Van Duijn Research Articles

Temporal analysis of hospital network data by hierarchical Bayesian p2 models with covariates

Abstract Motivated by an application about interhospital connections, we propose a modelling approach for data referred to a temporal network. The approach may be seen as an extension of the one recently proposed in Bianchi et al. (2020) and, in turn, of the popular p1 and p2 models by Holland and Leinhardt (1981) and van Duijn et al. (2004), on which the latter is built. The proposed extension consists in the introduction of covariates and in the adoption of a hierarchical Bayesian inferential approach that shows advantages in the specific application. For Bayesian inference we rely on a Markov chain Monte Carlo algorithm that produces samples from the posterior distribution of the model parameters. The application is based on original data on patient referral relations among 127 hospitals serving a large regional community of patients in Italy from 2014 to 2018. Results indicate that interhospital collaborative behaviours are primarily local and that collaborative attitudes vary at different time occasions of the considered period and in accordance with the level of competition faced by hospital organisations.

Minimal cognition and stigmergic coordination: An everyday tale of building and bacteria

Van Duijn and colleagues propose that minimal cognition can be understood in terms of sensorimotor coordination – that is the coordination between sensory apparatus of an organism and the motor processes that move it around the environment (2006). Despite there being much to recommend this account it still faces some challenges. For example, it does not accord with the intuition that there are cognitive processes that have little to do with sensorimotor coupling, it relies on a strong distinction between metabolic and cognitive processes, and perhaps counterintuitively it denies cognition to plants but grants it to the bacteria on their roots that perform various functions for them. Moreover, it is difficult to see how to account for cognition over the transition from single to multicellular organisms. This paper proposes taking a more radical view of cognition to be what happens in swarms – the coordination of multiple processes through the traces of their actions in the environment. Key to this approach is the observation that the structure of the environment plays an active coordinative role and that this structure results in part from the actions of the system that it helps coordinate. Systems develop sensitivity to the appropriate trace variables in the environment. Viewed as collections of processes bacteria, biofilms, plants, animals can be viewed as cognitive systems in this framework and it has the potential to be applied to the social world.

Stigmergic coordination and minimal cognition in plants

The tricky question in the plant cognition debate is what theory of cognition should be used to fix the reference of cognitive concepts without skewing the debate too much one way or the other. After all, plants are rather different to animals in many respects: they are not motile, do not possess central nervous systems or even neurons, do not exhibit an invariant morphology, interact with the world in a distributed multi-centred manner, and behave through changes in their physiology. Nonetheless, there is a significant strand in the debate that asserts that plants are indeed cognitive. But what theory of cognition makes sense of this claim without baking in prior zoological assumptions? The aim of this paper is to try out a theory of minimal cognition that makes the claim of plant cognition plausible. It is primarily inspired by the distributed cognition literature and the sensorimotor coordination theory of cognition proposed by van Duijn et al. (2006) . We take a cognitive system to be a coordinated set of semi-autonomous processes running over the organism and items in its environment. Coordination is characterised in terms of two functional conditions that ensure that the system generates goal-directed action in the world. The system is stigmergic in the sense that the material results of its actions in the environment are a crucial part of the processes that coordinate further actions. The account possesses a degree of scale invariance and helps unify cognitive explanation across microorganisms, plants and animals.

Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer's disease.

Translating human genetic findings (genome-wide association studies [GWAS]) to pathobiology and therapeutic discovery remains a major challenge for Alzheimer's disease (AD). We present a network topology-based deep learning framework to identify disease-associated genes (NETTAG). We leverage non-coding GWAS loci effects on quantitative trait loci, enhancers and CpG islands, promoter regions, open chromatin, and promoter flanking regions under the protein-protein interactome. Via NETTAG, we identified 156 AD-risk genes enriched in druggable targets. Combining network-based prediction and retrospective case-control observations with 10 million individuals, we identified that usage of four drugs (ibuprofen, gemfibrozil, cholecalciferol, and ceftriaxone) is associated with reduced likelihood of AD incidence. Gemfibrozil (an approved lipid regulator) is significantly associated with 43% reduced risk of AD compared with simvastatin using an active-comparator design (95% confidence interval 0.51-0.63, p<0.0001). In summary, NETTAG offers a deep learning methodology that utilizes GWAS and multi-genomic findings to identify pathobiology and drug repurposing in AD.

Corrigendum: Uncertainties shaping parental educational decisions: The case of Syrian refugee children in Turkey

The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.In the published article, the reference for [Dustron, 2019] was removed in author's proof. However, it still exists in the published article. The citation [Durston, 2019] and its reference [Durston, S., Duncalf, J., Alkassem, M., and Serdar, F. (2019). Evaluation of UNICEF's support to Education Personnel in the Syria Crisis Response in Turkey.] should be removed.PAGE \* Arabic \* MERGEFORMAT 3The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.In the published article, there was an error in Ethic Statement. In this way, it seems that the research protocol has been approved by an individual rather than a committee:The text appears as "The studies involving human participants were reviewed and approved by Dr. Marijtje A.J. van Duijn Groningen University. The patients/participants provided their written informed consent to participate in this study."The correct statement should be as "The studies involving human participants were reviewed and approved by Dr. Marijtje A.J. van Duijn, the head of the Research Ethics Committee at the Department of Sociology at University of Groningen. The participants provided their written informed consent to participate in this study."

Mathematical theory and simulations of thermoporoelasticity

In this paper we study the equations of semi-linear thermoporoelasticity. Starting point is the dimensionless formulation in van Duijn et al. (2019), which was obtained by a formal two-scale expansion. Nonlinearities in the equations arise through the fluid viscosity and the thermal conductivity, both may depend on temperature, and through the coupling in the heat convection by the Darcy discharge in the energy equation. The coupled system of equations involves as unknowns the skeleton displacement, Darcy discharge, fluid pressure and temperature. We treat the system in its incremental (i.e. time-discrete) form. We prove existence by applying a fundamental theorem of Brézis on pseudo-monotone operators. Moreover we show that the free energy of the system acts as a Lyapunov functional. This yields global stability in the time-stepping process. Our theoretical results are substantiated with two-dimensional numerical tests using a monolithic formulation. Temporal discretization is based on the backward Euler scheme and finite elements are employed for the spatial discretization. The semi-linear discrete system is solved with Newton’s method. In the proposed numerical examples, different source terms are employed and spatial mesh refinement studies show computational convergence.

Wetting fronts in unsaturated porous media: The combined case of hysteresis and dynamic capillary pressure

This paper extends the work of van Duijn et al. (2018) where travelling wave solutions for wetting fronts were considered under the presence of only capillary hysteresis effect and only dynamic capillary effect. In this work, we investigate how the gravity driven wetting fronts behave while moving through long vertical homogeneous porous columns, under the combined effect of capillary hysteresis and dynamic capillarity. It is shown that the developed saturation profiles will exhibit non-monotone behaviour if certain parametric conditions are satisfied. The characteristics of the profiles are explained in detail for all the cases. Moreover, parametric conditions that inhibit the fronts from reaching full saturation are laid out. The analysis agrees well with experimental observations. Finally, numerical results are shown that confirm all the theoretical predictions.

A priori error analysis for transient problems using Enhanced Velocity approach in the discrete-time setting

Time discretization along with space discretization is important in the numerical simulation of subsurface flow applications for long run. In this paper, we derive theoretical convergence error estimates in discrete-time setting for transient problems with the Dirichlet boundary condition. Enhanced Velocity Mixed FEM as domain decomposition method is used in the space discretization and the backward Euler method and the Crank-Nicolson method are considered in the discrete-time setting. Enhanced Velocity scheme was used in the adaptive mesh refinement dealing with heterogeneous porous media [1, 2] for single phase flow and transport and demonstrated as mass conservative and efficient method. Numerical tests validating the backward Euler theory are presented. This error estimates are useful in the determining of time step size and the space discretization size. References. [1] Yerlan Amanbek, Gurpreet Singh, Mary F Wheeler, and Hans van Duijn. Adaptive numerical homogenization for upscaling single phase flow and transport. ICES Report,12:17, 2017. [2] Gurpreet Singh, Yerlan Amanbek, and Mary F Wheeler. Adaptive homogenization for upscaling heterogeneous porous medium. In SPE Annual Technical Conference and Exhibition. Society of Petroleum Engineers, 2017.

Демографический дайджест

&#x0D; Balistreri K.S., K. Joyner, G. Kao. Trading Youth for Citizenship? The Spousal Age Gap in Cross-Border Marriages. &#x0D; Kolk M., M. Hällsten. Demographic and Educational Success of Lineages in Northern Sweden. &#x0D; Monnet E., C. Wolf. Demographic cycles, migration and housing investment. &#x0D; Lee R., Y. Zhou. Does Fertility or Mortality Drive Contemporary Population Aging? The Revisionist View Revisited. &#x0D; Cahill K.E., M.D. Giandrea, J.F. Quinn. To What Extent is Gradual Retirement a Product of Financial Necessity? &#x0D; Damman M., R. Van Duijn. Intergenerational Support in the Transition From Work to Retirement. &#x0D; DeWaard J., J.T. Ha, J. Raymer, A. Wiśniowski. Migration from New-Accession Countries and Duration Expectancy in the EU-15: 2002–2008.&#x0D; Vidal S., J. Huinink, M. Feldhaus. Fertility Intentions and Residential Relocations. &#x0D; Schlaffer J.S. Financing Public Education Facilities: The Role of Elderly Populations and Geographic Mobility.&#x0D; Grow A., C. Schnor, J. Van Bavel. The reversal of the gender gap in education and relative divorce risks: A matter of alternatives in partner choice? &#x0D; Zarulli V., J.A.B. Jones, A. Oksuzyan, R. Lindahl-Jacobsen, K. Christensen, J.W. Vaupel. Women live longer than men even during severe famines and epidemics. &#x0D; Kashnitsky I., J. Schöley. Regional population structures at a glance. &#x0D;

Editorial introduction

One year ago, in July 2017, 173 statisticians from all around the world gathered in Groningen, (The Netherlands) for a whole week to celebrate the 32nd International Workshop on Statistical Modelling (IWSM) 2017. The scientific program of IWSM 2017 comprised a one-day short course on Statistical Models for Social Network Dynamics, five invited keynote talks, 57 contributed talks, and 51 poster contributions. As usual for the IWSM workshop series, nearly all topical fields of Statistical Modelling were covered, and the peer-reviewed contributions were of high scientific quality. Fortunately, Marijtje van Duijn from the editorial board of Statistica Neerlandica had a great idea and suggested to launch a Statistica Neerlandica special issue on Statistical Modelling, featuring selected IWSM 2017 contributions. In my role as chair of the IWSM, I liked this idea to bundle some of the most interesting contributions in a special issue, and fortunately, the whole editorial board of Statistica Neerlandica supported Marijtje's idea as well. During last year's IWSM workshop, we selected the most appropriate contributions and invited the presenters to submit scientific papers on their works. To ensure the highest scientific quality, all submitted papers underwent a strict peer review process, and only the finally accepted papers have been published in this special issue. This is the special issue that so many statistical modellers have been waiting for: It consists of 11 articles with an average length of exactly 20 pages (standard deviation: 6.47), and I am convinced that the papers are representative of typical IWSM contributions. Moreover, I hope that the reader will enjoy reading the 11 articles as much as I enjoyed editing them. I thank the Statistical Modelling Society (Amsterdam) for giving me the opportunity to host the IWSM in Groningen in 2017. My thanks also go to the editorial board of Statistica Neerlandica for supporting the idea to launch a special issue on Statistical Modelling and for making me the responsible guest editor of this special issue. I also would like to thank all the members of the scientific committee and the local organizing committee for the support before and at the IWSM 2017. Special thanks go to the sponsors of IWSM 2017, especially to the “Koninklijke Nederlandse Akademie van Wetenschappen” (KNAW), the “Netherlands Organisation for Scientific Research” (NWO), the Dutch “Stochastics - Theoretical and Applied Research” (STAR) cluster, R studio, the province and city of Groningen, C. R. Rao Stichting, and the Toyota Motor Corporation. Finally yet importantly, I would like to thank all the authors who contributed to this special issue. On a personal note, I would like to add that I am very happy that the contributing authors, the editorial board of Statistica Neerlandica, and the editors of Wiley worked so hard and efficiently, so that I can keep my promise, namely that the special issue will have been published in July 2018. This paper is in pleasant anticipation of the IWSM 2018, which will shortly take place in Bristol, England (15–20 July 2018).

Rapid Detection of Urinary Tract Infections via Bacterial Nuclease Activity

Rapid and accurate bacterial detection methods are needed for clinical diagnostic, water, and food testing applications. The wide diversity of bacterial nucleases provides a rich source of enzymes that could be exploited as signal amplifying biomarkers to enable rapid, selective detection of bacterial species. With the exception of the use of micrococcal nuclease activity to detect Staphylococcus aureus, rapid methods that detect bacterial pathogens via their nuclease activities have not beendeveloped. Here, we identify endonuclease I as a robust biomarker for E.coli and develop a rapid ultrasensitive assay that detects its activity. Comparison of nuclease activities of wild-type and nuclease-knockout E.coli clones revealed that endonuclease I is the predominant DNase in E.coli lysates. Endonuclease I is detectable by immunoblot and activity assays in uropathogenic E.coli strains. A rapid assay that detects endonuclease I activity in patient urine with an oligonucleotide probe exhibited substantially higher sensitivity for urinary tract infections than that reported for rapid urinalysis methods. The 3hr turnaround time is much shorter than that of culture-based methods, thereby providing a means for expedited administration of appropriate antimicrobial therapy. We suggest this approach could address various unmet needs for rapid detection of E.coli.

Homogenization of a pore scale model for precipitation and dissolution in porous media

In this article, we employ homogenization techniques to provide a rigorous derivation of the Darcy scale model for precipitation and dissolution in porous media. The starting point is the pore scale model in van Duijn & Pop (2004 ), which is a coupled system of evolution equations, involving a parabolic equation which models ion transport in the fluid phase of a periodic porous medium, coupled to an ordinary differential equations modelling dissolution and precipitation at the grains boundary. The main challenge is in dealing with the dissolution and precipitation rates, which involve a monotone but possibly discontinuous function. In order to pass to the limit in these rate functions at the boundary of the grains, we prove strong two-scale convergence for the concentrations at the microscopic boundary and use refined arguments in order to identify the form of the macroscopic dissolution rate, which is again a discontinuous function. The resulting upscaled model is consistent with the Darcy scale model proposed in Knabner et al . (1995 ).

Editorial

A few months ago, Philip Hans Franses stepped down as editor of Statistica Neerlandica after a tenure of many years. Let me start this editorial by thanking him for the excellent job he has achieved for such a long time. It is a testimony to the enormous size of Philip Hans' shoes that we have felt the need to fill them not with one but with three new editors: myself (Eric Cator), Marijtje van Duijn and Erik van Zwet. Roughly speaking, I will focus on mathematical statistics, Marijtje on statistics for the behavioural sciences and Erik on biostatistics. Statistica Neerlandica has always had a very wide scope, covering all areas of statistics, from theoretical to applied. The diversity of our editorial team will ensure the continuation of this tradition and hopefully send a message to a broad range of authors to consider us for their work. The change in editorship has also meant that we have renewed much of the editorial board. While several associate editors have been very kind to stay on, we say goodbye to Paul Eilers, Rob Eisinga, Patrick Groenen, Geurt Jongbloed, Alfred Stein and Peter van der Heijden. We thank them for all their selfless help in the past few years. We are very excited to welcome Ismael Castillo, Lutz Dümbgen, Anuska Ferligoj, Richard Gill, Jelle J. Goeman, Peter Grünwald, Alexandre Tsybakov, Mark J. van der Laan, Aad van der Vaart, Michel van der Wel and Jon Wellner as new associate editors. We look forward to working with them (some might say: harassing them) and learning from them. The editorial board continues its commitment to a fast and fair reviewing process and will judge submissions on quality, correctness, relevance and originality. Statistica Neerlandica encourages transparency and reproducibility and offers online resources to make data, code, simulation results and other additional materials publicly available. We have many plans for the future. In particular, we would like to dedicate special issues to conferences, and in fact, we already made a tentative start with the IBS 2015 Channel Meeting in Utrecht. Special issues around topics of current interest are also high on our list, and your (the reader's) suggestions are very welcome. Statistica Neerlandica has been the journal of the Netherlands Society for Statistics and Operations Research since 1946. We are honoured to edit a journal with such a long and venerable history but, even more than that, we look forward to an exciting future. We will not be able to do much without your support, though, so please keep sending us your work!

Both Targeted Mass Spectrometry and Flow Sorting Analysis Methods Detected the Decreased Serum Apolipoprotein E Level in Alzheimer's Disease Patients

Apolipoprotein E (ApoE) polymorphism has been appreciated as a valuable predictor of Alzheimer disease (AD), and the associated ε4 allele has been recognized as an indicator of susceptibility to this disease. However, serum ApoE levels have been a controversial issue in AD, due to the great variability regarding the different target detection methods, ethnicity, and the geographic variations of cohorts. The aim of this study was to validate serum ApoE levels in relation to AD, particularly using two distinct detection methods, liquid chromatography-selected reaction monitoring (SRM) mass spectrometry and microsphere-based fluorescence-activated cell sorting (FACS) analysis, to overcome experimental variations. Also, comparison of serum ApoE levels was performed between the level of protein detection by FACS and peptide level by SRM in both control and AD patients. Results from the two detection methods were cross-confirmed and validated. Both methods produced fairly consistent results, showing a significant decrease of serum ApoE levels in AD patients relative to those of a control cohort (43 control versus 45 AD, p < 0.0001). Significant correlation has been revealed between results from FACS and SRM (p < 0.0001) even though lower serum ApoE concentration values were measured in protein by FACS analysis than in peptide-level detections by SRM. Correlation study suggested that a decrease of the serum ApoE level in AD is related to the mini-mental state exam score in both results from different experimental methods, but it failed to show consistent correlation with age, gender, or clinical dementia rating.

Cognitive Deficits and Disruption of Neurogenesis in a Mouse Model of Apolipoprotein E4 Domain Interaction

Apolipoprotein E4 (apoE4) allele is the major genetic risk factor for sporadic Alzheimer disease (AD) due to the higher prevalence and earlier onset of AD in apoE4 carriers. Accumulating data suggest that the interaction between the N- and the C-terminal domains in the protein may be the main pathologic feature of apoE4. To test this hypothesis, we used Arg-61 mice, a model of apoE4 domain interaction, by introducing the domain interaction feature of human apoE4 into native mouse apoE. We carried out hippocampus-dependent learning and memory tests and related cellular and molecular assays on 12- and 3-month-old Arg-61 and age-matched background C57BL/6J mice. Learning and memory task performance were impaired in Arg-61 mice at both old and young ages compared with C57BL/6J mice. Surprisingly, young Arg-61 mice had more mitotic doublecortin-positive cells in the subgranular zone; mRNA levels of brain-derived neurotrophic factor (BDNF) and TrkB were also higher in 3-month-old Arg-61 hippocampus compared with C57BL/6J mice. These early-age neurotrophic and neurogenic (proliferative) effects in the Arg-61 mouse may be an inadequate compensatory but eventually detrimental attempt by the system to "repair" itself. This is supported by the higher cleaved caspase-3 levels in the young animals that not only persisted, but increased in old age, and the lower levels of doublecortin at old age in the hippocampus of Arg-61 mice. These results are consistent with human apoE4-dependent cognitive and neuro-pathologic changes, supporting the principal role of domain interaction in the pathologic effect of apoE4. Domain interaction is, therefore, a viable therapeutic/prophylactic target for cognitive impairment and AD in apoE4 subjects.

OP0263-PARE Patient Involvement in E-Health Research and Intervention Development

BackgroundResults from early E-health research for patients with several chronic somatic conditions including rheumatoid arthritis are promising [1]. Despite obvious advantages of E-health interventions for patients, research also shows high...

THU0590 The Patient-Therapist Relationship as An Indicator for Treatment Success in E-Health Treatments for Patients with Rheumatoid Arthritis and Psorias

BackgroundThe popularity of E-health is rising and research has shown that E-health interventions can be effective [1]. However, they also offer new challenges and questions in clinical practice and research,...

Special issue “Mathematics of Porous Media,” dedicated to Professor C.J. van Duijn on the occasion of his 60th anniversary

This special issue contains selected contributions from the conference “The Mathematics of Porous Media,” organized in Split (Croatia), June 13–15, 2011. This meeting has celebrated the 60th anniversary of Prof. Dr. Ir. Cornelis Johannes (Hans) van Duijn, who is one of the founding editors of this journal. Hans van Duijn was born in 1950 in Rotterdam, The Netherlands, but he grew up in the city of Middelburg in Zeeland. Coming from a family background where high school education was not self-evident, Hans graduated only with a “middle” level which did not allow for university studies. After having gained a degree at a technical college only after 3 years in time, it was certainly a big step for him to enroll in 1972 at Eindhoven University of Technology in Physics. Three years later, having earned an “engineer” degree with distinction and with his interest in applied mathematics ignited, Hans made an even more fundamental step when he entered the office of Bert Peletier of the Mathematics Department of Delft University of Technology. Peletier was so impressed by this young man with the “wrong” degree that he offered him a position as PhD student. When in 1977 Peletier moved to Leiden University, Hans moved too, and in 1979,

We screen newborns, don't we?: realizing the promise of public health genomics.

Genomics and public health have been uneasy bedfellows for some time. Most efforts to improve population health through genomic approaches have focused on the assessment of risks for common diseases, with the aim of tailoring interventions and screening.1 However, the improvement of population health through such an approach has remained elusive.2 Now, rapid progress in affordable, robust DNA sequencing offers a promising opportunity. By expanding the field’s focus from common to rare diseases, it may be possible to realize the promise of public health genomics by identifying those millions of individuals who unknowingly carry mutations that confer a dramatic predisposition to preventable diseases.

BiotecVisions 2013, March

BiotecVisions 2013, March