Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Detection and validated quantification of 21 benzodiazepines and 3 "z-drugs" in human hair by LC-MS/MS

A method for detection and quantification of 21 benzodiazepines and the pharmacologically related "z-drugs" in human hair samples was developed and fully validated using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). After methanolic and methanolic/aqueous extraction, the analytes were separated using two different LC-MS systems (AB Sciex 3200 QTRAP and AB Sciex 5500 QTRAP). Separation columns, mobile phases and MS modes for both systems were: Phenomenex Kinetex, 2.6μm, 50/2.1; 5mM ammonium formate buffer pH 3.5/methanol, total flow 0.75mL/min; electrospray ionization (ESI), multiple reaction monitoring (MRM), information dependent acquisition (IDA), enhanced product ion scan (EPI). The assays were found to be selective for the tested compounds (alprazolam, 7-aminoclonazepam, 7-aminoflunitrazepam, bromazepam, chlordiazepoxide, clonazepam, N-desalkylflurazepam, diazepam, flunitrazepam, flurazepam, alpha-hydroxymidazolam, lorazepam, lormetazepam, midazolam, nitrazepam, nordazepam, oxazepam, phenazepam, prazepam, temazepam, triazolam, zaleplon, zolpidem and zopiclone), all validation criteria were in the required ranges according to international guidelines, except for bromazepam. Matrix effects, and process efficiencies were in the acceptable ranges evaluated using the post-extraction addition approach. Lower limits of quantification were between 0.6 and 16pg/mg of hair. The LC-MS/MS assay has proven to be applicable for determination of the studied analytes in human hair in numerous authentic cases (n=175)

Detection and validated quantification of the phosphodiesterase type 5 inhibitors sildenafil, vardenafil, tadalafil, and 2 of their metabolites in human blood plasma by LC-MS/MS-application to forensic and therapeutic drug monitoring cases

INTRODUCTION: Phosphodiesterase type 5 inhibitors such as sildenafil, vardenafil, and tadalafil are a class of drugs used primarily in the treatment of erectile dysfunction. Sildenafil and tadalafil are also approved for the treatment of pulmonary hypertension. The aim of this study was to develop and validate a procedure for the detection and quantification of these 3 drugs and some of their metabolites in human blood plasma. METHODS: After liquid-liquid extraction of 0.5 mL of blood plasma using diethyl ether-ethyl acetate (1:1), the analytes sildenafil, norsildenafil, vardenafil, norvardenafil, and tadalafil were separated using a Shimadzu Prominence High-Performance Liquid Chromatography System (C18 separation column, gradient elution, and a total flow of 0.5 mL/min). They were detected using an AB Sciex 3200 Q-Trap LC-MS-MS System (electrospray ionization and multiple reaction monitoring mode). The method was fully validated according to international guidelines. RESULTS: The assay was found to be selective for the tested compounds. It was linear from 5 to 1000 ng/mL for sildenafil, from 2 to 700 ng/mL for norsildenafil, from 0.5 to 350 ng/mL for vardenafil, from 0.5 to 200 ng/mL for norvardenafil, and from 5 to 1000 ng/mL for tadalafil. The recoveries were generally more than 50%. Matrix effects were not observed. Accuracy, repeatability, and intermediate precision were within the required limits (<15% or <20% near the limit of quantification). No instability was observed after repeated freezing and thawing or in processed samples. CONCLUSIONS: A liquid chromatography-tandem mass spectrometry assay for the determination of sildenafil, norsildenafil, vardenafil, norvardenafil, and tadalafil in human blood plasma was developed and validated. It has proven to be selective, linear, accurate, and precise for all studied drugs. The method has also proven to be applicable for forensic cases and for therapeutic drug monitoring

Metabolite to parent drug concentration ratios in hair for the differentiation of tramadol intake from external contamination and passive exposure

Tramadol was found in a man's hair sample during an abstinence test necessary to regain his driving license. The suspect denied having taken tramadol claiming external contamination as the reason for the positive result, as he was working in a tramadol production company. Nevertheless, low concentrations of both major metabolites, N-desmethyltramadol (NDMT) and O-desmethyltramadol (ODMT), were found in hair (180 and 6 pg/mg hair, respectively). To assess this case, tramadol concentrations and metabolite to parent drug concentration ratios were determined in hair samples of 75 patients taking tramadol and of eight employees working in the production and laboratory site of the same company. Additionally, wash water used for decontaminating hair was analyzed for both groups, patients and employees. Analysis of hair sample extracts was performed by LC-MS/MS using multiple reaction monitoring (MRM), information dependent acquisition (IDA) and enhanced product ion scan (EPI). High variations of metabolite to parent drug concentration ratios in hair samples of patients were observed. Differences in NDMT and ODMT to tramadol concentration ratios were found when comparing the cohort of patients to employees. The suspect could be included in the cohort of employees considering the ODMT to tramadol concentration ratio in hair and tramadol concentration ratio in wash water versus hair. Metabolite to parent drug concentration ratios of hair samples may represent a helpful tool for the differentiation of tramadol intake versus external contamination. Ratios of tramadol concentrations in wash water versus the subjects' hair may provide additional information for case assessments

Group hypnotherapy versus group relaxation for smoking cessation: an RCT study protocol

BACKGROUND: A significant number of smokers would like to stop smoking. Despite the demonstrated efficacy of pharmacological smoking cessation treatments, many smokers are unwilling to use them; however, they are inclined to try alternative methods. Hypnosis has a long-standing reputation in smoking cessation therapy, but its efficacy has not been scientifically proven. We designed this randomised controlled trial to evaluate the effects of group hypnosis as a method for smoking cessation, and we will compare the results of group hypnosis with group relaxation. METHODS/DESIGN: This is a randomised controlled trial (RCT) to compare the efficacy of a single session of hypnosis with that of relaxation performed in groups of 8-15 smokers. We intend to include at least 220 participants in our trial. The inclusion criteria include smoking at least 5 cigarettes per day, not using other cessation methods and being willing to quit smoking. The intervention is performed by a trained hypnotist/relaxation therapist. Both groups first receive 40 min of mental preparation that is based on motivational interviewing. Then, a state of deep relaxation is induced in the hypnosis condition, and superficial relaxation is induced in the control condition. Suggestions are made in the hypnosis condition that aim to switch the mental self-image of the participants from that of smokers to that of non-smokers. Each intervention lasts for 40 min. The participants also complete questionnaires that assess their smoking status and symptoms of depression and anxiety at baseline, 2 weeks and 6 months post-intervention. In addition, saliva samples are collected to assess cotinine levels at baseline and at 6 months post-intervention. We also assess nicotine withdrawal symptoms at 2 weeks post-intervention. DISCUSSION: To the best of our knowledge, this RCT is the first to test the efficacy of group hypnosis versus group relaxation. Issues requiring discussion in the outcome paper include the lack of standardisation of hypnotic interventions in smoking cessation, the debriefing of the participants, the effects of group dynamics and the reasons for dropouts. TRIAL REGISTRATION: Current Controlled Trials, ISRCTN72839675