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Article ; Online: Time-Varying Parameters in Econometrics: The editor’s foreword

Blasques, F. / Harvey, A.C. / Koopman, S.J. / Lucas, A.

Journal of Econometrics. 2023 Apr. 03, p.105439-

2023 , Page(s) 105439–

Abstract: The Themed Issue Time-Varying Parameters in Econometrics consists of eight papers where theoretical, methodological and empirical developments are reported. Particular attention is given to observation-driven time-varying parameter models of which score- ... ...

Abstract	The Themed Issue Time-Varying Parameters in Econometrics consists of eight papers where theoretical, methodological and empirical developments are reported. Particular attention is given to observation-driven time-varying parameter models of which score-driven models is a sub-class. We will introduce the Themed Issue and review its contributions.
Keywords	econometrics ; journals ; models ; wills ; C31 ; C32 ; Observation-driven time series models ; Score-driven time series models ; Financial econometrics
Language	English
Dates of publication	2023-0403
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	1460617-3
ISSN	0304-4076
ISSN	0304-4076
DOI	10.1016/j.jeconom.2023.03.007
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Effect of Population Partitioning on the Probability of Silent Circulation of Poliovirus.

Vallejo, Celeste / Pearson, Carl A B / Koopman, James S / Hladish, Thomas J

Bulletin of mathematical biology

2022 Volume 84, Issue 6, Page(s) 62

Abstract: Polio can circulate unobserved in regions that are challenging to monitor. To assess the probability of silent circulation, simulation models can be used to understand transmission dynamics when detection is unreliable. Model assumptions, however, impact ...

Abstract	Polio can circulate unobserved in regions that are challenging to monitor. To assess the probability of silent circulation, simulation models can be used to understand transmission dynamics when detection is unreliable. Model assumptions, however, impact the estimated probability of silent circulation. Here, we examine the impact of having distinct populations, rather than a single well-mixed population, with a discrete-individual model including environmental surveillance. We show that partitioning a well-mixed population into networks of distinct communities may result in a higher probability of silent circulation as a result of the time it takes for the detection of a circulation event. Population structure should be considered when assessing polio control in a region with many loosely interacting communities.
MeSH term(s)	Humans ; Mathematical Concepts ; Models, Biological ; Poliomyelitis/diagnosis ; Poliomyelitis/epidemiology ; Poliomyelitis/prevention & control ; Poliovirus ; Probability
Language	English
Publishing date	2022-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-022-01014-6
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Article ; Online: An investigation of pathways for rebuilding Australia’s sheep flock

Brien, F. D. / Pitchford, R. L. / Vogt, S. P. / Koopman, D. J.

Animal Production Science. 2023, v. 63, no. 13 p.1310-1323

2023

Abstract: ... products to Australia’s customers, which requires a more rapid rebuilding of the national sheep ...

Abstract	Context A significant opportunity remains to further increase the supply of premium sheepmeat products to Australia’s customers, which requires a more rapid rebuilding of the national sheep flock. To help meet this challenge, developing relevant information for sheep producers to assist them to achieve a profitable flock-rebuilding outcome is viewed as highly desirable. Aims (1) Develop flock-rebuild scenarios that track inventory, cashflow, profit and loss, and the overall balance sheet over a 5-year projection. (2) Model the impact on flock-rebuilding pathways of exposure to variation in supplementary-feed costs, purchase of stock and price received for sale animals and flock structure. (3) Model variation in benefits and costs for a range of production zones, enterprise types and flock-age profiles. Methods Fourteen flock-rebuilding pathways were assessed for up to nine flock types, using a spreadsheet model that tracked inventory, cashflow, profit and loss, and the overall balance sheet over 5years. Key results The top four pathways for profitability and capacity to rapidly rebuild flock numbers include retention of more older ewes, purchasing young ewes, purchasing older ewes (mostly 5–6-year olds) in Merino and Merino-cross flock types only and joining ewe lambs in Maternal and Cleanskin flock types only. These pathways were not sensitive to variation in the cost of supplementary feed, stock prices or flock structure, although joining Merino ewe lambs became one of the top four pathways when feed costs were lower. Conclusions and implications The well established practices of retaining ewes for longer and purchasing ewes, especially young ewes, have the most potential to both rapidly and profitably rebuild flock numbers. However, joining ewe lambs, particularly in Maternal and Cleanskin flocks, can also profitably contribute to rapid flock rebuilding. While reducing reproductive wastage or increasing reproductive potential were mostly profitable, they could not rapidly rebuild flock numbers. In contrast, accelerated lambing systems can rapidly rebuild flock numbers, but are only marginally profitable.
Keywords	Merino ; animal production ; balance sheet ; business enterprises ; ewes ; feed supplements ; flocks ; inventories ; models ; prices ; profitability ; drought ; joining ; modelling ; rebuilding ; reproduction ; restocking ; sheep
Language	English
Size	p. 1310-1323.
Publishing place	CSIRO Publishing
Document type	Article ; Online
ZDB-ID	2472524-9
ISSN	1836-5787 ; 1836-0939
ISSN (online)	1836-5787
ISSN	1836-0939
DOI	10.1071/AN22121
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Article ; Online: A framework for building comprehensive cancer center's capacity for bidirectional engagement.

Trapl, Erika S / Koopman Gonzalez, Sarah / Austin, Kristina

Cancer causes & control : CCC

2024

Abstract: Purpose: Community engagement has benefits for cancer centers' work and for its researchers. This study examined the experiences and perceptions of community engagement by members of the Case Comprehensive Cancer Center (Case CCC) to create and ... ...

Abstract	Purpose: Community engagement has benefits for cancer centers' work and for its researchers. This study examined the experiences and perceptions of community engagement by members of the Case Comprehensive Cancer Center (Case CCC) to create and implement a framework to meet the needs of the entire cancer center. Methods: This study included three phases: 1) Semi-structured interviews with 12 researchers from a basic science program to identify needs and suggestions for the support of community engagement; 2) Preliminary interview results informed the development of a survey of 86 cancer center members' about their awareness of and readiness to integrate community outreach and engagement into their research; and 3) The Case CCC Office of Community Outreach and Engagement reviewed the results from phases 1 and 2 to develop and then utilize a framework of engagement opportunities. Results: In the interviews and surveys, cancer center members recognized the importance of community engagement and expressed an interest in participating in COE-organized opportunities for bidirectional engagement. While participation barriers include communication issues, limited awareness of opportunities, and competing priorities, members were open to learning new skills, changing approaches, and utilizing services to facilitate engagement. The framework outlines engagement opportunities ranging from high touch, low reach to low touch, and high reach and was used to develop specific services. Conclusion: This study identified varying needs around community engagement using an approach aimed at understanding the perspectives of a community of scientists. Implementing the framework enables reaching scientists in different ways and facilitates scientists' recognition of and engagement with opportunities.
Language	English
Publishing date	2024-02-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1064022-8
ISSN	1573-7225 ; 0957-5243
ISSN (online)	1573-7225
ISSN	0957-5243
DOI	10.1007/s10552-023-01848-y
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Article ; Online: Humans need only 200 ms to generate posture-specific muscle activation patterns for successful vertical jumps in reaction to an auditory trigger.

Bobbert, Maarten F / Koopman, Axel S

Frontiers in sports and active living

2023 Volume 5, Page(s) 1123335

Abstract: Introduction: It is currently unknown how the central nervous system controls ballistic whole-body movements like vertical jumps. Here we set out to study the time frame of generating muscle activation patterns for maximum-effort jumps from different ... ...

Abstract	Introduction: It is currently unknown how the central nervous system controls ballistic whole-body movements like vertical jumps. Here we set out to study the time frame of generating muscle activation patterns for maximum-effort jumps from different initial postures. Methods: We had ten healthy male participants make a slow countermovement from an upright position and initiate a maximal vertical jump as soon as possible following an auditory trigger. The trigger was produced when hip height dropped below one of three preselected values, unknown in advance to the participant, so that the participant was uncertain about the posture from which to initiate the jump. Furthermore, we determined the ensuing bottom postures reached during jumps, and from these postures had the participants perform maximum-effort squat jumps in two conditions: whenever they felt ready, or as soon as possible following an auditory trigger. Kinematics and ground reaction forces were measured, and electromyograms were collected from gluteus maximus, biceps femoris, rectus femoris, vastus lateralis, gastrocnemius and soleus. For each muscle, we detected activation onsets, as well as reaction times defined as the delay between trigger onset and activation onset. Results: In the jumps preceded by a slow countermovement, the posture from which to initiate the jump was unknown before trigger onset. Nevertheless, in these jumps, posture-specific muscle activation patterns were already released within 200 ms after trigger onset and reaction times were not longer and jump heights not less than in squat jumps from corresponding bottom postures. Discussion: Our findings suggest that the generation of muscle activation patterns for jumping does not start before trigger onset and requires only about 200 ms.
Language	English
Publishing date	2023-05-17
Publishing country	Switzerland
Document type	Journal Article
ISSN	2624-9367
ISSN (online)	2624-9367
DOI	10.3389/fspor.2023.1123335
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Article ; Online: Models and analyses to understand threats to polio eradication.

Koopman, James S

BMC medicine

2017 Volume 15, Issue 1, Page(s) 221

Abstract: To achieve complete polio eradication, the live oral poliovirus vaccine (OPV) currently used must be phased out after the end of wild poliovirus transmission. However, poorly understood threats may arise when OPV use is stopped. To counter these threats, ...

Abstract	To achieve complete polio eradication, the live oral poliovirus vaccine (OPV) currently used must be phased out after the end of wild poliovirus transmission. However, poorly understood threats may arise when OPV use is stopped. To counter these threats, better models than those currently available are needed. Two articles recently published in BMC Medicine address these issues. Mercer et al. (BMC Med 15:180, 2017) developed a statistical model analysis of polio case data and characteristics of cases occurring in several districts in Pakistan to inform resource allocation decisions. Nevertheless, despite having the potential to accelerate the elimination of polio cases, their analyses are unlikely to advance our understanding OPV cessation threats. McCarthy et al. (BMC Med 15:175, 2017) explored one such threat, namely the emergence and transmission of serotype 2 circulating vaccine derived poliovirus (cVDPV2) after OPV2 cessation, and found that the risk of persistent spread of cVDPV2 to new areas increases rapidly 1-5 years after OPV2 cessation. Thus, recently developed models and analysis methods have the potential to guide the required steps to surpass these threats. 'Big data' scientists could help with this; however, datasets covering all eradication efforts should be made readily available.Please see related articles: https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-017-0937-y and https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-017-0941-2 .
MeSH term(s)	Disease Eradication ; Disease Outbreaks/prevention & control ; Humans ; Pakistan ; Poliomyelitis/epidemiology ; Poliovirus/immunology ; Poliovirus Vaccine, Oral/immunology
Chemical Substances	Poliovirus Vaccine, Oral
Language	English
Publishing date	2017--22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
ISSN	1741-7015
ISSN (online)	1741-7015
DOI	10.1186/s12916-017-0991-5
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Article: Performance evaluation of air-source heat pump based on a pressure drop embedded model.

Koopman, Tim / Zhu, Tingting / Rohlfs, Wilko

Heliyon

2024 Volume 10, Issue 4, Page(s) e24634

Abstract: ... has been developed. The model is capable of computing the heat pump's coefficient of performance (COP ... for three different refrigerants, R410A, R32 and R290, are compared. The model's accuracy is validated ...

Abstract	An air-source heat pump simulation model, accounting for evaporator and condenser pressure drop, has been developed. The model is capable of computing the heat pump's coefficient of performance (COP) under different ambient temperatures and relative humidities above frosting conditions. This research extends an existing iterative simulation method that relies on the equalization of logarithmic mean temperature differences (LMTDs) calculated through two different approaches by adding a pressure drop simulation. Frictional and acceleration pressure drop is considered, computed iteratively. Simulation results for three different refrigerants, R410A, R32 and R290, are compared. The model's accuracy is validated by comparing simulated COP values with measured COP values from the reference heat pump datasheet. The model closely replicates the measured COP values above frosting conditions, with only a slight underestimation of approximately 1.5%. Results show a substantial impact of ambient temperature on the COP. For instance, an ambient temperature of 20
Language	English
Publishing date	2024-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e24634
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Article ; Online: Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules.

Koopman, Jeroen / Grimme, Stefan

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 12, Page(s) 2226–2242

Abstract: Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass ... ...

Abstract	Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.
MeSH term(s)	Mass Spectrometry
Language	English
Publishing date	2022-11-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.2c00209
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Article ; Online: Modeling the dynamics of SARS-CoV-2 immunity waning, antigenic drifting, and population serology patterns

Koopman, J. S. / Simon, C. P.

Abstract: Reinfection with SARS-CoV-2 can result from either waning immunity, a drift in the virus that escapes previously stimulated immunity, or both. The nature of such reinfection risks will affect the choice of control tactics and vaccines. We constructed an ... ...

Abstract	Reinfection with SARS-CoV-2 can result from either waning immunity, a drift in the virus that escapes previously stimulated immunity, or both. The nature of such reinfection risks will affect the choice of control tactics and vaccines. We constructed an SIR transmission model of waning and drifting that can be fitted to cross-neutralization serological data. In this model, waning occurs in individuals who have recovered from previous infections while drifting occurs during transmission to a previously infected individual. Interactions at the population level generate complex dynamics that cause drifting to occur in unanticipated but explainable ways across waning and drifting parameter sets. In particular, raising the fraction of transmissions where drifting occurs slows the rise of drifted strains to high levels and changes the equilibrium distribution of strains from {cup} shaped (extreme strains dominate) to {cap} shaped (central strains dominate). In {cup} shaped parameter regimes, endemic infection levels can rise after many years to above the original epidemic peak. The model simulates results from cross-neutralization assays given sera from previously infected individuals when multiple drifted strains are used in the assays. Fitting the model to such assay data can estimate waning and drifting parameters. Given the parameters, the model predicts infection patterns. We propose a process for using fits of our model to serological and other data called Decision Robustness and Identifiability Analysis (DRIA). This can inform decisions about vaccine options such as whether to prepare for changes in vaccine composition because the virus is changing to escape immunity.
Keywords	covid19
Publisher	MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.09.10.20192153
Database	COVID19

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Article ; Online: Live-Cell Assessment of Reactive Oxygen Species Levels Using Dihydroethidine.

Grefte, Sander / Koopman, Werner J H

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2275, Page(s) 291–299

Abstract: Reactive oxygen species (ROS) play an important role in cellular (patho)physiology. Empirical evidence suggests that mitochondria are an important source of ROS, especially under pathological conditions. Here, we describe a method for ROS measurement ... ...

Abstract	Reactive oxygen species (ROS) play an important role in cellular (patho)physiology. Empirical evidence suggests that mitochondria are an important source of ROS, especially under pathological conditions. Here, we describe a method for ROS measurement using dihydroethidium (HEt) and live-cell microscopy.
MeSH term(s)	Cells, Cultured ; Dicarbethoxydihydrocollidine/analogs & derivatives ; Dicarbethoxydihydrocollidine/chemistry ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Fluorescent Dyes/chemistry ; HEK293 Cells ; Humans ; Membrane Potential, Mitochondrial ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Myoblasts/cytology ; Reactive Oxygen Species/analysis ; Skin/cytology ; Skin/metabolism
Chemical Substances	Fluorescent Dyes ; Reactive Oxygen Species ; dihydroethidine ; Dicarbethoxydihydrocollidine (632-93-9)
Language	English
Publishing date	2021-06-12
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1262-0_18
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