailand: a non-randomised interventional study 
BMJ Open  2012;2(1):e000539.
Objectives
To understand the incidence and types of medication prescribing errors in a low resource setting ophthalmology clinic and to determine the impact of a preprinted prescription based on the hospital formulary (FormularyScript) on medication prescribing errors.
Design
Non-randomised interventional study.
Setting
Ophthalmology clinic in a teaching hospital in northeast Thailand.
Participants
4349 handwritten prescriptions collected from October 2009 to December 2009, and 4146 FormularyScripts collected from February 2010 to May 2010.
Primary and secondary outcome measures
All prescriptions from the handwritten and FormularyScript groups were analysed for medication error rates by types (legibility, ambiguous, incomplete, abbreviation and accuracy) and subtypes (drug name, strength, which eye, route and dispensed amount).
Results
Comparison of error rates in the two groups showed a 10-fold reduction in the overall error rate using FormularyScript (32.9%–3.5%, p<0.001). FormularyScripts were associated with statistically significant (p<0.001) decreases in the following error types: legibility (16.1%–0.1%), incomplete (16.1%–0.1%) and abbreviation (3.1%–0.3%). There was no statistically significant change in accuracy errors (0.8%–0.6%, p=0.21). Ambiguous errors increased with FormularyScripts (0.6%–2.5%, p<0.001), likely due to the introduction of new ways to make errors. Decreases were seen in all legibility, abbreviation and accuracy error subtypes, and four out of six incomplete error subtypes. There were statistically significant increases in both ambiguous error subtypes: which eye (0.3%–2.5%, p<0.001) and drug name (0.3%–0.6%, p=0.03).
Conclusions
In our study population, outpatient medication prescribing errors were common and primarily due to legibility and incomplete error types. A preprinted prescription form has the potential to decrease medication prescribing errors related to legibility, incomplete prescribing information and use of unacceptable abbreviations without changing the overall rate of accuracy errors. However, new error types can occur.
Article summary
Article focus
Little is known about the frequency and types of medication prescribing errors in developing countries, especially outpatient settings.
Computerised prescribing systems are usually not feasible in low resource settings; however, a preprinted form may be an alternative.
Key messages
Medication prescribing errors are common in outpatient ophthalmology clinics and are primarily due to legibility and incomplete information.
Preprinted prescription forms have the potential to decrease medication prescribing errors related to legibility, incomplete prescribing information and use of unacceptable abbreviations without changing the overall rate of accuracy errors, but new error types can be introduced.
Any new medication prescribing system needs to be carefully monitored for unintended consequences. Working closely with physicians and pharmacists to optimise design and providing adequate training for users are important considerations in minimising the introduction of new ways of making errors.
Strengths and limitations of this study
The main strengths of this study are that it demonstrates that a low cost alternative to computerised prescribing exists and is effective at reducing the most common types of medication prescribing errors.
Important limitations of this study are that it is a non-randomised study conducted at a single site, the subjective nature of determining and classifying error types such as legibility, the FormularyScript did not include all necessary medications and physicians were aware that the prescriptions were being analysed for prescribing errors.
doi:10.1136/bmjopen-2011-000539
PMCID: PMC3289984  PMID: 22365953
22.  Psychoemotional Features in Irritable Bowel Syndrome 
Journal of Medicine and Life  2012;5(4):398-409.
Objective. To delineate the psychological profile of individuals with irritable bowel syndrome (IBS).
Method. A triple questionnaire of 614 items (including psychological and medical ones) was given to 10192 respondents and the results were analyzed by means of Cronbach alpha and Chi square test, together with an ad-hoc designed method that implied ranking and outliers detecting.
Results and conclusions. Anxiety and depression are general psychological tendencies unspecifcally linked with IBS. Among the features with a relatively more specific correlation with IBS, tension has the strongest association, followed by the inclination to endure unacceptable situations, preoccupation for health, and susceptibility, and then by fear of failure and sense of demanding profession.
IBS individuals readily accept a subordinate position, which may be connected to their history of tyrannical parents, and also to their preoccupation for authority factors. The sense of being treated unfairly by the authority persons during the school years nuances this last feature. Some features that bring some nuances to this psychological portrait are: contemplative nature and analyzing tendency, preoccupation with health issues, a reserved, unsociable, and precautious nature, clinging to known circumstances.
Abbreviations: ChiSq = chi-square; OdRa = odds ratio; OdRaCL = OdRa confidence limits; ErrProb = probability of error; SS = statistically significant; CrA = Cronbach alpha; a / m = the calculations were done by taking into account the average/ maximal score; P / M = psychological / medical category; PaMm / PmMa / PmMm / PaMa = the calculations were done by taking into account the average score for the PsyCt and the maximal score for the MedCt / the maximal score for PsyCt and the average score for the MedCt / and the maximal score for both / and the average score for both; FD = functional dyspepsia; IBS = irritable bowel syndrome; IBSCt = IBS category; MedCt = medical category; PsyCt / PsyIt = psychological category / item.
PMCID: PMC3539839  PMID: 23346240
colonic functional disorders; personality inventory; psychological profile; psychological predisposition to disease
23.  Abbreviated neuropsychological assessment in schizophrenia 
The aim of this study was to identify the best subset of neuropsychological tests for prediction of several different aspects of functioning in a large (n = 236) sample of older people with schizophrenia. While the validity of abbreviated assessment methods has been examined before, there has never been a comparative study of the prediction of different elements of cognitive impairment, real-world outcomes, and performance-based measures of functional capacity. Scores on 10 different tests from a neuropsychological assessment battery were used to predict global neuropsychological (NP) performance (indexed with averaged scores or calculated general deficit scores), performance-based indices of everyday-living skills and social competence, and case-manager ratings of real-world functioning. Forward entry stepwise regression analyses were used to identify the best predictors for each of the outcomes measures. Then, the analyses were adjusted for estimated premorbid IQ, which reduced the magnitude, but not the structure, of the correlations. Substantial amounts (over 70%) of the variance in overall NP performance were accounted for by a limited number of NP tests. Considerable variance in measures of functional capacity was also accounted for by a limited number of tests. Different tests constituted the best predictor set for each outcome measure. A substantial proportion of the variance in several different NP and functional outcomes can be accounted for by a small number of NP tests that can be completed in a few minutes, although there is considerable unexplained variance. However, the abbreviated assessments that best predict different outcomes vary across outcomes. Future studies should determine whether responses to pharmacological and remediation treatments can be captured with brief assessments as well.
doi:10.1080/13803390802251386
PMCID: PMC2668735  PMID: 18720182
Schizophrenia; Disability; Neuropsychological assessment; Functional capacity; Abbreviated assessments
24.  MEDLARS Abbreviations for Medical Journal Titles 
The National Library of Medicine announces its adoption of the Anglo-American standard for the formulation of journal title abbreviations according to the American National Standard for the Abbreviation of Titles of Periodicals (1969), with individual words abbreviated, in turn, according to the International List of Periodical Title Word Abbreviations (1970).
The history of the activity of the specific Z39 Committee of USASI (now ANSI) concerned with journal title abbreviations is reviewed, covering the period from 1962 to the present. A history of the National Clearinghouse for Periodical Title Word Abbreviations and of the International List is also given.
Former NLM usage is compared with the forms of the present International List and examples show the major changes in NLM abbreviations.
The NLM Rules for Abbreviation of Periodical Titles as derived from the new standard are appended.
PMCID: PMC197609  PMID: 5146764
25.  Consenting Operative Orthopaedic Trauma Patients: Challenges and Solutions 
ISRN Surgery  2014;2014:354239.
Guidelines exist to obtain informed consent before any operative procedure. We completed an audit cycle starting with retrospective review of 50 orthopaedic trauma procedures (Phase 1 over three months to determine the quality of consenting documentation). The results were conveyed and adequate training of the staff was arranged according to guidelines from BOA, DoH, and GMC. Compliance in filling consent forms was then prospectively assessed on 50 consecutive trauma surgeries over further three months (Phase 2). Use of abbreviations was significantly reduced (P = 0.03) in Phase 2 (none) compared to 10 (20%) in Phase 1 with odds ratio of 0.04. Initially, allocation of patient's copy was dispensed in three (6% in Phase 1) cases compared to 100% in Phase 2, when appropriate. Senior doctors (registrars or consultant) filled most consent forms. However, 7 (14%) consent forms in Phase 1 and eleven (22%) in Phase 2 were signed by Core Surgical Trainees year 2, which reflects the difference in seniority amongst junior doctors. The requirement for blood transfusion was addressed in 40% of cases where relevant and 100% cases in Phase 2. Consenting patients for trauma surgery improved in Phase 2. Regular audit is essential to maintain expected national standards.
doi:10.1155/2014/354239
PMCID: PMC3933397  PMID: 24653843

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