Space-Variant Gabor Decomposition for Filtering 3D Medical Images

This is an experimental paper in which we introduce the possibility to analyze and to synthesize 3D medical images by using multivariate Gabor frames with Gaussian windows. Our purpose is to apply a space-variant filter-like operation in the space-frequency domain to correct medical images corrupted by different types of acquisitions errors. The Gabor frames are constructed with Gaussian windows sampled on non-separable lattices for a better packing of the space-frequency plane. An implementable solution for 3D-Gabor frames with non-separable lattice is given and numerical tests on simulated data are presented.Austrian Science Fund (FWF) P2751

A "Candidate-Interactome" Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a “candidate interactome” (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms

A “Candidate-Interactome” Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a "candidate interactome" (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms

Pheochromocytoma in Denmark during 1977–2016: validating diagnosis codes and creating a national cohort using patterns of health registrations

Andreas Ebbehoj,1,2 Sarah Forslund Jacobsen,3 Christian Trolle,1 Maciej Grzegorz Robaczyk,4 Åse Krogh Rasmussen,3 Ulla Feldt-Rasmussen,3 Reimar Wernich Thomsen,5 Per Løgstrup Poulsen,1 Kirstine Stochholm,1 Esben Søndergaard1 1Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark; 2Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; 3Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark; 4Department of Endocrinology, Aalborg University Hospital, Aalborg, Denmark; 5Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark Background: Pheochromocytoma and catecholamine-secreting paraganglioma (PPGL) are rare but potentially life-threatening tumors. We aimed to validate diagnosis codes for PPGL in the Danish National Patient Registry, the Danish National Pathology Registry, and the Danish Registry of Causes of Death and to create a national cohort of incident PPGL patients by linking these three registries. Patients and methods: We obtained data from the three abovementioned registries for all individuals registered with pheochromocytoma or catecholamine hypersecretion in Denmark during 1977–2016 (average population 5.30 million). We then reviewed health records for all individuals living in the North Denmark Region and Central Denmark Region (average population 1.75 million) to validate the diagnosis of PPGL. We tested a number of algorithms for accurately identifying true cases of PPGL to maximize positive predictive values (PPVs) and completeness. The best algorithm was subsequently validated in an external sample. Results: We identified 2626 individuals with a PPGL diagnosis code in Denmark, including 787 (30.0%) in the North Denmark Region and Central Denmark Region. In this subsample, we retrieved the health records of 771/787 (98.0%) individuals and confirmed 198 incident PPGL patients (25.3%). The PPV of PPGL diagnosis codes was 21.7% in the Danish National Patient Registry, 50.0% in the Danish Registry of Causes of Death, and 79.5% in the Danish National Pathology Registry. By combining patterns of registrations in the three registries, we could increase the PPV to 93.1% (95% confidence interval [CI]: 88.5–96.3) and completeness to 88.9% (95% CI: 83.7–92.9), thus creating a national PPGL cohort of 588 patients. PPV for the optimal algorithm was 95.3% (95% CI: 88.5–98.7) in the external validation sample. Conclusion: Diagnosis codes for pheochromocytoma had low PPV in several individual health registries. However, with a combination of registries we were able to identify a near-complete national cohort of PPGL patients in Denmark, as a valuable source for epidemiological research. Keywords: registry-based research, International Classification of Diseases, ICD, Systematized Nomenclature of Medicine, SNOMED, hospital register diagnoses, pathology register, cause of death registe

Challenges and opportunities for integrating lake ecosystem modelling approaches

A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others (‘reinventing the wheel’). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available (‘having tunnel vision’). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and trait-based models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its ‘leading principle’, there are many opportunities for combining approaches. We take the point of view that a single ‘right’ approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem model

Airborne trace elements near a petrochemical industrial complex in Thailand assessed by the lichen Parmotrema tinctorum (Despr. ex Nyl.) Hale

7siSeveral trace elements discharged by the petrochemical industry are toxic to humans and the ecosystem. In this study, we assessed airborne trace elements in the vicinity of the Map Ta Phut petrochemical industrial complex in Thailand by transplanting the lichen Parmotrema tinctorum to eight industrial, two rural, and one clean air sites between October 2013 and June 2014. After 242 days, the concentrations of As, Cd, Co, Cr, Cu, Hg, Mo, Ni, Pb, Sb, Ti, V, and Zn in lichens at most industrial sites were higher than those at the rural and the control sites; in particular, As, Cu, Mo, Sb, V, and Zn were significantly higher than at the control site (p < 0.05). Contamination factors (CFs) indicated that Cd, Cu, Mo, and Sb, which have severe health impacts, heavily contaminated at most industrial sites. Principal component analysis (PCA) showed that most elements were associated with industry, with lesser contributions from traffic and agriculture. Based on the pollution load indexes (PLIs), two industrial sites were highly polluted, five were moderately polluted, and one had a low pollution level, whereas the pollution load at the rural sites was comparable to background levels. This study reinforces the utility of lichens as cost-effective biomonitors of airborne elements, suitable for use in developing countries, where adequate numbers of air monitoring instruments are unavailable due to financial, technical, and policy constraints.partially_openopenBoonpeng, Chaiwat; Polyiam, Wetchasart; Sriviboon, Chutima; Sangiamdee, Duangkamon; Watthana, Santi; Nimis, Pier Luigi; Boonpragob, KansriBoonpeng, Chaiwat; Polyiam, Wetchasart; Sriviboon, Chutima; Sangiamdee, Duangkamon; Watthana, Santi; Nimis, Pierluigi; Boonpragob, Kansr