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Article ; Online: Methods of Computational Analysis in Kidney Development.

Tikka, Pauli / Schaefer, Franz

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

2019 Volume 1926, Page(s) 235–246

Abstract: This chapter reviews some currently available methodologies for constructing mathematical models in kidney development. Mammalian nephrogenesis is a complex biological process, which in its earliest stages involves migration, condensation, proliferation, ...

Abstract	This chapter reviews some currently available methodologies for constructing mathematical models in kidney development. Mammalian nephrogenesis is a complex biological process, which in its earliest stages involves migration, condensation, proliferation, and differentiation of metanephric mesenchymal (MM) cells interacting with the uroepithelial cells of the ureteric bud (UB). First, the mathematical modelling in biology is generally described. Secondly, some accounts to biological pattern formation in modelling are given in general, including models that transcend the Turing model. This is followed by a short assessment on the main branch of models in the kidney development, the evaluation of the branching morphogenesis of the kidney. Finally, two alternative models in the early kidney development processes are given as an example. They also elucidate the difficulties in the model building process. Firstly, a computational model building with the CompuCell3D program for the early nephron progenitor cell movements with the key extracellular signaling effectors is depicted. This collective migration leads to the first pretubular aggregate (PTA). The simulation parameters of the program imitate the program's cell sorting example with different adhesions and chemoattractants. The program utilizes Cellular Potts Model (CPM) to describe the development. Secondly, an example of PTA to renal vesicle (RV) transition modelling is described. In that case, the model is unique, where the model process is based on the chemoattractants from UB.
MeSH term(s)	Animals ; Cell Differentiation/genetics ; Cell Differentiation/physiology ; Kidney/cytology ; Kidney/physiology ; Organ Culture Techniques/methods ; Organogenesis/genetics ; Organogenesis/physiology
Language	English
Publishing date	2019-02-11
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9021-4_19
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Prevalence of Short Peer Reviews in 3 Leading General Medical Journals.

Geldsetzer, Pascal / Heemann, Markus / Tikka, Pauli / Wang, Grace / Cusick, Marika Mae / Lenjani, Ali / Krishnan, Nandita

JAMA network open

2023 Volume 6, Issue 12, Page(s) e2347607

Abstract: Importance: High-quality peer reviews are often thought to be essential to ensuring the integrity of the scientific publication process, but measuring peer review quality is challenging. Although imperfect, review word count could potentially serve as a ...

Abstract	Importance: High-quality peer reviews are often thought to be essential to ensuring the integrity of the scientific publication process, but measuring peer review quality is challenging. Although imperfect, review word count could potentially serve as a simple, objective metric of review quality. Objective: To determine the prevalence of very short peer reviews and how often they inform editorial decisions on research articles in 3 leading general medical journals. Design, setting, and participants: This cross-sectional study compiled a data set of peer reviews from published, full-length original research articles from 3 general medical journals (The BMJ, PLOS Medicine, and BMC Medicine) between 2003 and 2022. Eligible articles were those with peer review data; all peer reviews used to make the first editorial decision (ie, accept vs revise and resubmit) were included. Main outcomes and measures: Prevalence of very short reviews was the primary outcome, which was defined as a review of fewer than 200 words. In secondary analyses, thresholds of fewer than 100 words and fewer than 300 words were used. Results were disaggregated by journal and year. The proportion of articles for which the first editorial decision was made based on a set of peer reviews in which very short reviews constituted 100%, 50% or more, 33% or more, and 20% or more of the reviews was calculated. Results: In this sample of 11 466 reviews (including 6086 in BMC Medicine, 3816 in The BMJ, and 1564 in PLOS Medicine) corresponding to 4038 published articles, the median (IQR) word count per review was 425 (253-575) words, and the mean (SD) word count was 520.0 (401.0) words. The overall prevalence of very short (<200 words) peer reviews was 1958 of 11 466 reviews (17.1%). Across the 3 journals, 843 of 4038 initial editorial decisions (20.9%) were based on review sets containing 50% or more very short reviews. The prevalence of very short reviews and share of editorial decisions based on review sets containing 50% or more very short reviews was highest for BMC Medicine (693 of 2585 editorial decisions [26.8%]) and lowest for The BMJ (76 of 1040 editorial decisions [7.3%]). Conclusion and relevance: In this study of 3 leading general medical journals, one-fifth of initial editorial decisions for published articles were likely based at least partially on reviews of such short length that they were unlikely to be of high quality. Future research could determine whether monitoring peer review length improves the quality of peer reviews and which interventions, such as incentives and norm-based interventions, may elicit more detailed reviews.
MeSH term(s)	Humans ; Cross-Sectional Studies ; Peer Review/standards ; Periodicals as Topic/standards ; Prevalence ; Publications
Language	English
Publishing date	2023-12-01
Publishing country	United States
Document type	Journal Article
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2023.47607
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Book ; Online ; Thesis: Modelling of Cell Movements and Aggregations During Early Nephrogenesis

Tikka, Pauli [Verfasser] / Schaefer, Franz [Akademischer Betreuer]

2021

Author's details	Pauli Tikka ; Betreuer: Franz Schaefer
Keywords	Naturwissenschaften ; Science
Subject code	sg500
Language	English
Publisher	Universitätsbibliothek Heidelberg
Publishing place	Heidelberg
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article: Ptch2 is a Potential Regulator of Mesenchymal Stem Cells.

Juuri, Emma / Tikka, Pauli / Domanskyi, Andrii / Corfe, Ian / Morita, Wataru / Mckinnon, Peter J / Jandova, Nela / Balic, Anamaria

Frontiers in physiology

2022 Volume 13, Page(s) 877565

Abstract: Ptch receptors 1 and 2 mediate Hedgehog signaling pivotal for organ development and homeostasis. In contrast to embryonic ... ...

Abstract	Ptch receptors 1 and 2 mediate Hedgehog signaling pivotal for organ development and homeostasis. In contrast to embryonic lethal
Language	English
Publishing date	2022-04-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2022.877565
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Article: Healthcare Worker Attendance During the Early Stages of the COVID-19 Pandemic: A Longitudinal Analysis of Daily Fingerprint-Verified Data from All Public-Sector Secondary and Tertiary Care Facilities in Bangladesh.

Do, Duy / Sarker, Malabika / Chen, Simiao / Lenjani, Ali / Tikka, Pauli / Bärnighausen, Till / Geldsetzer, Pascal

medRxiv : the preprint server for health sciences

2020

Abstract: Background: The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires healthcare workers (HCWs) to be present at work, particularly in low- and middle-income countries ( ... ...

Abstract	Background: The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires healthcare workers (HCWs) to be present at work, particularly in low- and middle-income countries (LMICs) where they are already in critically low supply. To inform whether and to what degree policymakers in Bangladesh, and LMICs more broadly, should expect a drop in HCW attendance as COVID-19 continues to spread, this study aims to determine how HCW attendance has changed during the early stages of the COVID-19 pandemic in Bangladesh. Methods: This study analyzed daily fingerprint-verified attendance data from all 527 public-sector secondary and tertiary care facilities in Bangladesh to describe HCW attendance from January 26, 2019 to March 22, 2020, by cadre, hospital type, and geographic division. We then regressed HCW attendance onto fixed effects for day-of-week, month, and hospital, as well as indicators for each of three pandemic periods: a China-focused period (January 11, 2020 [first confirmed COVID-19 death in China] until January 29, 2020), international-spread period (January 30, 2020 [World Health Organization declared a global emergency] until March 6, 2020), and local-spread period (March 7, 2020 [first confirmed COVID-19 case in Bangladesh] until the end of the study period). Findings: On average between January 26, 2019 and March 22, 2020, 34.1% of doctors, 64.6% of nurses, and 70.6% of other healthcare staff were present for their scheduled shift. Attendance rate increased with time in 2019 among all cadres. Attendance level of nurses dropped by 2.5% points (95% CI; -3.2% to -1.8%) and 3.5% points (95% CI; -4.5% to -2.5%) during the international-spread and the local-spread periods of the COVID-19 pandemic, relative to the China-focused period. Similarly, the attendance level of other healthcare staff declined by 0.3% points (95% CI; -0.8% to 0.2%) and 2.3% points (95% CI; -3.0% to -1.6%) during the international-spread and local-spread periods, respectively. Among doctors, however, the international-spread and local-spread periods were associated with a statistically significant increase in attendance by 3.7% points (95% CI; 2.5% to 4.8%) and 4.9% points (95% CI; 3.5% to 6.4%), respectively. The reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals, where the majority of COVID-19 testing and treatment took place, than that at small hospitals. Conclusions: After a year of significant improvements, attendance levels among nurses and other healthcare staff (who form the majority of the healthcare workforce in Bangladesh) have declined during the early stages of the COVID-19 pandemic. This finding may portend an even greater decrease in attendance if COVID-19 continues to spread in Bangladesh. Policymakers in Bangladesh and similar LMICs should undertake major efforts to achieve high attendance levels among HCWs, particularly nurses, such as by providing sufficient personal protective equipment as well as monetary and non-monetary incentives.
Keywords	covid19
Language	English
Publishing date	2020-09-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.09.01.20186445
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Healthcare worker attendance during the early stages of the COVID-19 pandemic: A longitudinal analysis of fingerprint-verified data from all public-sector secondary and tertiary care facilities in Bangladesh.

Do, Duy / Sarker, Malabika / Chen, Simiao / Lenjani, Ali / Tikka, Pauli / Bärnighausen, Till / Geldsetzer, Pascal

Journal of global health

2020 Volume 10, Issue 2, Page(s) 20509

Abstract: Background: The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires health care workers (HCWs) to be present at work, particularly in low- and middle-income countries ( ... ...

Abstract	Background: The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires health care workers (HCWs) to be present at work, particularly in low- and middle-income countries (LMICs) where they are already in critically low supply. To inform whether and to what degree policymakers in Bangladesh, and LMICs more broadly, should expect a drop in HCW attendance as COVID-19 continues to spread, this study aims to determine how HCW attendance has changed during the early stages of the COVID-19 pandemic in Bangladesh. Methods: This study analyzed daily fingerprint-verified attendance data from all 527 public-sector secondary and tertiary care facilities in Bangladesh to describe HCW attendance from January 26, 2019 to March 22, 2020, by cadre, hospital type, and geographic division. We then regressed HCW attendance onto fixed effects for day-of-week, month, and hospital, as well as indicators for each of three pandemic periods: a China-focused period (January 11, 2020 (first confirmed COVID-19 death in China) until January 29, 2020), international-spread period (January 30, 2020 (World Health Organization's declaration of a global emergency) until March 6, 2020), and local-spread period (March 7, 2020 (first confirmed COVID-19 case in Bangladesh) until the end of the study period). Findings: On average between January 26, 2019 and March 22, 2020, 34.1% of doctors, 64.6% of nurses, and 70.6% of other health care staff were present for their scheduled shift. HCWs' attendance rate increased with time in 2019 among all cadres. Nurses' attendance level dropped by 2.5% points (95% confidence interval (CI) = -3.2% to -1.8%) and 3.5% points (95% CI = -4.5% to -2.5%) during the international-spread and the local-spread periods of the COVID-19 pandemic, relative to the China-focused period. Similarly, the attendance level of other health care staff declined by 0.3% points (95% CI = -0.8% to 0.2%) and 2.3% points (95% CI = -3.0% to -1.6%) during the international-spread and local-spread periods, respectively. Among doctors, however, the international-spread and local-spread periods were associated with a statistically significant increase in attendance by 3.7% points (95% CI = 2.5% to 4.8%) and 4.9% points (95% CI = 3.5% to 6.4%), respectively. The reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals, where the majority of COVID-19 testing and treatment took place, than that at small hospitals. Conclusions: After a year of significant improvements, HCWs' attendance levels among nurses and other health care staff (who form the majority of Bangladesh's health care workforce) have declined during the early stages of the COVID-19 pandemic. This finding may portend an even greater decrease in attendance if COVID-19 continues to spread in Bangladesh. Policymakers in Bangladesh and similar LMICs should undertake major efforts to achieve high attendance levels among HCWs, particularly nurses, such as by providing sufficient personal protective equipment as well as monetary and non-monetary incentives.
MeSH term(s)	Adult ; Bangladesh/epidemiology ; Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Female ; Health Workforce/statistics & numerical data ; Hospitals, Public/statistics & numerical data ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral ; SARS-CoV-2 ; Secondary Care/organization & administration ; Secondary Care/statistics & numerical data ; Tertiary Healthcare/organization & administration ; Tertiary Healthcare/statistics & numerical data
Keywords	covid19
Language	English
Publishing date	2020-08-27
Publishing country	Scotland
Document type	Journal Article
ZDB-ID	2741629-X
ISSN	2047-2986 ; 2047-2986
ISSN (online)	2047-2986
ISSN	2047-2986
DOI	10.7189/jogh.10.020509
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Healthcare Worker Attendance During the Early Stages of the COVID-19 Pandemic: A Longitudinal Analysis of Daily Fingerprint-Verified Data from All Public-Sector Secondary and Tertiary Care Facilities in Bangladesh

Do, Duy / Sarker, Malabika / Chen, Simiao / Lenjani, Ali / Tikka, Pauli / Barnighausen, Till / Geldsetzer, Pascal

medRxiv

Abstract: Background. The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires healthcare workers (HCWs) to be present at work, particularly in low- and middle-income countries ( ... ...

Abstract	Background. The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires healthcare workers (HCWs) to be present at work, particularly in low- and middle-income countries (LMICs) where they are already in critically low supply. To inform whether and to what degree policymakers in Bangladesh, and LMICs more broadly, should expect a drop in HCW attendance as COVID-19 continues to spread, this study aims to determine how HCW attendance has changed during the early stages of the COVID-19 pandemic in Bangladesh. Methods. This study analyzed daily fingerprint-verified attendance data from all 527 public-sector secondary and tertiary care facilities in Bangladesh to describe HCW attendance from January 26, 2019 to March 22, 2020, by cadre, hospital type, and geographic division. We then regressed HCW attendance onto fixed effects for day-of-week, month, and hospital, as well as indicators for each of three pandemic periods: a China-focused period (January 11, 2020 [first confirmed COVID-19 death in China] until January 29, 2020), international-spread period (January 30, 2020 [World Health Organization declared a global emergency] until March 6, 2020), and local-spread period (March 7, 2020 [first confirmed COVID-19 case in Bangladesh] until the end of the study period). Findings. On average between January 26, 2019 and March 22, 2020, 34.1% of doctors, 64.6% of nurses, and 70.6% of other healthcare staff were present for their scheduled shift. Attendance rate increased with time in 2019 among all cadres. Attendance level of nurses dropped by 2.5% points (95% CI; -3.2% to -1.8%) and 3.5% points (95% CI; -4.5% to -2.5%) during the international-spread and the local-spread periods of the COVID-19 pandemic, relative to the China-focused period. Similarly, the attendance level of other healthcare staff declined by 0.3% points (95% CI; -0.8% to 0.2%) and 2.3% points (95% CI; -3.0% to -1.6%) during the international-spread and local-spread periods, respectively. Among doctors, however, the international-spread and local-spread periods were associated with a statistically significant increase in attendance by 3.7% points (95% CI; 2.5% to 4.8%) and 4.9% points (95% CI; 3.5% to 6.4%), respectively. The reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals, where the majority of COVID-19 testing and treatment took place, than that at small hospitals. Conclusions. After a year of significant improvements, attendance levels among nurses and other healthcare staff (who form the majority of the healthcare workforce in Bangladesh) have declined during the early stages of the COVID-19 pandemic. This finding may portend an even greater decrease in attendance if COVID-19 continues to spread in Bangladesh. Policymakers in Bangladesh and similar LMICs should undertake major efforts to achieve high attendance levels among HCWs, particularly nurses, such as by providing sufficient personal protective equipment as well as monetary and non-monetary incentives.
Keywords	covid19
Language	English
Publishing date	2020-09-03
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.09.01.20186445
Database	COVID19

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Article: Healthcare worker attendance during the early stages of the COVID-19 pandemic: A longitudinal analysis of fingerprint-verified data from all public-sector secondary and tertiary care facilities in Bangladesh

Do, Duy / Sarker, Malabika / Chen, Simiao / Lenjani, Ali / Tikka, Pauli / Bärnighausen, Till / Geldsetzer, Pascal

J Glob Health

Abstract: Background: The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires health care workers (HCWs) to be present at work, particularly in low- and middle-income countries ( ... ...

Abstract	Background: The COVID-19 pandemic has overwhelmed hospitals in several areas in high-income countries. An effective response to this pandemic requires health care workers (HCWs) to be present at work, particularly in low- and middle-income countries (LMICs) where they are already in critically low supply. To inform whether and to what degree policymakers in Bangladesh, and LMICs more broadly, should expect a drop in HCW attendance as COVID-19 continues to spread, this study aims to determine how HCW attendance has changed during the early stages of the COVID-19 pandemic in Bangladesh. Methods: This study analyzed daily fingerprint-verified attendance data from all 527 public-sector secondary and tertiary care facilities in Bangladesh to describe HCW attendance from January 26, 2019 to March 22, 2020, by cadre, hospital type, and geographic division. We then regressed HCW attendance onto fixed effects for day-of-week, month, and hospital, as well as indicators for each of three pandemic periods: a China-focused period (January 11, 2020 (first confirmed COVID-19 death in China) until January 29, 2020), international-spread period (January 30, 2020 (World Health Organization's declaration of a global emergency) until March 6, 2020), and local-spread period (March 7, 2020 (first confirmed COVID-19 case in Bangladesh) until the end of the study period). Findings: On average between January 26, 2019 and March 22, 2020, 34.1% of doctors, 64.6% of nurses, and 70.6% of other health care staff were present for their scheduled shift. HCWs' attendance rate increased with time in 2019 among all cadres. Nurses' attendance level dropped by 2.5% points (95% confidence interval (CI) = -3.2% to -1.8%) and 3.5% points (95% CI = -4.5% to -2.5%) during the international-spread and the local-spread periods of the COVID-19 pandemic, relative to the China-focused period. Similarly, the attendance level of other health care staff declined by 0.3% points (95% CI = -0.8% to 0.2%) and 2.3% points (95% CI = -3.0% to -1.6%) during the international-spread and local-spread periods, respectively. Among doctors, however, the international-spread and local-spread periods were associated with a statistically significant increase in attendance by 3.7% points (95% CI = 2.5% to 4.8%) and 4.9% points (95% CI = 3.5% to 6.4%), respectively. The reduction in attendance levels across all HCWs during the local-spread period was much greater at large hospitals, where the majority of COVID-19 testing and treatment took place, than that at small hospitals. Conclusions: After a year of significant improvements, HCWs' attendance levels among nurses and other health care staff (who form the majority of Bangladesh's health care workforce) have declined during the early stages of the COVID-19 pandemic. This finding may portend an even greater decrease in attendance if COVID-19 continues to spread in Bangladesh. Policymakers in Bangladesh and similar LMICs should undertake major efforts to achieve high attendance levels among HCWs, particularly nurses, such as by providing sufficient personal protective equipment as well as monetary and non-monetary incentives.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #895671
Database	COVID19

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Article ; Online: Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis.

Tikka, Pauli / Mercker, Moritz / Skovorodkin, Ilya / Saarela, Ulla / Vainio, Seppo / Ronkainen, Veli-Pekka / Sluka, James P / Glazier, James A / Marciniak-Czochra, Anna / Schaefer, Franz

Mathematical biosciences

2021 Volume 344, Page(s) 108759

Abstract: During early kidney organogenesis, nephron progenitor (NP) cells move from the tip to the corner region of the ureteric bud (UB) branches in order to form the pretubular aggregate, the early structure giving rise to nephron formation. NP cells derive ... ...

Abstract	During early kidney organogenesis, nephron progenitor (NP) cells move from the tip to the corner region of the ureteric bud (UB) branches in order to form the pretubular aggregate, the early structure giving rise to nephron formation. NP cells derive from metanephric mesenchymal cells and physically interact with them during the movement. Chemotaxis and cell-cell adhesion differences are believed to drive the cell patterning during this critical period of organogenesis. However, the effect of these forces to the cell patterns and their respective movements are known in limited details. We applied a Cellular Potts Model to explore how these forces and organizations contribute to directed cell movement and aggregation. Model parameters were estimated based on fitting to experimental data obtained in ex vivo kidney explant and dissociation-reaggregation organoid culture studies. Our simulations indicated that optimal enrichment and aggregation of NP cells in the UB corner niche requires chemoattractant secretion from both the UB epithelial cells and the NP cells themselves, as well as differences in cell-cell adhesion energies. Furthermore, NP cells were observed, both experimentally and by modelling, to move at higher speed in the UB corner as compared to the tip region where they originated. The existence of different cell speed domains along the UB was confirmed using self-organizing map analysis. In summary, we saw faster NP cell movements near aggregation. The applicability of Cellular Potts Model approach to simulate cell movement and patterning was found to be good during for this early nephrogenesis process. Further refinement of the model should allow us to recapitulate the effects of developmental changes of cell phenotypes and molecular crosstalk during further organ development.
MeSH term(s)	Cell Movement ; Computer Simulation ; Kidney ; Nephrons ; Organogenesis/genetics ; Stem Cells
Language	English
Publishing date	2021-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1126-5
ISSN	1879-3134 ; 0025-5564
ISSN (online)	1879-3134
ISSN	0025-5564
DOI	10.1016/j.mbs.2021.108759
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