Takshan/R1 huggingface dataset:
Non-retrieval of inferior vena cava filters as a patient safety concern: evaluation of a new process improvement project to increase retrieval rates in a vascular and interventional radiology clinic.

Background: Retrieval of inferior vena cava filters (IVCFs) is important to decrease the long-term risk of complications associated with indwelling devices. Our hospital experienced low retrieval rates and implemented a low-cost intervention and evaluation for quality improvement. The working hypothesis was that a simple, mailed letter intervention could increase retrieval rates by increasing patient and primary care provider knowledge of the need for retrieval. Methods: For all prospective patients who received a retrievable IVCF during the intervention period from January 1, 2014 to February 29, 2016, patients and their primary care providers were mailed letters encouraging contact with the clinic for evaluation of eligibility for retrieval. The main outcome was retrieval of the IVCF if clinically indicated with a secondary outcome of time-to-retrieval. A pre-intervention control group from October 1, 2011 to December 31, 2013 was used to evaluate the impact of the intervention. Competing risks, time-to-event analysis was used to compare the pre- and post-intervention period retrieval rates correcting for patients who died during follow-up. Results: Between the pre- and post-intervention periods, crude retrieval rates increased from 4.4% to 8.1% with a 12-fold change at comparable time points. The time-to-retrieval in the pre-intervention period was a mean (SD) of 503 (207) days with a median (IQR) of 505 (301-742). In the post-intervention period, time-to-retrieval was a mean (SD) of 119 (83) days and with median (IQR) of 128 (38-164) days. Conclusions: This low-cost intervention significantly increased retrieval rates in a single clinic. However, retrieval rates remain low and can be further improved. Ongoing interventions, including improved patient follow-up and physician education, are being implemented to further improve retrieval and use of inferior vena cava filters. Implanting clinics should implement quality improvement initiatives to improve patient care and follow-up with IVCFs to ensure retrievals occur once clinically relevant in order to minimize long-term complications.
Efficacy and safety of secukinumab administration by autoinjector in patients with psoriatic arthritis: results from a randomized, placebo-controlled trial (FUTURE 3).

BACKGROUND: The study aimed to assess 52-week efficacy and safety of secukinumab self-administration by autoinjector in patients with active psoriatic arthritis (PsA) in the FUTURE 3 study ( ClinicalTrials.gov NCT01989468). METHODS: Patients (≥ 18 years of age; N = 414) with active PsA were randomized 1:1:1 to subcutaneous (s.c.) secukinumab 300 mg, 150 mg, or placebo at baseline, weeks 1, 2, 3, and 4, and every 4 weeks thereafter. Per clinical response, placebo-treated patients were re-randomized to s.c. secukinumab 300 or 150 mg at week 16 (nonresponders) or week 24 (responders) and stratified at randomization by prior anti-tumor necrosis factor (TNF) therapy (anti-TNF-naïve, 68.1%; intolerant/inadequate response (anti-TNF-IR), 31.9%). The primary endpoint was the proportion of patients achieving at least 20% improvement in American College of Rheumatology response criteria (ACR20) at week 24. Autoinjector usability was evaluated by Self-Injection Assessment Questionnaire (SIAQ). RESULTS: Overall, 92.1% (300 mg), 91.3% (150 mg), and 93.4% (placebo) of patients completed 24 weeks, and 84.9% (300 mg) and 79.7% (150 mg) completed 52 weeks. In the overall population (combined anti-TNF-naïve and anti-TNF-IR), ACR20 response rate at week 24 was significantly higher in secukinumab groups (300 mg, 48.2% (p < 0.0001); 150 mg, 42% (p < 0.0001); placebo, 16.1%) and was sustained through 52 weeks. SIAQ results showed that more than 93% of patients were satisfied/very satisfied with autoinjector usage. Secukinumab was well tolerated with no new or unexpected safety signals reported. CONCLUSIONS: Secukinumab provided sustained improvements in signs and symptoms in active PsA patients through 52 weeks. High acceptability of autoinjector was observed. The safety profile was consistent with that reported previously. TRIAL REGISTRATION: ClinicalTrials.gov NCT01989468 . Registered 21 November 2013. EudraCT 2013-004002-25 . Registered 17 December 2013.
Risk factors for type 2 diabetes mellitus: An exposure-wide umbrella review of meta-analyses.

BACKGROUND: Type 2 diabetes mellitus (T2DM) is a global epidemic associated with increased health expenditure, and low quality of life. Many non-genetic risk factors have been suggested, but their overall epidemiological credibility has not been assessed. METHODS: We searched PubMed to capture all meta-analyses and Mendelian randomization studies for risk factors of T2DM. For each association, we estimated the summary effect size, its 95% confidence and prediction interval, and the I2 metric. We examined the presence of small-study effects and excess significance bias. We assessed the epidemiological credibility through a set of predefined criteria. RESULTS: We captured 86 eligible papers (142 associations) covering a wide range of biomarkers, medical conditions, and dietary, lifestyle, environmental and psychosocial factors. Adiposity, low hip circumference, serum biomarkers (increased level of alanine aminotransferase, gamma-glutamyl transferase, uric acid and C-reactive protein, and decreased level of adiponectin and vitamin D), an unhealthy dietary pattern (increased consumption of processed meat and sugar-sweetened beverages, decreased intake of whole grains, coffee and heme iron, and low adherence to a healthy dietary pattern), low level of education and conscientiousness, decreased physical activity, high sedentary time and duration of television watching, low alcohol drinking, smoking, air pollution, and some medical conditions (high systolic blood pressure, late menarche age, gestational diabetes, metabolic syndrome, preterm birth) presented robust evidence for increased risk of T2DM. CONCLUSIONS: A healthy lifestyle pattern could lead to decreased risk for T2DM. Future randomized clinical trials should focus on identifying efficient strategies to modify harmful daily habits and predisposing dietary patterns.
Paramutation-like features of multiple natural epialleles in tomato.

BACKGROUND: Freakish and rare or the tip of the iceberg? Both phrases have been used to refer to paramutation, an epigenetic drive that contravenes Mendel's first law of segregation. Although its underlying mechanisms are beginning to unravel, its understanding relies only on a few examples that may involve transgenes or artificially generated epialleles. RESULTS: By using DNA methylation of introgression lines as an indication of past paramutation, we reveal that the paramutation-like properties of the H06 locus in hybrids of Solanum lycopersicum and a range of tomato relatives and cultivars depend on the timing of sRNA production and conform to an RNA-directed mechanism. In addition, by scanning the methylomes of tomato introgression lines for shared regions of differential methylation that are absent in the S. lycopersicum parent, we identify thousands of candidate regions for paramutation-like behaviour. The methylation patterns for a subset of these regions segregate with non Mendelian ratios, consistent with secondary paramutation-like interactions to variable extents depending on the locus. CONCLUSION: Together these results demonstrate that paramutation-like epigenetic interactions are common for natural epialleles in tomato, but vary in timing and penetrance.
Epidemiology of pre-eclampsia and eclampsia at the KK Women's and Children's Hospital, Singapore.

INTRODUCTION: The incidences and characteristics of pre-eclampsia (PE) and eclampsia in KK Women's and Children's Hospital (KKH), a tertiary obstetrical referral centre in Singapore, were studied. METHODS: The incidences and types of PE between July 1999 and June 2003 were derived from the pregnancy disease databases. The characteristics of women with PE in relation to the general obstetric population were analysed on the age, race, parity, types of delivery, gestation at delivery and mortality. Case records of eclampsia were analysed. RESULTS: A total of 2,213 (3.6 percent) out of 61,595 deliveries were complicated by PE between July 1999 and June 2003. Incidence rates for mild or unspecified PE, severe PE, eclampsia and PE superimposed on hypertension were 2.47 percent (1,518), 0.97 percent (599), 0.02 percent (10) and 0.14 percent (85), respectively. The incidence increased with multiple pregnancies: from 3.5 percent in singletons to 7.5 percent in twins, 19.4 percent in triplets and 25.0 percent in quadruplets. The Caesarean section rate for PE was 46.1 percent compared with 23.7 percent in the hospital population. The proportion of premature birth (<37 weeks) in PE was 31.0 percent and that of severe prematurity (<32 weeks) was 5.7 percent, while hospital population proportions were 9.8 percent and 1.3 percent, respectively. The perinatal mortality rate (PMR) of PE was 11.0/1,000 births (population PMR was 4.4/1,000 births). There were only ten cases of eclampsia out of 61,595 deliveries (1:6160) giving an incidence of eclampsia of 16.2/100,000 deliveries. There was no stillbirth, neonatal and maternal death among the eclamptic patients. CONCLUSION: The incidence and outcome of eclampsia in KKH showed a significant reduction over the years due to improved obstetrical care. While PE is still common, eclampsia is now a very rare disease outcome.
Congenital anterior abdominal wall defects in England and Wales 1987-93: retrospective analysis of OPCS data.

OBJECTIVES: Analysis of incidence and characteristics of congenital abdominal wall defects, with special reference to the differences between the incidence of gastroschisis and exomphalos (omphalocele). DESIGN: Retrospective analysis using data from the Office of Population Censuses and Surveys (recoded to differentiate exomphalos and gastroschisis) and the National Congenital Malformation Notification Scheme. SETTING: England and Wales, 1987 to 1993. RESULTS: 1043 congenital anterior abdominal wall defects were notified within the seven year study period. Of these, 539 were classified as gastroschisis, 448 as exomphalos, 19 as "prune belly syndrome," and 37 as "unclassified." Gastroschisis doubled in incidence from 0.65 in 1987 to 1.35 per 10,000 total births in 1991, with little further change; the incidence of exomphalos decreased from 1.13 to 0.77 per 10000 births. The overall incidence of notified congenital abdominal wall defects was 2.15 per 10000 total births. Gastroschisis was associated with a lower overall maternal age than exomphalos and with a significantly lower proportion of additional reported congenital malformations (5.0%) than in the cohort with exomphalos (27.4%) (odds ratio 0.14, 95% confidence interval 0.09 to 0.22; P < 0.001). The sex ratio of the two cohorts was the same. The incidence of gastroschisis and exomphalos was higher in the northern regions of England than in the south east of the country. CONCLUSIONS: The national congenital malformation notification system showed an increasing trend in the incidence of fetuses born with gastroschisis and a progressive decreasing incidence of exomphalos in England and Wales between 1987 and 1993. Although the reasons for this are likely to be multifactorial, a true differential change seems likely. The observed increase in incidence of gastroschisis relative to exomphalos and the differentiation in maternal age have implications for resource management within the NHS and warrant further epidemiological monitoring. Regional differences may be due to a dietary or environmental factor, which requires further study.
Incremental Cost-Effectiveness Analysis of Gestational Diabetes Mellitus Screening Strategies in Singapore.

The objective of this study was to conduct an incremental cost-effectiveness analysis from the payer's perspective in Singapore of 3 gestational diabetes mellitus screening strategies: universal, targeted, or no screening. A decision tree model assessed the primary outcome: incremental cost per quality-adjusted life year (QALY) gained. Probabilities, costs, and utilities were derived from the literature, the Growing Up in Singapore Towards healthy Outcomes (GUSTO) birth cohort study, and the KK Women's and Children's Hospital's database. Relative to targeted screening using risk factors, universal screening generates an incremental cost-effectiveness ratio (ICER) of $USD10 630/QALY gained. Sensitivity analyses show that disease prevalence rates and intervention effectiveness of glycemic management have the biggest impacts on the ICERs. Based on the model and best available data, universal screening is a cost-effective approach for reducing the complications of gestational diabetes mellitus in Singapore as compared with the targeted screening approach or no screening.
Ethnic differences translate to inadequacy of high-risk screening for gestational diabetes mellitus in an Asian population: a cohort study.

BACKGROUND: Universal and high-risk screening for gestational diabetes mellitus (GDM) has been widely studied and debated. Few studies have assessed GDM screening in Asian populations and even fewer have compared Asian ethnic groups in a single multi-ethnic population. METHODS: 1136 pregnant women (56.7% Chinese, 25.5% Malay and 17.8% Indian) from the Growing Up in Singapore Towards healthy Outcomes (GUSTO) birth cohort study were screened for GDM by 75-g oral glucose tolerance test (OGTT) at 26-28 weeks of gestation. GDM was defined using the World Health Organization (WHO) criteria. High-risk screening is based on the guidelines of the UK National Institute for Health and Clinical Excellence. RESULTS: Universal screening detected significantly more cases than high-risk screening [crude OR 2.2 (95% CI 1.7-2.8)], particularly for Chinese women [crude OR = 3.5 (95% CI 2.5-5.0)]. Pre-pregnancy BMI > 30 kg/m2 (adjusted OR = 3.4, 95% CI 1.5-7.9) and previous GDM history (adjusted OR = 6.6, 95% CI 1.2-37.3) were associated with increased risk of GDM in Malay women while GDM history was the only significant risk factor for GDM in Chinese women (adjusted OR = 4.7, 95% CI 2.0-11.0). CONCLUSION: Risk factors used in high-risk screening do not sufficiently predict GDM risk and failed to detect half the GDM cases in Asian women. Asian women, particularly Chinese, should be screened to avoid under-diagnosis of GDM and thereby optimize maternal and fetal outcomes.
Association between ABCG2 Q141K polymorphism and gout risk affected by ethnicity and gender: a systematic review and meta-analysis.

AIM: Original studies have employed various genetic models in association analysis between ABCG2 Q141K (rs2231142) with gout risk and different or conflicting results, especially regarding the role of gender in this association. In addition, it is not clear whether the association varies by ethnicity. METHOD: Articles published before September 1, 2013 were extracted and registered into databases for the systematic review of this polymorphism. The quality of each study was scored based on predefined criteria. The genetic model was identified through stratification analysis, then a meta-analysis including all publically available data was preformed to test the association between rs2231142 and gout risk. Potential sources of heterogeneity were sought out via stratification analysis and meta-regression analysis. RESULTS: Nine case-control studies involving 17 942 individuals were eligible for the meta-analysis of rs2231142. Codominant model was the most appropriate genetic model to interpret the susceptibility cause. It showed that the rs2231142 T allele obviously increased gout risk, and TT was much stronger than GT (TT vs. GG: OR, 4.10; 95% CI, 2.90-5.80; GT vs. GG: OR, 1.71, 95% CI, 1.39-2.10). In addition, gender and ethnicity were found to affect the association between the susceptibility of gout and rs2231142. CONCLUSION: ABCG2 rs2231142 is an important genetic factor in increasing gout risk, and the difference in genetic association has been found between male and female populations. In addition, the degree of association has been found to vary with ethnicity.
Loss of PTEN in high grade advanced stage triple negative breast ductal cancers in African American women.

INTRODUCTION: PTEN is a tumor suppressor gene that inhibits cell proliferation by inhibiting the phosphoinositide 3-kinase (PI3 K) signaling pathway. The significance of PTEN mutations resulting in variable PTEN expression and their impact on prognosis of breast cancer is not well established. The objective of our study was to correlate the immunohistochemical expression of PTEN in the four major subtypes of breast carcinoma (Luminal A, Luminal B, HER2 positive, and Triple Negative) in a population of 202 African-American (AA) females with other clinicopathological factors. MATERIALS AND METHODS: Tissue microarrays (TMAs) were constructed from FFPE tumor blocks from primary ductal breast carcinomas in 202 African-American females. Five micrometer sections were stained with a mouse monoclonal antibody against PTEN. The sections were evaluated for the intensity of cytoplasmic and nuclear reactivity. Bivariate analysis was done via χ2 analysis and survivability data was calculated via the generation of Kaplan-Meier curves (SPSS v19). RESULTS: Loss of PTEN expression was associated with ER negative (p = 0.021), PR negative (p = 0.024) and triple negative (p = 0.0024) breast ductal cancers. It was marginally associated with distant metastasis (p = 0.074). There was no association between PTEN loss and recurrence-free survival or overall survival. CONCLUSION: In our study, a statistically significant association between PTEN loss and the triple negative breast cancers (TNBC) was found in AA women. PTEN inhibits PI3 K resulting in decreased activation of downstream effector, mammalian target of rapamycin (mTOR). Loss of PTEN results in cell proliferation through activation of mTOR. Targeted therapy with mTOR inhibitors might be useful in the treatment of TNBC.
Simple decision rules for classifying human cancers from gene expression profiles.

MOTIVATION: Various studies have shown that cancer tissue samples can be successfully detected and classified by their gene expression patterns using machine learning approaches. One of the challenges in applying these techniques for classifying gene expression data is to extract accurate, readily interpretable rules providing biological insight as to how classification is performed. Current methods generate classifiers that are accurate but difficult to interpret. This is the trade-off between credibility and comprehensibility of the classifiers. Here, we introduce a new classifier in order to address these problems. It is referred to as k-TSP (k-Top Scoring Pairs) and is based on the concept of 'relative expression reversals'. This method generates simple and accurate decision rules that only involve a small number of gene-to-gene expression comparisons, thereby facilitating follow-up studies. RESULTS: In this study, we have compared our approach to other machine learning techniques for class prediction in 19 binary and multi-class gene expression datasets involving human cancers. The k-TSP classifier performs as efficiently as Prediction Analysis of Microarray and support vector machine, and outperforms other learning methods (decision trees, k-nearest neighbour and naïve Bayes). Our approach is easy to interpret as the classifier involves only a small number of informative genes. For these reasons, we consider the k-TSP method to be a useful tool for cancer classification from microarray gene expression data. AVAILABILITY: The software and datasets are available at http://www.ccbm.jhu.edu CONTACT: actan@jhu.edu.
Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data.

MOTIVATION: DNA microarray data analysis has been used previously to identify marker genes which discriminate cancer from normal samples. However, due to the limited sample size of each study, there are few common markers among different studies of the same cancer. With the rapid accumulation of microarray data, it is of great interest to integrate inter-study microarray data to increase sample size, which could lead to the discovery of more reliable markers. RESULTS: We present a novel, simple method of integrating different microarray datasets to identify marker genes and apply the method to prostate cancer datasets. In this study, by applying a new statistical method, referred to as the top-scoring pair (TSP) classifier, we have identified a pair of robust marker genes (HPN and STAT6) by integrating microarray datasets from three different prostate cancer studies. Cross-platform validation shows that the TSP classifier built from the marker gene pair, which simply compares relative expression values, achieves high accuracy, sensitivity and specificity on independent datasets generated using various array platforms. Our findings suggest a new model for the discovery of marker genes from accumulated microarray data and demonstrate how the great wealth of microarray data can be exploited to increase the power of statistical analysis. CONTACT: leixu@jhu.edu.
A bibliometric analysis of the published road traffic injuries research in India, post-1990.

BACKGROUND: Globally, road traffic injuries are the leading cause of death among those aged 15-29 years. However, road traffic injury research has not received adequate attention from the scientific community in low- and middle-income countries, including India. The present study aims to provide a bibliometric overview of research assessing road traffic injuries in India. METHODS: We used Scopus to extract relevant research in road traffic injuries published from 1991 to 2017. This study presented the key bibliometric indicators such as trends of annual publications and citations, top 10 authors, journals, institutions and highly cited articles, citation analysis of articles, co-occurrence of keywords, etc. Analysis was performed using Scopus, Microsoft Excel, and VOS-viewer. RESULTS: A total of 242 articles were retrieved with an h-index of 18, excluding self-citations. A steadfast growth of publications was documented in last decade, especially after the year 2010. The h-index of the top 10 authors, institutions, journals and highly cited articles did not surpass single digits. A network visualisation map showed that 'traffic accident', 'male', 'adolescent' and 'child' were the most commonly encountered key terms. The prominent authors were Gururaj G, Dandona R, and Hyder AA, whereas the top journals were the Indian Journal of Forensic Medicine and Toxicology, Medico Legal Update, and the International Journal of Applied Engineering Research and top institutions were the All India Institute of Medical Sciences, New Delhi, the Indian Institute of Technology, Delhi, and the Administrative Staff College of India. CONCLUSION: In India, road traffic injuries research is inadequate in quantity and quality, warranting greater attention from researchers and policy planners to address the burden of road traffic injuries.