Miracle-dz/UniFAR-FTUs huggingface dataset:
Sociodemographic Differences Between Alcohol Use and Sickness Absence: Pooled Analysis of Four Cohort Studies

Aims We examined differences in sickness absence in relation to at-risk drinking and abstinence, taking into account potential changes in consumption. Methods We used individual-participant data (n = 46,514) from four prospective cohort studies from Finland, France and the UK. Participants responded to a survey on alcohol use at two time points 4-6 years apart, and were linked to records of sickness absence for an ~6-year follow-up after the latter survey. Abstainers were those reporting no alcohol use in either survey. At-risk drinkers at T1 were labelled as 'former', at-risk drinkers at T2 as 'current' and at-risk drinkers at both times as 'consistent' at-risk drinkers. The reference group was low-risk drinkers at both times. Study-specific analyses were stratified by sex and socioeconomic status (SES) and the estimates were pooled using meta-analysis. Results Among men (n = 17,285), abstainers (6%), former (5%), current (5%) and consistent (7%) at-risk drinkers had an increased risk of sickness absence compared with consistent low-risk drinkers (77%). Among women (n = 29,229), only abstainers (12%) had a higher risk of sickness absence compared to consistent low-risk drinkers (74%). After adjustment for lifestyle and health, abstaining from alcohol was associated with sickness absence among people with intermediate and high SES, but not among people with low SES. Conclusions The U-shaped alcohol use-sickness absence association is more consistent in men than women. Abstinence is a risk factor for sickness absence among people with higher rather than lower SES. Healthy worker effect and health selection may partly explain the observed differences. Short summary In a pooled analysis from four cohort studies from three European countries, we demonstrated a U-shaped association between alcohol use and sickness absence, particularly among men. Abstinence from alcohol was associated with increased sickness absenteeism among both sexes and across socioeconomic strata, except those with low SES.
A framework of comfort for practice: An integrative review identifying the multiple influences on patients’ experience of comfort in healthcare settings

Purpose Comfort is central to patient experience but the concept of comfort is poorly defined. This review aims to develop a framework representing patients' complex perspective of comfort to inform practice and guide initiatives to improve the quality of healthcare. Data sources CINAHL, MEDLINE Complete, PsycINFO and Google Scholar (November 2016); reference lists of included publications. Study selection Qualitative and theoretical studies advancing knowledge about the concept of comfort in healthcare settings. Studies rated for methodological quality and relevance to patients' perspectives. Data extraction Data on design, methods, features of the concept of comfort, influences on patients' comfort. Data were systematically coded and categorized using Framework method. Results of data synthesis Sixty-two studies (14 theoretical and 48 qualitative) were included. Qualitative studies explored patient and staff perspectives in varying healthcare settings including hospice, emergency departments, paediatric, medical and surgical wards and residential care for the elderly. From patients' perspective, comfort is multidimensional, characterized by relief from physical discomfort and feeling positive and strengthened in one's ability to cope with the challenges of illness, injury and disability. Different factors are important to different individuals. We identified 10 areas of influence within four interrelated levels: patients' use of self-comforting strategies; family presence; staff actions and behaviours; and environmental factors. Conclusion Our data provide new insights into the nature of comfort as a highly personal and contextual experience influenced in different individuals by different factors that we have classified into a framework to guide practice and quality improvement initiatives.
Androgen receptor gene status in plasma DNA associates with worse outcome on enzalutamide or abiraterone for castration-resistant prostate cancer: a multi-institution correlative biomarker study

Abstract Background There is an urgent need to identify biomarkers to guide personalized therapy in castration-resistant prostate cancer (CRPC). We aimed to clinically qualify androgen receptor (AR) gene status measurement in plasma DNA using multiplex droplet digital PCR (ddPCR) in pre- and post-chemotherapy CRPC. Methods We optimized ddPCR assays for AR copy number and mutations and retrospectively analyzed plasma DNA from patients recruited to one of the three biomarker protocols with prospectively collected clinical data. We evaluated associations between plasma AR and overall survival (OS) and progression-free survival (PFS) in 73 chemotherapy-naïve and 98 post-docetaxel CRPC patients treated with enzalutamide or abiraterone (Primary cohort) and 94 chemotherapy-naïve patients treated with enzalutamide (Secondary cohort; PREMIERE trial). Results In the primary cohort, AR gain was observed in 10 (14%) chemotherapy-naïve and 33 (34%) post-docetaxel patients and associated with worse OS [hazard ratio (HR), 3.98; 95% CI 1.74–9.10; P < 0.001 and HR 3.81; 95% CI 2.28–6.37; P < 0.001, respectively], PFS (HR 2.18; 95% CI 1.08–4.39; P = 0.03, and HR 1.95; 95% CI 1.23–3.11; P = 0.01, respectively) and rate of PSA decline ≥50% [odds ratio (OR), 4.7; 95% CI 1.17–19.17; P = 0.035 and OR, 5.0; 95% CI 1.70–14.91; P = 0.003, respectively]. AR mutations [2105T>A (p.L702H) and 2632A>G (p.T878A)] were observed in eight (11%) post-docetaxel but no chemotherapy-naïve abiraterone-treated patients and were also associated with worse OS (HR 3.26; 95% CI 1.47–not reached; P = 0.004). There was no interaction between AR and docetaxel status (P = 0.83 for OS, P = 0.99 for PFS). In the PREMIERE trial, 11 patients (12%) with AR gain had worse PSA-PFS (sPFS) (HR 4.33; 95% CI 1.94–9.68; P < 0.001), radiographic-PFS (rPFS) (HR 8.06; 95% CI 3.26–19.93; P < 0.001) and OS (HR 11.08; 95% CI 2.16–56.95; P = 0.004). Plasma AR was an independent predictor of outcome on multivariable analyses in both cohorts. Conclusion Plasma AR status assessment using ddPCR identifies CRPC with worse outcome to enzalutamide or abiraterone. Prospective evaluation of treatment decisions based on plasma AR is now required. Clinical Trial number NCT02288936 (PREMIERE trial).
Inflammatory Differences in Plaque Erosion and Rupture in Patients With ST‐Segment Elevation Myocardial Infarction

Background Plaque erosion causes 30% of ST‐segment elevation myocardial infarctions, but the underlying cause is unknown. Inflammatory infiltrates are less abundant in erosion compared with rupture in autopsy studies. We hypothesized that erosion and rupture are associated with significant differences in intracoronary cytokines in vivo. Methods and Results Forty ST‐segment elevation myocardial infarction patients with <6 hours of chest pain were classified as ruptured fibrous cap (RFC) or intact fibrous cap (IFC) using optical coherence tomography. Plasma samples from the infarct‐related artery and a peripheral artery were analyzed for expression of 102 cytokines using arrays; results were confirmed with ELISA. Thrombectomy samples were analyzed for differential mRNA expression using quantitative real‐time polymerase chain reaction. Twenty‐three lesions were classified as RFC (58%), 15 as IFC (38%), and 2 were undefined (4%). In addition, 12% (12 of 102) of cytokines were differentially expressed in both coronary and peripheral plasma. I‐TAC was preferentially expressed in RFC (significance analysis of microarrays adjusted P<0.001; ELISA IFC 10.2 versus RFC 10.8 log2 pg/mL; P=0.042). IFC was associated with preferential expression of epidermal growth factor (significance analysis of microarrays adjusted P<0.001; ELISA IFC 7.42 versus RFC 6.63 log2 pg/mL, P=0.036) and thrombospondin 1 (significance analysis of microarrays adjusted P=0.03; ELISA IFC 10.4 versus RFC 8.65 log2 ng/mL, P=0.0041). Thrombectomy mRNA showed elevated I‐TAC in RFC (P=0.0007) epidermal growth factor expression in IFC (P=0.0264) but no differences in expression of thrombospondin 1. Conclusions These results demonstrate differential intracoronary cytokine expression in RFC and IFC. Elevated thrombospondin 1 and epidermal growth factor may play an etiological role in erosion.
Neutrophil-to-lymphocyte ratio as prognostic indicator in gastrointestinal cancers: a systematic review and meta-analysis

An accurate, time efficient, and inexpensive prognostic indicator is needed to reduce cost and assist with clinical decision making for cancer management. The neutrophil-to-lymphocyte ratio (NLR), which is derived from common serum testing, has been explored in a variety of cancers. We sought to determine its prognostic value in gastrointestinal cancers and performed a meta-analysis of published studies using the Meta-analysis Of Observational Studies in Epidemiology guidelines. Included were randomized control trials and observational studies that analyzed humans with gastrointestinal cancers that included NLR and hazard ratios (HR) with overall survival (OS), disease-free survival (DFS), progression-free survival (PFS), and/or cancer-specific survival (CSS). We analyzed 144 studies comprising 45,905 patients, two-thirds of which were published after 2014. The mean, median, and mode cutoffs for NLR reporting OS from multivariate models were 3.4, 3.0, 5.0 (±IQR 2.5-5.0), respectively. Overall, NLR greater than the cutoff was associated with a HR for OS of 1.63 (95% CI, 1.53-1.73; P < 0.001). This association was observed in all subgroups based on tumor site, stage, and geographic region. HR for elevated NLR for DFS, PFS, and CSS were 1.70 (95% CI, 1.52-1.91, P < 0.001), 1.64 (95% CI, 1.36-1.97, P < 0.001), and 1.83 (95% CI, 1.50-2.23, P < 0.001), respectively. Available evidence suggests that NLR greater than the cutoff reduces OS, independent of geographic location, gastrointestinal cancer type, or stage of cancer. Furthermore, DFS, PFS, and CSS also have worse outcomes with elevated NLR.
Disparity in Race-Specific Comorbidities Associated With Central Venous Catheter–Related Bloodstream Infection (AHRQ-PSI7)

Studies of racial disparities in hospital-level patient safety outcomes typically apply a race-common approach to risk adjustment. Risk factors specific to a minority population may not be identified in a race-common analysis if they represent only a small percentage of total cases. This study identified patient comorbidities and characteristics associated with the likelihood of a venous catheter–related bloodstream infection (Agency for Healthcare Research and Quality Patient Safety Indicator 7 [PSI7]) separately for blacks and whites using race-specific logistic regression models. Hospitals were ranked by the racial disparity in PSI7 and segmented into 4 groups. The analysis identified both black- and white-specific risk factors associated with PSI7. Age showed race-specific reverse association, with younger blacks and older whites more likely to have a PSI7 event. These findings suggest the need for race-specific covariate adjustments in patient outcomes and provide a new context for examining racial disparities.
Research on Optimization and Application of Slope One Algorithm in Personalized Recommendation System

Slope one algorithm is a kind of collaborative filtering algorithm to predict the user's preference value for new items, based on the average preference difference between the new items and items the user has rated, which has been widely used in the network recommendation system since it was proposed in 2005. Due to the intermediate process of algorithm, memory consumption, it greatly affects the practical application effect. In this paper, combining the design and actual development of personalized recommendation system on cloud computing platform, it introduces similarity information of employment information content in Slope one algorithm, which can reduce uncertainty intermediate process, at the same time, with the use of Map Reduce distributed computing to deal with massive data analysis and calculation. Experimental results show that the proposed method can effectively enhance the efficiency of Slope one algorithm in the personalized recommendation system, further improve the user experience of the front.
Sinogram synthesis using convolutional-neural-network for sparsely view-sampled CT

Reducing the number of projections in computed tomography (CT) has been exploited as a low-dose option in conjunction with advanced iterative image reconstruction algorithms. While such iterative image reconstruction methods do provide useful images and valuable insights of the inverse imaging problems, it is an intriguing issue whether missing view projection data in the sinogram can be successfully recovered. There have been reported several approaches to interpolating the missing sinogram data. Deep-learning based super-resolution techniques in the field of natural image enhancement have been recently introduced and showed promising results. Inspired by the super-resolution techniques, we have earlier proposed a sinogram inpainting method that uses a convolutional-neural-network for sparsely viewsampled CT. Despite of the encouraging initial results, our previously proposed method had two drawbacks. The measured sinogram was contaminated in the process of filling the missing sinogram by the deep learning network. Additionally, the sum of the interpolated sinogram in the direction of detector row at each view angle was not preserved. In this study, we improve our previously developed deep-learning based sinogram synthesis method by adding new layers and modifying the size of receptive field in the deep learning network to overcome the above limitations. From the quantitative evaluations on the image accuracy and quality using real patients’ CT images, we show that the new approach synthesizes more accurate sinogram and thus leads to higher quality of CT image than the previous one.
A Comparison of Pain Beliefs and Coping Strategies and Their Association with Chronic Pain Adjustment Between Singapore and United States

Objectives Research examining the importance of pain beliefs and coping strategies to chronic pain adjustment has been performed almost exclusively using Western populations. The purpose of this study was to examine empirically the generalizability of this research to Singapore. Methods Employing a cross-sectional design, measures assessing pain beliefs, coping strategies, pain intensity, pain interference, and depressive symptoms were administered to 101 patients with chronic pain from Singapore. Analyses examined the means of belief and coping strategies measures and their associations with measures of pain intensity, pain interference, and depressive symptoms and compared the results with the data of a sample of 100 patients with chronic pain from a previously published study from the United States. Results Mean differences between the Singapore and US samples were found for four of the seven belief scales, and four of the eight coping scales. When significant, associations between belief and coping strategies with measures of pain and dysfunction were in the hypothesized directions in both samples. We also found that the strength of four out of 30 of the associations between beliefs/coping strategies and measures of pain and dysfunction were different between the Singapore and US samples. Conclusion The ﬁndings provide further support for the potential influence of culture on how individuals view and cope with pain. However, the many similarities found in direction and strength of the associations between beliefs/coping strategies and measures of pain/dysfunction provide preliminary support for the appropriateness of the use of cognitive behavioral therapy developed in the United States with the Singapore population.
Effectiveness of Supplementary Cognitive-Behavioral Therapy for Pharmacotherapy-Resistant Depression: A Randomized Controlled Trial.

OBJECTIVE Antidepressant medication is efficacious in the treatment of depression, but not all patients improve with antidepressant medication alone. Despite this treatment gap, limited evidence regarding the effectiveness of supplementing psychotherapy for pharmacotherapy-resistant depression is available. Therefore, we investigated the effectiveness of supplementing usual medication management (treatment as usual [TAU]) with cognitive-behavioral therapy (CBT) in patients with pharmacotherapy-resistant depression seeking psychiatric specialty care. METHODS A 16-week assessor-masked randomized controlled trial with a 12-month follow-up was conducted in 1 university hospital and 1 psychiatric hospital from September 2008 to December 2014. Outpatients aged 20-65 years with pharmacotherapy-resistant depression (taking antidepressant medications for ≥ 8 weeks, 17-item GRID-Hamilton Depression Rating Scale [GRID-HDRS₁₇] score ≥ 16, Maudsley Staging Method for treatment-resistant depression score ≥ 3, and DSM-IV criteria for major depressive disorder) were randomly assigned (1:1) to CBT combined with TAU or to TAU alone. The primary outcome was the alleviation of depressive symptoms, as measured by change in the total GRID-HDRS₁₇ score from baseline to 16 weeks; primary analysis was done on an intention-to-treat basis. RESULTS A total of 80 patients were randomized; 78 (97.5%) were assessed for the primary outcome, and 73 (91.3%) were followed up for 12 months. Supplementary CBT significantly alleviated depressive symptoms at 16 weeks, as shown by greater least squares mean changes in GRID-HDRS₁₇ scores in the intervention group than in the control group (-12.7 vs -7.4; difference = -5.4; 95% CI, -8.1 to -2.6; P < .001), and the treatment effect was maintained for at least 12 months (-15.4 vs -11.0; difference = -4.4; 95% CI, -7.2 to -1.6; P = .002). CONCLUSIONS Patients with pharmacotherapy-resistant depression treated in psychiatric specialty care settings may benefit from supplementing usual medication management with CBT. TRIAL REGISTRATION UMIN Clinical Trials Registry identifier: UMIN000001218​​.
Social support as a mediator variable of the relationship between depression and life satisfaction in a sample of Saudi caregivers of patients with Alzheimer's disease

The authors would like to apologise for an error made in the acknowledgement of the above mentioned article. In the acknowledgement section of the article, paragraph ‘This project was funded by the Deanship of Scientific Research (DSR), at King Abdulaziz University, Jeddah, under grant no. (G-282/ 724246/1436). The authors, therefore, acknowledge with thanks DSR for technical and financial support’. Should read: This project was funded by the Deanship of Scientific Research (DSR), at King Abdulaziz University, Jeddah, under grant no. (G-282-246-36). The authors, therefore, acknowledge with thanks DSR for technical and financial support’.
Dynamic Sensing Strategies for Efficient Spectrum Utilization in Cognitive Radio Networks

For cognitive radio (CR) networks with user hierarchy, the sensing strategy with "listen-before-talk" (LBT) policy plays a key role in spectrum utilization and primary user (PU) protection. However, existing sensing strategies do not handle satisfactorily the randomness of both user locations and channel conditions in the network environment, resulting in inefficient spectrum utilization. To cope with such randomness, this paper develops three dynamic sensing strategies that can adaptively schedule the sensing slots/cycles according to the online link conditions without assuming knowledge of the PU traffic model. The proposed strategies can improve the efficiency of spectrum utilization while being robust with respect to the uncertainty in the PU traffic pattern. To maximize spectrum utilization, the proposed strategies are formulated through closed-form expressions. Efficient methods are introduced to compute the optimal values of the parameters used in the strategies, such as sensing time and sensing threshold. Simulations verify that the proposed sensing strategies offer an evident improvement on the spectrum utilization of the CR network.
Characterization of pyrazinamide resistance in consecutive multidrug-resistant mycobacterium tuberculosis isolates in sweden between 2003 and 2015

Background: The first line anti-tuberculosis drug pyrazinamide (PZA) is important when treating PZA susceptible multidrug-resistant tuberculosis (MDR-TB). Several drug resistance surveys have however reported PZA resistance among a significant proportion of multidrug-resistant (MDR) cases and this undoubtedly highlights the need for accurate and reliable detection of PZA resistance. Unfortunately, the testing of PZA susceptibility is associated with technical difficulties and even though the introduction of pncA sequencing has helped to address this issue, misclassification may still occur. In this study, we determined the prevalence and characteristics of PZA resistance in Swedish MDR-TB strains. Materials and Methods: 153 MDR-TB strains isolated in Sweden between 2003 and 2015 were analyzed for PZA resistance by considering both phenotypic and genotypic data. Results: The phenotypic test showed that 58% of the multidrug-resistant isolates were PZA resistant and the correlation between phenotype and genotype was solid, although a small number of isolates deviate from the expected phenotypic-genotypic pattern. Conclusion: The results indicate that the prevalence of pyrazinamide resistance among Swedish MDR cases is increasing.
Experimental analysis and modelling of the behavioural interactions underlying the coordination of collective motion and the propagation of information in fish schools

Fish schools are systems in which thousands of individuals can move in a synchronised manner in a changing environment, with endogenous perturbations (e.g. when a congener leaves the group) or exogenous (e.g. the attack of a predator). The coordination of fish schools, decentralised, is not completely understood yet. If the mechanisms underlying social interactions discussed in previous studies qualitatively match the social patterns observed in nature, the quantification of these interactions and the quantitative match between individual measurements and collective patterns are still sparse in recent works and are the main focus of this thesis. This work combines closely experimental and modelling methods in order to investigate the links between the individual behaviours and the patterns observed at the collective scale. We have characterised and quantified the interactions and mechanisms at the origin of, first, the coordination of individuals in fish schools and, second, the propagation of information, when the group is under endogenous or exogenous perturbations. This thesis focuses on one freshwater fish species, the rummy-nose tetra (Hemigrammus rhodostomus), and is the result of a diversity of experimental methods, statistical analyses and modelling, at the interface of ethology, statistical physics and computational sciences.
DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival

Breast cancer patients with Luminal A disease generally have a good prognosis, but among this patient group are patients with good prognosis that are currently overtreated with adjuvant chemotherapy, and also patients that have a bad prognosis and should be given more aggressive treatment. There is no available method for subclassification of this patient group. Here we present a DNA methylation signature (SAM40) that segregates Luminal A patients based on prognosis, and identify one good prognosis group and one bad prognosis group. The prognostic impact of SAM40 was validated in four independent patient cohorts. Being able to subdivide the Luminal A patients may give the two-sided benefit of identifying one subgroup that may benefit from a more aggressive treatment than what is given today, and importantly, identifying a subgroup that may benefit from less treatment.