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Sökning: WFRF:(Ahmad Tariq)

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  • Ahmad, Tariq, et al. (författare)
  • Machine Learning Methods Improve Prognostication, Identify Clinically Distinct Phenotypes, and Detect Heterogeneity in Response to Therapy in a Large Cohort of Heart Failure Patients
  • 2018
  • Ingår i: Journal of the American Heart Association : Cardiovascular and Cerebrovascular Disease. - WILEY. - 2047-9980. ; 7:8
  • Tidskriftsartikel (refereegranskat)abstract
    • Background-Whereas heart failure (HF) is a complex clinical syndrome, conventional approaches to its management have treated it as a singular disease, leading to inadequate patient care and inefficient clinical trials. We hypothesized that applying advanced analytics to a large cohort of HF patients would improve prognostication of outcomes, identify distinct patient phenotypes, and detect heterogeneity in treatment response. Methods and Results-The Swedish Heart Failure Registry is a nationwide registry collecting detailed demographic, clinical, laboratory, and medication data and linked to databases with outcome information. We applied random forest modeling to identify predictors of 1-year survival. Cluster analysis was performed and validated using serial bootstrapping. Association between clusters and survival was assessed with Cox proportional hazards modeling and interaction testing was performed to assess for heterogeneity in response to HF pharmacotherapy across propensity-matched clusters. Our study included 44 886 HF patients enrolled in the Swedish Heart Failure Registry between 2000 and 2012. Random forest modeling demonstrated excellent calibration and discrimination for survival (C-statistic=0.83) whereas left ventricular ejection fraction did not (C-statistic=0.52): there were no meaningful differences per strata of left ventricular ejection fraction (1-year survival: 80%, 81%, 83%, and 84%). Cluster analysis using the 8 highest predictive variables identified 4 clinically relevant subgroups of HF with marked differences in 1-year survival. There were significant interactions between propensity-matched clusters (across age, sex, and left ventricular ejection fraction and the following medications: diuretics, angiotensin-converting enzyme inhibitors, )i-blockers, and nitrates, Pamp;lt;0.001, all). Conclusions-Machine learning algorithms accurately predicted outcomes in a large data set of HF patients. Cluster analysis identified 4 distinct phenotypes that differed significantly in outcomes and in response to therapeutics. Use of these novel analytic approaches has the potential to enhance effectiveness of current therapies and transform future HF clinical trials.
  • Ahmad, Waqas, et al. (författare)
  • Computationally Efficient Light Field Image Compression Using a Multiview HEVC Framework
  • 2019
  • Ingår i: IEEE Access. ; 7, s. 143002-143014
  • Tidskriftsartikel (refereegranskat)abstract
    • The acquisition of the spatial and angular information of a scene using light eld (LF) technologies supplement a wide range of post-processing applications, such as scene reconstruction, refocusing, virtual view synthesis, and so forth. The additional angular information possessed by LF data increases the size of the overall data captured while offering the same spatial resolution. The main contributor to the size of captured data (i.e., angular information) contains a high correlation that is exploited by state-of-the-art video encoders by treating the LF as a pseudo video sequence (PVS). The interpretation of LF as a single PVS restricts the encoding scheme to only utilize a single-dimensional angular correlation present in the LF data. In this paper, we present an LF compression framework that efciently exploits the spatial and angular correlation using a multiview extension of high-efciency video coding (MV-HEVC). The input LF views are converted into multiple PVSs and are organized hierarchically. The rate-allocation scheme takes into account the assigned organization of frames and distributes quality/bits among them accordingly. Subsequently, the reference picture selection scheme prioritizes the reference frames based on the assigned quality. The proposed compression scheme is evaluated by following the common test conditions set by JPEG Pleno. The proposed scheme performs 0.75 dB better compared to state-of-the-art compression schemes and 2.5 dB better compared to the x265-based JPEG Pleno anchor scheme. Moreover, an optimized motionsearch scheme is proposed in the framework that reduces the computational complexity (in terms of the sum of absolute difference [SAD] computations) of motion estimation by up to 87% with a negligible loss in visual quality (approximately 0.05 dB).
  • Cleynen, Isabelle, et al. (författare)
  • Inherited determinants of Crohn's disease and ulcerative colitis phenotypes a genetic association study
  • 2016
  • Ingår i: The Lancet. - New York, USA : Elsevier. - 0140-6736. ; 387:10014, s. 156-167
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Crohn's disease and ulcerative colitis are the two major forms of inflammatory bowel disease; treatment strategies have historically been determined by this binary categorisation. Genetic studies have identified 163 susceptibility loci for inflammatory bowel disease, mostly shared between Crohn's disease and ulcerative colitis. We undertook the largest genotype association study, to date, in widely used clinical subphenotypes of inflammatory bowel disease with the goal of further understanding the biological relations between diseases.Methods This study included patients from 49 centres in 16 countries in Europe, North America, and Australasia. We applied the Montreal classification system of inflammatory bowel disease subphenotypes to 34,819 patients (19,713 with Crohn's disease, 14,683 with ulcerative colitis) genotyped on the Immunochip array. We tested for genotype-phenotype associations across 156,154 genetic variants. We generated genetic risk scores by combining information from all known inflammatory bowel disease associations to summarise the total load of genetic risk for a particular phenotype. We used these risk scores to test the hypothesis that colonic Crohn's disease, ileal Crohn's disease, and ulcerative colitis are all genetically distinct from each other, and to attempt to identify patients with a mismatch between clinical diagnosis and genetic risk profile.Findings: After quality control, the primary analysis included 29,838 patients (16,902 with Crohn's disease, 12,597 with ulcerative colitis). Three loci (NOD2, MHC, and MST1 3p21) were associated with subphenotypes of inflammatory bowel disease, mainly disease location (essentially fixed over time; median follow-up of 10·5 years). Little or no genetic association with disease behaviour (which changed dramatically over time) remained after conditioning on disease location and age at onset. The genetic risk score representing all known risk alleles for inflammatory bowel disease showed strong association with disease subphenotype (p=1·65 × 10(-78)), even after exclusion of NOD2, MHC, and 3p21 (p=9·23 × 10(-18)). Predictive models based on the genetic risk score strongly distinguished colonic from ileal Crohn's disease. Our genetic risk score could also identify a small number of patients with discrepant genetic risk profiles who were significantly more likely to have a revised diagnosis after follow-up (p=6·8 × 10(-4)).Interpretation: Our data support a continuum of disorders within inflammatory bowel disease, much better explained by three groups (ileal Crohn's disease, colonic Crohn's disease, and ulcerative colitis) than by Crohn's disease and ulcerative colitis as currently defined. Disease location is an intrinsic aspect of a patient's disease, in part genetically determined, and the major driver to changes in disease behaviour over time.Funding: International Inflammatory Bowel Disease Genetics Consortium members funding sources (see Acknowledgments for full list).
  • Craddock, Nick, et al. (författare)
  • Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
  • 2010
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
  • Tidskriftsartikel (refereegranskat)abstract
    • Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
  • Franke, Andre, et al. (författare)
  • Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
  • 2010
  • Ingår i: Nature Genetics. - 1061-4036. ; 42:12, s. 1118-1125
  • Tidskriftsartikel (refereegranskat)abstract
    • We undertook a meta-analysis of six Crohn's disease genome-wide association studies (GWAS) comprising 6,333 affected individuals (cases) and 15,056 controls and followed up the top association signals in 15,694 cases, 14,026 controls and 414 parent-offspring trios. We identified 30 new susceptibility loci meeting genome-wide significance (P < 5 × 10⁻⁸). A series of in silico analyses highlighted particular genes within these loci and, together with manual curation, implicated functionally interesting candidate genes including SMAD3, ERAP2, IL10, IL2RA, TYK2, FUT2, DNMT3A, DENND1B, BACH2 and TAGAP. Combined with previously confirmed loci, these results identify 71 distinct loci with genome-wide significant evidence for association with Crohn's disease.
  • Ghafoor, Mubeen, et al. (författare)
  • Perceptually Lossless Surgical Telementoring System Based on Non-Parametric Segmentation
  • 2019
  • Ingår i: Journal of Medical Imaging and Health Informatics. - 2156-7018. ; 9:3, s. 464-473
  • Tidskriftsartikel (refereegranskat)abstract
    • Bandwidth constraint is one of the significant concerns of surgical telementoring, especially in rural areas. High-Efficiency Video Coding (H.265/HEVC) based video compression techniques have shown promising results for telementoring applications. However, there is a tradeoff between the quality of video received by the remote surgeon and the bandwidth resources required for video transmission. In order to efficiently compress and transmit real-time surgical videos, a hybrid lossless-lossy approach is proposed where surgical incision region (location of surgery) is coded in high quality while the background (non-incision) region is coded in medium to low quality depending on the nature of the region. The surgical incision region is detected based on an efficient color and location-based non-parametric segmentation approach. This approach takes explicitly into account the physiological nature of the human visual system and efficiently encodes the video by providing good overall visual impact in the location of surgery. The results of the proposed approach are shown in terms of video quality metrics such as Bjontegaard delta bitrate (BD-BR), Bjontegaard delta peak signal-to-noise ratio (BD-PSNR), and structural similarity index measurement (SSIM). Experimental results showed that in comparison with default full-frame HEVC encoding, the proposed surgical incision region based encoding achieved an average BD-BR reduction of 77.5% at high-quality settings (QP in range of 0 to 20 in surgical incision region and an increasing QP in skin and background region). The average gain in BD-PSNR of the proposed algorithm was 6.99 dB in surgical incision region at high-quality setting, and the average SSIM index came out to be 0.9926 which is only 0.006% less than the default full-frame HEVC coding. Based on these results, the proposed encoding algorithm can be considered as an efficient and effective solution for surgical telementoring systems for limited bandwidth networks.
  • Hassan, A., et al. (författare)
  • High Efficiency Video Coding (HEVC)–Based Surgical Telementoring System Using Shallow Convolutional Neural Network
  • 2019
  • Ingår i: Journal of digital imaging. - 0897-1889. ; 32:6, s. 1027-1043
  • Tidskriftsartikel (refereegranskat)abstract
    • Surgical telementoring systems have gained lots of interest, especially in remote locations. However, bandwidth constraint has been the primary bottleneck for efficient telementoring systems. This study aims to establish an efficient surgical telementoring system, where the qualified surgeon (mentor) provides real-time guidance and technical assistance for surgical procedures to the on-spot physician (surgeon). High Efficiency Video Coding (HEVC/H.265)–based video compression has shown promising results for telementoring applications. However, there is a trade-off between the bandwidth resources required for video transmission and quality of video received by the remote surgeon. In order to efficiently compress and transmit real-time surgical videos, a hybrid lossless-lossy approach is proposed where surgical incision region is coded in high quality whereas the background region is coded in low quality based on distance from the surgical incision region. For surgical incision region extraction, state-of-the-art deep learning (DL) architectures for semantic segmentation can be used. However, the computational complexity of these architectures is high resulting in large training and inference times. For telementoring systems, encoding time is crucial; therefore, very deep architectures are not suitable for surgical incision extraction. In this study, we propose a shallow convolutional neural network (S-CNN)–based segmentation approach that consists of encoder network only for surgical region extraction. The segmentation performance of S-CNN is compared with one of the state-of-the-art image segmentation networks (SegNet), and results demonstrate the effectiveness of the proposed network. The proposed telementoring system is efficient and explicitly considers the physiological nature of the human visual system to encode the video by providing good overall visual impact in the location of surgery. The results of the proposed S-CNN-based segmentation demonstrated a pixel accuracy of 97% and a mean intersection over union accuracy of 79%. Similarly, HEVC experimental results showed that the proposed surgical region–based encoding scheme achieved an average bitrate reduction of 88.8% at high-quality settings in comparison with default full-frame HEVC encoding. The average gain in encoding performance (signal-to-noise) of the proposed algorithm is 11.5 dB in the surgical region. The bitrate saving and visual quality of the proposed optimal bit allocation scheme are compared with the mean shift segmentation–based coding scheme for fair comparison. The results show that the proposed scheme maintains high visual quality in surgical incision region along with achieving good bitrate saving. Based on comparison and results, the proposed encoding algorithm can be considered as an efficient and effective solution for surgical telementoring systems for low-bandwidth networks.
  • Heap, Graham A., et al. (författare)
  • Clinical Features and HLA Association of 5-Aminosalicylate (5-ASA)-induced Nephrotoxicity in Inflammatory Bowel Disease
  • 2016
  • Ingår i: Journal of Crohn's & Colitis. - Oxford University Press. - 1873-9946. ; 10:2, s. 149-158
  • Tidskriftsartikel (refereegranskat)abstract
    • Background and Aims: Nephrotoxicity is a rare idiosyncratic reaction to 5-aminosalicylate (5-ASA) therapies. The aims of this study were to describe the clinical features of this complication and identify clinically useful genetic markers so that these drugs can be avoided or so that monitoring can be intensified in high-risk patients.Methods: Inflammatory bowel disease patients were recruited from 89 sites around the world. Inclusion criteria included normal renal function prior to commencing 5-ASA, >= 50% rise in creatinine any time after starting 5-ASA, and physician opinion implicating 5-ASA strong enough to justify drug withdrawal. An adjudication panel identified definite and probable cases from structured case report forms. A genome-wide association study was then undertaken with these cases and 4109 disease controls.Results: After adjudication, 151 cases of 5-ASA-induced nephrotoxicity were identified. Sixty-eight percent of cases were males, with nephrotoxicity occurring at a median age of 39.4 years (range 6-79 years). The median time for development of renal injury after commencing 5-ASA was 3.0 years (95% confidence interval [CI] 2.3-3.7). Only 30% of cases recovered completely after drug withdrawal, with 15 patients requiring permanent renal replacement therapy. A genome-wide association study identified a suggestive association in the HLA region (p = 1 x 10(-7)) with 5-ASA-induced nephrotoxicity. A sub-group analysis of patients who had a renal biopsy demonstrating interstitial nephritis (n = 55) significantly strengthened this association (p = 4 x 10(-9), odds ratio 3.1).Conclusions: This is the largest and most detailed study of 5-ASA-induced nephrotoxicity to date. It highlights the morbidity associated with this condition and identifies for the first time a significant genetic predisposition to drug-induced renal injury.
  • Heap, Graham A., et al. (författare)
  • HLA-DQA1-HLA-DRB1 variants confer susceptibility to pancreatitis induced by thiopurine immunosuppressants
  • 2014
  • Ingår i: Nature Genetics. - Nature Publishing Group. - 1061-4036. ; 46:10, s. 1131-1134
  • Tidskriftsartikel (refereegranskat)abstract
    • Pancreatitis occurs in approximately 4% of patients treated with the thiopurines azathioprine or mercaptopurine. Its development is unpredictable and almost always leads to drug withdrawal. We identified patients with inflammatory bowel disease (IBD) who had developed pancreatitis within 3 months of starting these drugs from 168 sites around the world. After detailed case adjudication, we performed a genome-wide association study on 172 cases and 2,035 controls with IBD. We identified strong evidence of association within the class II HLA region, with the most significant association identified at rs2647087 (odds ratio 2.59, 95% confidence interval 2.07-3.26, P = 2 x 10(-16)). We replicated these findings in an independent set of 78 cases and 472 controls with IBD matched for drug exposure. Fine mapping of the H LA region identified association with the HLA-DQA1*02:01-HLA-DRB1*07:01 haplotype. Patients heterozygous at rs2647087 have a 9% risk of developing pancreatitis after administration of a thiopurine, whereas homozygotes have a 17% risk.
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