Prevalence of resistance genes and antibiotic resistance profile among Stenotrophomonas maltophilia isolates from hospitalized patients in Iran

Stenotrophomonas maltophilia has emerged as an important nosocomial pathogen. Treatment of S. maltophilia infections is difficult due to increasing resistance to multiple antibacterial agents. In this 12-month cross-sectional study, from 2017 to 2018, 117 isolates were obtained from different clinical sources and identified by conventional biochemical methods. Antibiotic susceptibility tests were performed according to CLSI 2018. Minocycline disk (30 μg) and E-test strips for ceftazidime, trimethoprim-sulfamethoxazole and chloramphenicol were used. PCR confirmed isolates. The frequency of different classes of integrons (I, II) and resistance gene cassettes (sul1, sul2, dfrA1, dfrA5 and aadB) were determined by PCR. The results showed the highest frequency of resistance to chloramphenicol and ceftazidime with 32 cases (27.11%). Among strains, 12 cases (10.25%) were resistant to trimethoprim-sulfamethoxazole (the lowest frequency of resistance), while 19 (16.1%) isolates were resistant to minocycline. Frequency of sul1, int1, aadB, sul2, dfrA5 genes were 64 (55.08%), 26 (22.3 %), 18 (15.25%) and 17 (14.4%), 14 (11.86%), respectively. int2 and dfrA1 were not detected. Although we have not yet reached a high level of resistance to effective antibiotics such as trimethoprim-sulfamethoxazole, as these resistances can be carried by a plasmid, greater precision should be given to the administration of these antibiotics.

Real-world effectiveness, its predictors and onset of action of cholinesterase inhibitors and memantine in dementia: retrospective health record study

BACKGROUND

The efficacy of acetylcholinesterase inhibitors and memantine in the symptomatic treatment of Alzheimer's disease is well-established. Randomised trials have shown them to be associated with a reduction in the rate of cognitive decline.

AIMS

To investigate the real-world effectiveness of acetylcholinesterase inhibitors and memantine for dementia-causing diseases in the largest UK observational secondary care service data-set to date.

METHOD

We extracted mentions of relevant medications and cognitive testing (Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) scores) from de-identified patient records from two National Health Service (NHS) trusts. The 10-year changes in cognitive performance were modelled using a combination of generalised additive and linear mixed-effects modelling.

RESULTS

The initial decline in MMSE and MoCA scores occurs approximately 2 years before medication is initiated. Medication prescription stabilises cognitive performance for the ensuing 2-5 months. The effect is boosted in more cognitively impaired cases at the point of medication prescription and attenuated in those taking antipsychotics. Importantly, patients who are switched between agents at least once do not experience any beneficial cognitive effect from pharmacological treatment.

CONCLUSIONS

This study presents one of the largest real-world examination of the efficacy of acetylcholinesterase inhibitors and memantine for symptomatic treatment of dementia. We found evidence that 68% of individuals respond to treatment with a period of cognitive stabilisation before continuing their decline at the pre-treatment rate.

Plasma lipids and risk of aortic valve stenosis: a Mendelian randomization study

Background

Aortic valve stenosis is commonly considered a degenerative disorder with no recommended preventive intervention, with only valve replacement surgery or catheter intervention as treatment options.

Purpose

We sought to assess the causal association between exposure to lipid levels and risk of aortic stenosis.

Methods

Causality of association was assessed using two-sample Mendelian Randomization (MR) framework through different statistical methods. MR approach uses instrumental variable analysis to mimic the randomization process that underpins causal inference in clinical trials. It takes advantage of the naturally-occurring random allocation of alleles inherited by offspring from their parents during the formation of the zygote. We retrieved summary estimations of 157 genetic variants that have been shown to be associated with plasma lipid levels in the Global Lipids Genetics Consortium that included 188,577 participants, mostly European ancestry, and genetic association with aortic stenosis as the main outcome from a total of 432,173 participants in the UK Biobank. Secondary negative control outcomes included aortic regurgitation and mitral regurgitation.

Results

The odds ratio (OR) for developing aortic stenosis per unit increase in lipid parameter was 1.52 (95% confidence interval [CI], 1.22 to 1.90; per 0.98 mmol/L) for low-density lipoprotein (LDL) cholesterol, 1.03 (95% CI, 0.80 to 1.31; per 0.41 mmol/L) for high-density lipoprotein (HDL) cholesterol, and 1.38 (95% CI 0.92 to 2.07; per 1 mmol/L) for triglycerides. There was no evidence of a causal association between any of the lipid parameters and aortic or mitral regurgitation.

Conclusion

Lifelong exposure to high LDL-cholesterol increases the risk of symptomatic aortic stenosis, suggesting that LDL-lowering treatment may be effective in its prevention.

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation

Genetic susceptibility, elevated blood pressure and risk of atrial fibrillation

Background

Whether elevated blood pressure (BP) is a modifiable risk factor for atrial fibrillation (AF) is not established.

Purpose

We tested (1) whether the association between BP and risk of AF is causal, (2) whether it varies according to individual's genetic susceptibility for AF, and (3) the extent to which specific BP-lowering drugs are expected to reduce this risk.

Methods

First, causality of association was assessed through two-sample Mendelian Randomization (MR), using data from two independent genome-wide association studies that included a total of one million European population. Second, UK Biobank individual participant data of 329,237 participants at baseline was used to study the effect of BP on AF according to genetic susceptibility of developing AF. Third, a possible treatment effect with BP-lowering drug classes on AF risk was predicted through genetic variants in druggable genes that code proteins related to the function of each drug class. Estimated drug effects were compared with effects on incident coronary heart disease, for which direct trial evidence exists.

Results

The two-sample MR analysis indicated that on average each 10-mm Hg increment in systolic BP increased the risk of AF (odds ratio [OR]: 1.23 [1.11 to 1.36]). This association was replicated in the UK biobank using individual participant data. However, in a further genetic risk-stratified analysis, there was evidence for a linear gradient in the relative effects of systolic BP on AF; while there was no conclusive evidence of an effect in those with low genetic risk, a strong effect was observed among those with high genetic susceptibility for AF (Figure). The indirect comparison of predicted treatment effects using genetic proxies for three main drug classes (angiotensin-converting enzyme inhibitors, beta-blockers and calcium channel blockers) suggested similar average effects for prevention of atrial fibrillation and coronary heart disease.

Conclusions

The association between elevated BP and higher risk of AF is likely to be causal, suggesting that BP-lowering treatment may be effective in AF prevention. However, average effects masked clinically important variations, with a more pronounced effect in individuals with high genetic susceptibility.

Figure 1

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation

Evaluating the antibiotic resistance and frequency of adhesion markers among Escherichia coli isolated from type 2 diabetes patients with urinary tract infection and its association with common polymorphism of mannose-binding lectin gene

The present paper aims to determine the frequency and antibiotic resistance patterns of pathogenic bacteria, the virulence factor profile of Escherichia coli and mannose-binding lectin (MBL) gene polymorphism in individuals with diabetes mellitus (DM) and urinary tract infection (UTI). The population under study was 130 individuals with type 2 diabetes mellitus (T2DM) and UTI. The patients' clinical characteristics and urine and blood samples (5 mL) were collected. Antibiotic resistance was determined using a disc diffusion method, and the results were interpreted according to CLSI. The presence of virulence genes was detected by multiplex PCR. To detect the MBL gene polymorphism, PCR and restriction fragment length polymorphism methods were applied. The predominant Gram-negative and Gram-positive bacteria included E. coli and Streptococcus spp.viridans group, respectively. Women were more susceptible to the incidence of UTI than men. The E. coli isolates showed a high level of resistance to amoxicillin-clavulanic acid (87.35%), and nitrofurantoin and ceftizoxime were the most effective antimicrobial agents for E. coli. Cefotaxime and ceftizoxime were the most effective antimicrobial agents for Enterobacter spp., norfloxacin and ciprofloxacin were the most effective antimicrobial agents for Staphylococcus epidermidis and Staphylococcus saprophyticus. papGII (52.87%) and papEF (1.14%) had the highest and lowest frequency among examined genes in E. coli isolates, respectively. The GG genotype had the highest frequency among patients with T2DM and UTI. Results showed that the detection of E. coli in individuals with an AA genotype, codon 54 of the MBL gene, can play an important role in the molecular diagnosis and timely treatment of bacterial infections in individuals with diabetes.

Digital methods to enhance the usefulness of patient experience data in services for long-term conditions: the DEPEND mixed-methods study

Background

Collecting NHS patient experience data is critical to ensure the delivery of high-quality services. Data are obtained from multiple sources, including service-specific surveys and widely used generic surveys. There are concerns about the timeliness of feedback, that some groups of patients and carers do not give feedback and that free-text feedback may be useful but is difficult to analyse.

Objective

To understand how to improve the collection and usefulness of patient experience data in services for people with long-term conditions using digital data capture and improved analysis of comments.

Design

The DEPEND study is a mixed-methods study with four parts: qualitative research to explore the perspectives of patients, carers and staff; use of computer science text-analytics methods to analyse comments; co-design of new tools to improve data collection and usefulness; and implementation and process evaluation to assess use of the tools and any impacts.

Setting

Services for people with severe mental illness and musculoskeletal conditions at four sites as exemplars to reflect both mental health and physical long-terms conditions: an acute trust (site A), a mental health trust (site B) and two general practices (sites C1 and C2).

Participants

A total of 100 staff members with diverse roles in patient experience management, clinical practice and information technology; 59 patients and 21 carers participated in the qualitative research components.

Interventions

The tools comprised a digital survey completed using a tablet device (kiosk) or a pen and paper/online version; guidance and information for patients, carers and staff; text-mining programs; reporting templates; and a process for eliciting and recording verbal feedback in community mental health services.

Results

We found a lack of understanding and experience of the process of giving feedback. People wanted more meaningful and informal feedback to suit local contexts. Text mining enabled systematic analysis, although challenges remained, and qualitative analysis provided additional insights. All sites managed to collect feedback digitally; however, there was a perceived need for additional resources, and engagement varied. Observation indicated that patients were apprehensive about using kiosks but often would participate with support. The process for collecting and recording verbal feedback in mental health services made sense to participants, but was not successfully adopted, with staff workload and technical problems often highlighted as barriers. Staff thought that new methods were insightful, but observation did not reveal changes in services during the testing period.

Conclusions

The use of digital methods can produce some improvements in the collection and usefulness of feedback. Context and flexibility are important, and digital methods need to be complemented with alternative methods. Text mining can provide useful analysis for reporting on large data sets within large organisations, but qualitative analysis may be more useful for small data sets and in small organisations.

Limitations

New practices need time and support to be adopted and this study had limited resources and a limited testing time.

Future work

Further research is needed to improve text-analysis methods for routine use in services and to evaluate the impact of methods (digital and non-digital) on service improvement in varied contexts and among diverse patients and carers.

Funding

This project was funded by the NIHR Health Services and Delivery Research programme and will be published in full in Health Services and Delivery Research; Vol. 8, No. 28. See the NIHR Journals Library website for further project information.

P5313The association between coffee and caffeine consumption and renal function: insight from individual-level data, Mendelian randomization, and meta-analysis

Background

The reported relationship between coffee intake and renal function is poorly understood.

Purpose

By applying on two-sample Mendelian randomization (MR) and systematic review and meta-analysis we investigated the association between caffeine and coffee intake with prevalent CKD and markers of renal function.

Methods

For the individual data analysis we analysed the NHANES data on renal function markers and caffeine intake. MR was implemented by using summary-level data from genome-wide association studies conducted on coffee intake (N=91,462) and kidney function (N=133,413). Inverse variance weighted method (IVW), weighted median-based method, MR-Egger, MR-RAPS, MR-PRESSO were applied. Random effects models and generic inverse variance methods were used for the meta-analysis.

Results

Finally, we included the data of 18,436 participants, 6.9% had prevalent CKD (based on eGFR). Caffeine intake for general population was 131.1±1.1 mg. The % of pts. with CKD, by caffeine quartile was 16.6% in Q1 (lowest), 13.9% in Q2, 12.2% in Q3 and 11.0% in Q4 (p<0.001). After adjustment, for increasing quartiles for caffeine consumption, mean urine albumin, albumin-creatinine ratio and eGFR did not change significantly (p>0.234). In fully adjusted logistic regression models, there was no significant difference in chances of CKD prevalence (p-trend=0.745) (Table). In the same line, results of MR showed no impact of coffee intake on CKD (IVW=β: −0.0191, SE: 0.069, p=0.781) (Figure), on eGFR (overall= IVW= β: −0.0005, SE: 0.005, p=0.926) both in diabetic (IVW= β: −0.006, SE: 0.009, p=0.478), and non-diabetic patients (IVW= β: −6.772, SE: 0.006, p=0.991). Results from the meta-analysis indicted that coffee consumption was not significantly associated with CKD (OR: 0.85, 95% CI 0.71–1.02, p=0.090, n=6 studies, I2=0.32). These findings were robust in sensitivity analyses.

Levels of CKD markers across caffeine Qs Characteristics Quartiles of Caffeine p-value First Second Third Fourth Number of participants (n) 4609 4611 4608 4608 Log Urine Albumin (mg/L) 2.20±0.02 2.16±0.02 2.19±0.02 2.17±0.02 0.239 Serum Creatinine (mg/dL) 0.89±0.003 0.90±0.004 0.91±0.002 0.88±0.003 0.234 Log ACR (mg/g) 2.14±0.02 2.10±0.02 2.11±0.02 2.16±0.02 0.352 eGFR (ml/min/1.73m2) 91.2±0.7 92.8±0.4 90.2±0.5 89.6±0.3 0.415

MR on the impact of coffee intake on CKD

Conclusions

By implementing on different strategies we have highlighted no significant association between coffee consumption with renal function and chance of CKD.

Acknowledgement/Funding

None

Automatic mining of symptom severity from psychiatric evaluation notes

OBJECTIVES

As electronic mental health records become more widely available, several approaches have been suggested to automatically extract information from free-text narrative aiming to support epidemiological research and clinical decision-making. In this paper, we explore extraction of explicit mentions of symptom severity from initial psychiatric evaluation records. We use the data provided by the 2016 CEGS N-GRID NLP shared task Track 2, which contains 541 records manually annotated for symptom severity according to the Research Domain Criteria.

METHODS

We designed and implemented 3 automatic methods: a knowledge-driven approach relying on local lexicalized rules based on common syntactic patterns in text suggesting positive valence symptoms; a machine learning method using a neural network; and a hybrid approach combining the first 2 methods with a neural network.

RESULTS

The results on an unseen evaluation set of 216 psychiatric evaluation records showed a performance of 80.1% for the rule-based method, 73.3% for the machine-learning approach, and 72.0% for the hybrid one.

CONCLUSIONS

Although more work is needed to improve the accuracy, the results are encouraging and indicate that automated text mining methods can be used to classify mental health symptom severity from free text psychiatric notes to support epidemiological and clinical research.

Learning to identify Protected Health Information by integrating knowledge- and data-driven algorithms: A case study on psychiatric evaluation notes

De-identification of clinical narratives is one of the main obstacles to making healthcare free text available for research. In this paper we describe our experience in expanding and tailoring two existing tools as part of the 2016 CEGS N-GRID Shared Tasks Track 1, which evaluated de-identification methods on a set of psychiatric evaluation notes for up to 25 different types of Protected Health Information (PHI). The methods we used rely on machine learning on either a large or small feature space, with additional strategies, including two-pass tagging and multi-class models, which both proved to be beneficial. The results show that the integration of the proposed methods can identify Health Information Portability and Accountability Act (HIPAA) defined PHIs with overall F₁-scores of ∼90% and above. Yet, some classes (Profession, Organization) proved again to be challenging given the variability of expressions used to reference given information.

Exome-sequencing in a large population-based study reveals a rare Asn396Ser variant in the LIPG gene associated with depressive symptoms

Despite a substantial genetic component, efforts to identify common genetic variation underlying depression have largely been unsuccessful. In the current study we aimed to identify rare genetic variants that might have large effects on depression in the general population. Using high-coverage exome-sequencing, we studied the exonic variants in 1265 individuals from the Rotterdam study (RS), who were assessed for depressive symptoms. We identified a missense Asn396Ser mutation (rs77960347) in the endothelial lipase (LIPG) gene, occurring with an allele frequency of 1% in the general population, which was significantly associated with depressive symptoms (P-value=5.2 × 10^-08, β=7.2). Replication in three independent data sets (N=3612) confirmed the association of Asn396Ser (P-value=7.1 × 10^-03, β=2.55) with depressive symptoms. LIPG is predicted to have enzymatic function in steroid biosynthesis, cholesterol biosynthesis and thyroid hormone metabolic processes. The Asn396Ser variant is predicted to have a damaging effect on the function of LIPG. Within the discovery population, carriers also showed an increased burden of white matter lesions (P-value=3.3 × 10^-02) and a higher risk of Alzheimer's disease (odds ratio=2.01; P-value=2.8 × 10^-02) compared with the non-carriers. Together, these findings implicate the Asn396Ser variant of LIPG in the pathogenesis of depressive symptoms in the general population.

Intake of different types of dairy and its prospective association with risk of type 2 diabetes: The Rotterdam Study

BACKGROUND AND AIMS

The prevalence of type 2 diabetes (T2DM) is increasing. Several studies have suggested a beneficial effect of several major dairy nutrients on insulin production and sensitivity. Conversely, harmful effects have been suggested as well. This study aimed to investigate the impact of the full-range of dairy products and its association with incidence T2DM in Dutch adults aged ≥55 years participating in the Rotterdam Study.

METHODS AND RESULTS

Dairy intake was assessed with a validated FFQ, including total, skimmed, semi-skimmed, full-fat, fermented, and non-fermented dairy, and subclasses of these product groups. Verified prevalent and incident diabetes were documented. Cox proportional hazards regression and spline regression were used to analyse data, adjusting for age, sex, alcohol, smoking, education, physical activity, body mass index, intake of total energy, energy-adjusted meat, and energy-adjusted fish intake. Median total dairy intake was 398 g/day (IQR 259-559 g/day). Through 9.5 ± 4.1 years of follow-up, 393 cases of incident T2DM were reported. Cox and spline regression did not point towards associations of total dairy consumption, dairy consumption based on fat content, non-fermented or fermented dairy consumption, or individual dairy product consumption with incident T2DM. The HR for total dairy intake and T2DM was 0.93 (95% CI: 0.70-1.23) in the upper quartile (P-for trend 0.76).

CONCLUSIONS

This prospective cohort study did not point towards an association between dairy consumption and T2DM.

Association of circulating total bilirubin with the metabolic syndrome and type 2 diabetes: A systematic review and meta-analysis of observational evidence

OBJECTIVE

Emerging evidence suggests that bilirubin levels might be associated with the metabolic syndrome (MetS) and type 2 diabetes (T2D), although the nature of the association remains unclear.

DESIGN

This systematic review and meta-analysis investigated the relationship between total plasma bilirubin and the risk of MetS and T2D.

DATA SOURCES

Relevant studies were identified using five databases (Embase, Medline [Ovid], Web of Science, PubMed, Cochrane Central and Google Scholar), with the last search done on 21 October 2015. Study references were checked and authors contacted to identify additional studies.

STUDY SELECTION

Randomized controlled trials, and cohort, case-control and cross-sectional studies of adults examining the association between blood bilirubin levels and MetS and T2D were included, irrespective of language and date of publication. Abstract and full-text selection was done by two independent reviewers, with a third reviewer available in case of disagreement.

DATA EXTRACTION

Data were extracted by two independent reviewers using a predesigned data collection form.

MAIN OUTCOMES AND MEASURES

MetS and T2D.

METHODS

Summary estimates were obtained by random-effects meta-analysis.

RESULTS

Of the 2313 searched references, 16 observational studies (11 cross-sectional, two prospective, one that was both cross-sectional and prospective, two retrospective and one national survey) met our inclusion criteria. Overall, data were available for 175,911 non-overlapping participants, including 7414 MetS cases and 9406 T2D cases. In the meta-analysis of seven cross-sectional studies, the pooled odds ratio (95% confidence interval) for MetS in a comparison of extreme tertiles of serum bilirubin levels was 0.70 (95% CI: 0.62, 0.78), whereas no significant association was found for the pooled estimated relative risk between two prospective studies (0.57, 95% CI: 0.11, 2.94). The corresponding estimate was 0.77 (95% CI: 0.67, 0.87) for T2D from four cross-sectional studies.

CONCLUSION

The available evidence, mainly from cross-sectional studies, supports an inverse association of bilirubin levels with adverse metabolic outcomes. Large-scale prospective studies are now needed to establish whether bilirubin levels may be useful in the prevention of MetS and T2D.

The long-term risk of recognized and unrecognized myocardial infarction for depression in older men

BACKGROUND

The association between myocardial infarction (MI) and depression is well described. Yet, the underlying mechanisms are unclear and the contribution of psychological factors is uncertain. We aimed to determine the risk of recognized (RMI) and unrecognized (UMI) myocardial infections on depression, as both have a similar impact on cardiovascular health but differ in psychological epiphenomena.

METHOD

Participants of the Rotterdam Study, 1823 men aged ⩾55 years, were followed for the occurrence of depression. RMI and UMI were ascertained using electrocardiography and medical history at baseline. We determined the strength of the association of RMI and UMI with mortality, and we studied the relationship of RMI and UMI with depressive symptoms and the occurrence of major depression.

RESULTS

The risk of mortality was similar in men with RMI [adjusted hazard ratio (aHR) 1.71, 95% confidence interval (CI) 1.45-2.03] and UMI (aHR 1.58, 95% CI 1.27-1.97). Men with RMI had on average [unstandardized regression coefficient (B) 1.14, 95% CI 0.07-2.21] higher scores for depressive symptoms. By contrast, we found no clear association between UMI and depressive symptoms (B 0.55, 95% CI -0.51 to 1.62) in men. Analysis including occurrence of major depression as the outcome were consistent with the pattern of association.

CONCLUSION

The discrepant association of RMI and UMI with mortality compared to depression suggests that the psychological burden of having experienced an MI contributes to the long-term risk of depression.

The role of global and regional DNA methylation and histone modifications in glycemic traits and type 2 diabetes: A systematic review

BACKGROUND

New evidence suggests the potential involvement of epigenetic mechanisms in type 2 diabetes (T2D) as a crucial interface between the effects of genetic predisposition and environmental influences.

AIM

To systematically review studies investigating the association between epigenetic marks (DNA methylation and histone modifications) with T2D and glycemic traits (glucose and insulin levels, insulin resistance measured by HOMA-IR).

METHOD AND RESULTS

Six bibliographic databases (Embase.com, Medline (Ovid), Web-of-Science, PubMed, Cochrane Central and Google Scholar) were screened until 28th August 2015. We included randomized controlled trials, cohort, case-control and cross-sectional studies in humans that examined the association between epigenetic marks (global, candidate or genome-wide methylation of DNA and histone modifications) with T2D, glucose and insulin levels and insulin metabolism. Of the initially identified 3879 references, 53 articles, based on 47 unique studies met our inclusion criteria. Overall, data were available on 10,823 participants, with a total of 3358 T2D cases. There was no consistent evidence for an association between global DNA-methylation with T2D, glucose, insulin and insulin resistance. The studies reported epigenetic regulation of several candidate genes for diabetes susceptibility in blood cells, muscle, adipose tissue and placenta to be related with T2D without any general overlap between them. Histone modifications in relation to T2D were reported only in 3 observational studies.

CONCLUSIONS AND RELEVANCE

Current evidence supports an association between epigenetic marks and T2D. However, overall evidence is limited, highlighting the need for further larger-scale and prospective investigations to establish whether epigenetic marks may influence the risk of developing T2D.

Using local lexicalized rules to identify heart disease risk factors in clinical notes

Heart disease is the leading cause of death globally and a significant part of the human population lives with it. A number of risk factors have been recognized as contributing to the disease, including obesity, coronary artery disease (CAD), hypertension, hyperlipidemia, diabetes, smoking, and family history of premature CAD. This paper describes and evaluates a methodology to extract mentions of such risk factors from diabetic clinical notes, which was a task of the i2b2/UTHealth 2014 Challenge in Natural Language Processing for Clinical Data. The methodology is knowledge-driven and the system implements local lexicalized rules (based on syntactical patterns observed in notes) combined with manually constructed dictionaries that characterize the domain. A part of the task was also to detect the time interval in which the risk factors were present in a patient. The system was applied to an evaluation set of 514 unseen notes and achieved a micro-average F-score of 88% (with 86% precision and 90% recall). While the identification of CAD family history, medication and some of the related disease factors (e.g. hypertension, diabetes, hyperlipidemia) showed quite good results, the identification of CAD-specific indicators proved to be more challenging (F-score of 74%). Overall, the results are encouraging and suggested that automated text mining methods can be used to process clinical notes to identify risk factors and monitor progression of heart disease on a large-scale, providing necessary data for clinical and epidemiological studies.

Role of vitamin D in flare ups of rheumatoid arthritis

INTRODUCTION

Rheumatoid arthritis (RA) is one of the most prevalent autoimmune diseases worldwide. Some researchers have suggested that the serum vitamin D (Vit D) level may relate to disease activity. The current study was designed to identify the correlation between vitamin D prescription and prevention of relapses in rheumatoid arthritis.

PATIENTS AND METHOD

A double blinded, randomized controlled trial study was performed using 80 RA patients. RA was controlled and patients were in remission during the past 2 months. Serum level of Vit D in the studied patients was below 30 ng/dl. Patients were randomly allocated to receive Vit D or placebo. In the 6-month follow-up period, the Disease Activity Score 28 (DAS28) was used in case of relapses as an index of RA activity to compare the two groups.

RESULTS

The flare rate was not different between two groups (p > 0.05). The odds ratio of the rate of decline in patients of the trial group compared with the control group was 1.17 (not significant; p > 0.05). The mean DAS28 between the two patient groups was not significant (p > 0.05).

CONCLUSION

A low Vit D level was not identified to be a risk factor for RA severity or flare ups; however, although not statistically significant, Vit D treatment might be clinically effective. Further studies are needed with more emphasis on the issue of cost effectiveness and clinical importance to provide more information.

A genetic variant in SLC6A20 is associated with Type 2 diabetes in white-European and Chinese populations

AIMS

To investigate whether polymorphisms in SLC6A20 are associated with susceptibility to Type 2 diabetes.

METHODS

In the Rotterdam Study, a prospective, population-based cohort (n = 5974), 22 tagging polymorphisms with minor allele frequencies>0.05 across SLC6A20 were studied. Replication studies were performed in an independent Dutch case-control study (DiaGene-Rotterdam Study 2 n = 3133), and in a Chinese Han case-control population (n = 2279). A meta-analysis of the results was performed.

RESULTS

In the Rotterdam study, the minor alleles of rs13062383, rs10461016 and rs2286489 increased the risk of Type 2 diabetes (hazard ratio 1.37, 95% CI 1.15-1.63, hazard ratio 1.30 95% CI 1.09-1.54 and hazard ratio 1.20, 95% CI 1.07-1.35, respectively). In the DiaGene/Rotterdam Study 2, the A allele of rs13062383 increased the risk of Type 2 diabetes (odds ratio 1.45, 95% CI 1.19-1.76). In the Chinese Han study, the rs13062383 A allele also increased the risk of Type 2 diabetes (odds ratio 1.21, 95% CI 1.03-1.42). Meta-analysis showed a highly significant association of rs13062383 with Type 2 diabetes (odds ratio 1.35, 95% CI 1.21-1.47; P = 3.3 × 10⁻⁸).

CONCLUSIONS

In conclusion, rs13062383 in SLC6A20 increased the susceptibility to Type 2 diabetes in populations with different genetic backgrounds.

Sex-specific effects of naturally occurring variants in the dopamine receptor D2 locus on insulin secretion and type 2 diabetes susceptibility

AIMS

Modulation of dopamine receptor D2 (DRD2) activity affects insulin secretion in both rodents and isolated pancreatic β-cells. We hypothesized that single nucleotide polymorphisms in the DRD2/ANKK1 locus may affect susceptibility to type 2 diabetes in humans.

METHODS

Four potentially functional variants in the coding region of the DRD2/ANKK1 locus (rs1079597, rs6275, rs6277, rs1800497) were genotyped and analysed for type 2 diabetes susceptibility in up to 25 000 people (8148 with type 2 diabetes and 17687 control subjects) from two large independent Dutch cohorts and one Danish cohort. In addition, 340 Dutch subjects underwent a 2-h hyperglycaemic clamp to investigate insulin secretion. Since sexual dimorphic associations related to DRD2 polymorphisms have been previously reported, we also performed a gender-stratified analysis.

RESULTS

rs1800497 at the DRD2/ANKK1 locus was associated with a significantly increased risk for type 2 diabetes in women (odds ratio 1.14 (1.06-1.23); P = 4.1*10⁴) but not in men (odds ratio 1.00 (95% CI 0.93-1.07); P = 0.92) or the combined group. Although rs1800497 was not associated with insulin secretion, we did find another single nucleotide polymorphism in this locus, rs6275, to be associated with increased first-phase glucose-stimulated insulin secretion in women (P = 5.5*10⁴) but again not in men (P = 0.34).

CONCLUSION

The present data identify DRD2/ANKK1 as a potential sex-specific type 2 diabetes susceptibility gene.

Dissecting the relationship between high-sensitivity serum C-reactive protein and increased fracture risk: the Rotterdam Study

Serum high-sensitivity C-reactive protein (CRP) is an inflammatory biomarker. We investigated the relationship between CRP and bone health in the Rotterdam Study. Serum high-sensitivity CRP was associated with fracture risk and lower femoral neck bending strength. Mendelian randomization analyses did not yield evidence for this relationship being causal.

INTRODUCTION

Inflammatory diseases are associated with bone pathology, reflected in a higher fracture risk. Serum high-sensitivity CRP is an inflammatory biomarker. We investigated the relationship between CRP and bone mineral density (BMD), hip bone geometry, and incident fractures in the Rotterdam Study, a prospective population-based cohort.

METHODS

At baseline, serum high-sensitivity CRP was measured. A weighted genetic risk score was compiled for CRP based on published studies (29 polymorphisms; Illumina HumanHap550 Beadchip genotyping and HapMap imputation). Regression models were reported per standard deviation increase in CRP adjusted for sex, age, and BMI. Complete data was available for 6,386 participants, of whom 1,561 persons sustained a fracture (mean follow-up, 11.6 years).

RESULTS

CRP was associated with a risk for any type of fracture [hazard ratio (HR) = 1.06; 95 % confidence interval (CI), 1.02-1.11], hip fractures (HR = 1.09; 1.02-1.17) and vertebral fractures [odds ratio (OR) = 1.34; 1.14-1.58]. An inverse relationship between CRP levels and section modulus (-0.011 cm(3); -0.020 to -0.003 cm(3)) was observed. The combined genetic risk score of CRP single nucleotide polymorphisms (SNPs) was associated with serum CRP levels (p = 9 × 10(-56)), but not with fracture risk (HR = 1.00; 0.99-1.00; p = 0.23).

CONCLUSIONS

Serum high-sensitivity CRP is associated with fracture risk and lower bending strength. Mendelian randomization analyses did not yield evidence for this relationship being causal. Future studies might reveal what factors truly underlie the relationship between CRP and fracture risk.

Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives

OBJECTIVE

Identification of clinical events (eg, problems, tests, treatments) and associated temporal expressions (eg, dates and times) are key tasks in extracting and managing data from electronic health records. As part of the i2b2 2012 Natural Language Processing for Clinical Data challenge, we developed and evaluated a system to automatically extract temporal expressions and events from clinical narratives. The extracted temporal expressions were additionally normalized by assigning type, value, and modifier.

MATERIALS AND METHODS

The system combines rule-based and machine learning approaches that rely on morphological, lexical, syntactic, semantic, and domain-specific features. Rule-based components were designed to handle the recognition and normalization of temporal expressions, while conditional random fields models were trained for event and temporal recognition.

RESULTS

The system achieved micro F scores of 90% for the extraction of temporal expressions and 87% for clinical event extraction. The normalization component for temporal expressions achieved accuracies of 84.73% (expression's type), 70.44% (value), and 82.75% (modifier).

DISCUSSION

Compared to the initial agreement between human annotators (87-89%), the system provided comparable performance for both event and temporal expression mining. While (lenient) identification of such mentions is achievable, finding the exact boundaries proved challenging.

CONCLUSIONS

The system provides a state-of-the-art method that can be used to support automated identification of mentions of clinical events and temporal expressions in narratives either to support the manual review process or as a part of a large-scale processing of electronic health databases.

Topic categorisation of statements in suicide notes with integrated rules and machine learning

We describe and evaluate an automated approach used as part of the i2b2 2011 challenge to identify and categorise statements in suicide notes into one of 15 topics, including Love, Guilt, Thankfulness, Hopelessness and Instructions. The approach combines a set of lexico-syntactic rules with a set of models derived by machine learning from a training dataset. The machine learning models rely on named entities, lexical, lexico-semantic and presentation features, as well as the rules that are applicable to a given statement. On a testing set of 300 suicide notes, the approach showed the overall best micro F-measure of up to 53.36%. The best precision achieved was 67.17% when only rules are used, whereas best recall of 50.57% was with integrated rules and machine learning. While some topics (eg, Sorrow, Anger, Blame) prove challenging, the performance for relatively frequent (eg, Love) and well-scoped categories (eg, Thankfulness) was comparatively higher (precision between 68% and 79%), suggesting that automated text mining approaches can be effective in topic categorisation of suicide notes.

Alternative treatment of ovarian cysts with Tribulus terrestris extract: a rat model

Tribulus terrestris has long been used in traditional medicine to treat impotency and improve sexual functions in man. The aim of this study was to evaluate the efficiency of T. terrestris extract in the treatment of polycystic ovary (PCO) in Wistar rat. Estradiol valerate was injected to 15 mature Wistar rats to induce PCO. Rats were randomly divided into three groups (control, low-dose and high-dose groups) of five each and received 0, 5 and 10 mg of T. terrestris extract, respectively.Treatments began on days 50 and 61 after estradiol injection; at the same time, vaginal smear was prepared. The ovaries were removed on day 62, and histological sections were prepared accordingly. The number and diameter of corpora lutea, thickness of the theca interna layer and the number of all follicles were evaluated in both ovaries. In comparison with the control group, the number of corpora lutea and primary and secondary follicles significantly increased following T. terrestris treatment; however, the number of ovarian cysts significantly decreased. It can be concluded that T. terrestris have a luteinizing effect on ovarian cysts, which may relate to its gonadotropin-like activity; also, a high dose of the extract can efficiently remove ovarian cysts and resume ovarian activity.

Association of an APOC3 promoter variant with type 2 diabetes risk and need for insulin treatment in lean persons

AIMS/HYPOTHESIS

An APOC3 promoter haplotype has been previously associated with type 1 diabetes. In this population-based study, we investigated whether APOC3 polymorphisms increase type 2 diabetes risk and need for insulin treatment in lean participants.

METHODS

In the Rotterdam Study, a population-based prospective cohort (n = 7,983), Cox and logistic regression models were used to analyse the associations and interactive effects of APOC3 promoter variants (-482C > T, -455T > C) and BMI on type 2 diabetes risk and insulin treatment. Analyses were followed by replication in an independent case-control sample (1,817 cases, 2,292 controls) and meta-analysis.

RESULTS

In lean participants, the -482T allele was associated with increased risk of prevalent and incident type 2 diabetes: OR -482CT 1.47 (95% CI 1.13-1.92), -482TT 1.40 (95% CI 0.83-2.35), p = 0.009 for trend; HR -482CT 1.35 (95% CI 0.96-1.89), -482TT 1.68 (95% CI 0.91-3.1), p = 0.03 for trend, respectively. These results were confirmed by replication. Meta-analysis was highly significant (-482T meta-analysis p = 1.1 × 10(-4)). A borderline significant interaction was observed for insulin use among participants with type 2 diabetes (-482CT*BMI p = 0.06, -455TC*BMI p = 0.02).

CONCLUSIONS/INTERPRETATION

At a population-based level, the influence of APOC3 promoter variants on type 2 diabetes risk varies with the level of adiposity. Lean carriers of the -482T allele had increased type 2 diabetes risk, while such an effect was not observed in overweight participants. Conversely, in overweight participants the -455C allele seemed protective against type 2 diabetes. The interaction of the variants with need for insulin treatment may indicate beta cell involvement in lean participants. Our findings suggest overlap in the genetic backgrounds of type 1 diabetes and type 2 diabetes in lean patients.

A clinical and molecular genetic study of 112 Iranian families with primary microcephaly

BACKGROUND

Primary microcephaly (MCPH) is a genetically heterogeneous disorder showing an autosomal recessive mode of inheritance. Affected individuals present with head circumferences more than three SDs below the age- and sex-matched population mean, associated with mild to severe mental retardation. Five genes (MCPH1, CDK5RAP2, ASPM, CENPJ, STIL) and two genomic loci, MCPH2 and MCPH4, have been identified so far.

METHODS AND RESULTS

In this study, we investigated all seven MCPH loci in patients with primary microcephaly from 112 Consanguineous Iranian families. In addition to a thorough clinical characterisation, karyotype analyses were performed for all patients. For Homozygosity mapping, microsatellite markers were selected for each locus and used for genotyping. Our investigation enabled us to detect homozygosity at MCPH1 (Microcephalin) in eight families, at MCPH5 (ASPM) in thirtheen families. Three families showed homozygosity at MCPH2 and five at MCPH6 (CENPJ), and two families were linked to MCPH7 (STIL). The remaining 81 families were not linked to any of the seven known loci. Subsequent sequencing revealed eight, 10 and one novel mutations in Microcephalin, ASPM and CENPJ, respectively. In some families, additional features such as short stature, seizures or congenital hearing loss were observed in the microcephalic patient, which widens the spectrum of clinical manifestations of mutations in known microcephaly genes.

CONCLUSION

Our results show that the molecular basis of microcephaly is heterogeneous; thus, the Iranian population may provide a unique source for the identification of further genes underlying this disorder.

Sacroiliitis as an initial presentation of acute lymphoblastic leukaemia

A 17-year-old male was admitted to the hospital because of fever, low back pain and knee pain which had started a couple of months ago. Pelvic CT-scan confirmed left sacroiliitis. Complete blood count revealed pancytopenia.A bone marrow biopsy and aspiration was performed under local anaesthesia. The pathologist reported Acute Lymphoblastic Leukaemia. The reported patient is the first case of acute lymphoblastic leukaemia, accompanied by sacroiliitis.

Causes and anatomical site of blindness and severe visual loss in Isfahan, Islamic Republic of Iran

This study in 2005 evaluated the causes and major anatomical site of blindness and severe visual loss at a school for blind children in Isfahan province, Islamic Republic of Iran. All 211 students were examined according to the modified WHO/PBL eye examination record: 70.4% were blind, 24.3% had severe visual loss and 5.3% were visually impaired. The major causes of abnormality were hereditary factors (42.7%), prenatal/neonatal (18.5%) and unknown etiology (35.5%). The main sites of abnormality were the retina (62.6%), whole globe (17.5%), lens (7.1%) and optic nerve (7.1%). A high proportion of parents were in a consanguineous marriage (49.2%). The pattern of blindness in Isfahan encompasses characteristics of both developed and developing countries.

An RBP4 promoter polymorphism increases risk of type 2 diabetes

AIMS/HYPOTHESIS

Retinol-binding protein 4 (RBP4), originally known for retinol transport, was recently identified as an adipokine affecting insulin resistance. The RBP4 -803GA promoter polymorphism influences binding of hepatic nuclear factor 1alpha and is associated with type 2 diabetes in case-control studies. We hypothesised that the RBP4 -803GA polymorphism increases type 2 diabetes risk at a population-based level. In addition, information on retinol intake and plasma vitamin A levels enabled us to explore the possible underlying mechanism.

METHODS

In the Rotterdam Study, a prospective, population-based, follow-up study, the -803GA polymorphism was genotyped. In Cox proportional hazards models, associations of the -803GA polymorphism and retinol intake with type 2 diabetes risk were examined. Moreover, the interaction of the polymorphism with retinol intake on type 2 diabetes risk was assessed. In a subgroup of participants the association of the polymorphism and vitamin A plasma levels was investigated.

RESULTS

Homozygous carriers of the -803A allele had increased risk of type 2 diabetes (HR 1.83; 95% CI 1.26-2.66). Retinol intake was not associated with type 2 diabetes risk and showed no interaction with the RBP4 -803GA polymorphism. Furthermore, there was no significant association of the polymorphism with plasma vitamin A levels.

CONCLUSIONS/INTERPRETATION

Our results provide evidence that homozygosity for the RBP4 -803A allele is associated with increased risk of type 2 diabetes in the Rotterdam population. This relationship was not clearly explained by retinol intake and vitamin A plasma levels. Therefore, we cannot differentiate between a retinol-dependent or -independent mechanism of this RBP4 variant.

Effect of silymarin on metabolic factors of food-restricted over conditioned Wistar rats

This study was conducted to evaluate the changes in serum metabolic factors of over conditioned pregnant rats treated with silymarin in food restriction condition. Sixty pregnant Wistar rats were divided into five equal groups. All rats received high energy diet before treatments. Control group were fed ad libitum (Non-FR). Rats in other groups received 50% of the food intake of Non-FR group and served as food-restricted (FR) groups. Three of five FR groups received 150, 200 and 400 mg kg(-1) silymarin, respectively (FR-150, 200, 400). Another FR group (FR-Con) and the Non-FR group did not receive any silymarin. Glucose, triglyceride, LDL and HDL cholesterol, total cholesterol, thyroid hormones and cortisol were measured in serum. All factors were significantly different between groups except free-T4 and T4. Serum glucose concentrations in FR-150 and 200 and Non-FR groups were lower than FR-Con and FR-400. Silymarin significantly increased serum triglycerides, LDL cholesterol and cholesterol contents in FR groups. The highest levels of these factors were noted in 200 mg silymarin-treated group. HDL cholesterol was highest in FR-Con; meanwhile FR-200 group had the lowest HDL cholesterol. Serum cortisol decreased in treated and untreated FR groups except FR-150 group. Free-T3 and T3 concentrations in FR-400 and FR-Con groups were higher than the other silymarin treated groups. In conclusion our results indicate that 200 mg kg(-1) of silymarin in Wistar rats is the best dosage to achieve metabolic benefits. Silymarin has positive effects on lipid metabolism and can modulate serum triglyceride and cholesterol concentrations in food restriction condition. Also, the present findings suggest that silymarin under food restriction situation exerts a decreasing effect upon peripheral conversion of T4 to T3.

The relationship of plasma levels of pyridostigmine to clinical effect in patients with myasthenia gravis

The relationship between plasma levels of pyridostigmine to clinical evaluation of muscle power was examined in nine patients with myasthenia gravis during treatment with pyridostigmine in doses of 60 to 1040 mg daily. Five of the nine subjects demonstrated a trend towards a positive correlation, but in only two of them was this statistically significant at p < 0.05. In addition, the presence or absence of a possible correlation between muscle power and plasma concentration was not related to the duration of the disease, additional prednisolone therapy or thymectomy.

The effect of neostigmine on pyridostigmine bioavailability in myasthenic patients after oral administration

Plasma levels of pyridostigmine and/or neostigmine were monitored in 8 myasthenic patients who were stabilised on oral pyridostigmine bromide only (60-540 mg per day), and in 9 patients who were stabilised on both neostigmine bromide (15-480 mg per day) and pyridostigmine bromide (240-1080 mg per day), over a period of 12 hr (8.00 a.m. - 8.00 p.m.). Maximum plasma concentrations of pyridostigmine in the first and second groups of patients ranged from 12.4 to 64.5 ng per ml and 15.3 to 144.0 ng per ml respectively. Despite this general intersubject variation in bioavailability of pyridostigmine, there was a direct relationship between the area under plasma concentration-time curves (AUC) and total daily dose in the first group of myasthenic patients (r = 0.95). However, no such observation was noticed neither in all 17 patients nor in the 9 patients who were treated with both drugs. Neostigmine was detected in only one of the second group of patients. It was suggested that neostigmine might interfere with the bioavailability of pyridostigmine when both drugs are concurrently administered orally.

Kinetics and metabolism of intramuscular neostigmine in myasthenia gravis

Neostigmine kinetics and metabolism were studied after intracellular administration to 8 patients with myasthenia gravis. The plasma neostigmine level declined monoexponentially from 21 +/- 2 to 9 +/- 1 ng/ml between 30 and 120 min. The data were interpreted in terms of a 1-compartment model. Estimates of plasma half-life (t1/2) ranged from 51.1 to 90.5 min; apparent volume of distribution varied from 32.0 to 60.6 1; and total body clearance from 434 to 549 ml/min. Approximately 80% of the drug was eliminated in urine within 24 hr either as unchanged neostigmine or its metabolites. Approximately 50% of the dose was eliminated as the unchanged drug, 15% as 3-hydroxyphenyltrimethylammonium, and 15% as other unidentified metabolites. The neostigmine t1/2, based on the urinary excretion of the unchanged drug, ranged from 90.2 to 118.7 min. It was concluded that neostigmine was eliminated by renal and extrarenal mechanisms.

The simultaneous monitoring of plasma levels of neostigmine and pyridostigmine in man

The synthesis of a series of pyridostigmine analogues wa reported. From these analogues N,N-dipropylcarbamoyloxy-1-methylpyridinium bromide was considered the most suitable compound for use as a common internal marker for the simultaneous determination of neostigmine and pyridostigmine in human plasma. The assay involved a preliminary ion-pair extraction of the drugs and the internal marker from plasma using potassium-iodide glycine buffer. The extract was analysed by a GC system (10% OV-17 on chromosorb W-AW, 100-120 mesh) linked to a nitrogensensitive detector. The calibration graphs of neostigmine and pyridostigmine were linear and reproducible over the range 5 ng to 100 ng per ml in 3 ml plasma samples. This assay procedure has been used to monitor simultaneously the plasma levels of neostigmine (4.7 to 33 ng per ml) and pyridostigmine (2.7 to 18.6 ng per ml) of a myasthenic patient over a period of twelve hours with repeated dosing of neostigmine bromide (30 mg) and pyridostigmine bromide (60 mg).