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Article ; Online: Simulation models for aggregated data meta-analysis: Evaluation of pooling effect sizes and publication biases.

van den Heuvel, Edwin R / Almalik, Osama / Zhan, Zhuozhao

2024 Volume 33, Issue 3, Page(s) 359–375

Abstract: Simulation studies are commonly used to evaluate the performance of newly developed meta-analysis methods. For methodology that is developed for an aggregated data meta-analysis, researchers often resort to simulation of the aggregated data directly, ... ...

Abstract	Simulation studies are commonly used to evaluate the performance of newly developed meta-analysis methods. For methodology that is developed for an aggregated data meta-analysis, researchers often resort to simulation of the aggregated data directly, instead of simulating individual participant data from which the aggregated data would be calculated in reality. Clearly, distributional characteristics of the aggregated data statistics may be derived from distributional assumptions of the underlying individual data, but they are often not made explicit in publications. This article provides the distribution of the aggregated data statistics that were derived from a heteroscedastic mixed effects model for continuous individual data and a procedure for directly simulating the aggregated data statistics. We also compare our simulation approach with other simulation approaches used in literature. We describe their theoretical differences and conduct a simulation study for three meta-analysis methods: DerSimonian and Laird method for pooling aggregated study effect sizes and the Trim & Fill and precision-effect test and precision-effect estimate with standard errors method for adjustment of publication bias. We demonstrate that the choice of simulation model for aggregated data may have an impact on (the conclusions of) the performance of the meta-analysis method. We recommend the use of multiple aggregated data simulation models to investigate the sensitivity in the performance of the meta-analysis method. Additionally, we recommend that researchers try to make the individual participant data model explicit and derive from this model the distributional consequences of the aggregated statistics to help select appropriate aggregated data simulation models.
MeSH term(s)	Humans ; Publication Bias ; Computer Simulation ; Bias
Language	English
Publishing date	2024-03-09
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	1136948-6
ISSN	1477-0334 ; 0962-2802
ISSN (online)	1477-0334
ISSN	0962-2802
DOI	10.1177/09622802231206474
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Article ; Online: Jointly pooling aggregated effect sizes and their standard errors from studies with continuous clinical outcomes.

Almalik, Osama / Zhan, Zhuozhao / Heuvel, Edwin R van den

Biometrical journal. Biometrische Zeitschrift

2022 Volume 64, Issue 7, Page(s) 1340–1360

Abstract: The DerSimonian-Laird (DL) weighted average method for aggregated data meta-analysis has been widely used for the estimation of overall effect sizes. It is criticized for its underestimation of the standard error of the overall effect size in the ... ...

Abstract	The DerSimonian-Laird (DL) weighted average method for aggregated data meta-analysis has been widely used for the estimation of overall effect sizes. It is criticized for its underestimation of the standard error of the overall effect size in the presence of heterogeneous effect sizes. Due to this negative property, many alternative estimation approaches have been proposed in the literature. One of the earliest alternative approaches was developed by Hardy and Thompson (HT), who implemented a profile likelihood instead of the moment-based approach of DL. Others have further extended this likelihood approach and proposed higher-order likelihood inferences (e.g., Bartlett-type corrections). In addition, corrections factors for the estimated DL standard error, like the Hartung-Knapp-Sidik-Jonkman (HKSJ) adjustment, and the restricted maximum likelihood (REML) estimation have been suggested too. Although these improvements address the uncertainty in estimating the between-study variance better than the DL method, they all assume that the true within-study standard errors are known and equal to the observed standard errors of the effect sizes. Here, we will treat the observed standard errors as estimators for the within-study variability and we propose a bivariate likelihood approach that jointly estimates the overall effect size, the between-study variance, and the potentially heteroskedastic within-study variances. We study the performance of the proposed method by means of simulation, and compare it to DL (with and without HKSJ), HT, their higher-order likelihood methods, and REML. Our proposed approach seems to have better or similar coverages compared to the other approaches and it appears to be less biased in the case of heteroskedastic within-study variances when this heteroskedasticty is correlated with the effect size.
MeSH term(s)	Computer Simulation ; Likelihood Functions ; Research Design ; Uncertainty
Language	English
Publishing date	2022-06-26
Publishing country	Germany
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ZDB-ID	131640-0
ISSN	1521-4036 ; 0323-3847 ; 0006-3452
ISSN (online)	1521-4036
ISSN	0323-3847 ; 0006-3452
DOI	10.1002/bimj.202100108
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Article ; Online: Constitutional

Al-Moghrabi, Nisreen / Al-Showimi, Maram / Alqahtani, Amal / Almalik, Osama / Alhusaini, Hamed / Almalki, Ghdah / Saad, Ajawhara / Alsunayi, Elaf

International journal of molecular sciences

2024 Volume 25, Issue 6

Abstract: Breast cancer (BC) and ovarian cancer (OC) are rapidly increasing in Saudi Arabia. ...

Abstract	Breast cancer (BC) and ovarian cancer (OC) are rapidly increasing in Saudi Arabia.
MeSH term(s)	Female ; Humans ; Triple Negative Breast Neoplasms/epidemiology ; Triple Negative Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Saudi Arabia/epidemiology ; Promoter Regions, Genetic ; BRCA1 Protein/genetics ; BRCA1 Protein/metabolism ; DNA Methylation ; Risk Factors ; Ovarian Neoplasms/epidemiology ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Genetic Predisposition to Disease ; DNA Modification Methylases/genetics ; DNA Modification Methylases/metabolism ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism
Chemical Substances	BRCA1 Protein ; RNA, Messenger ; BRCA1 protein, human ; MGMT protein, human (EC 2.1.1.63) ; DNA Modification Methylases (EC 2.1.1.-) ; Tumor Suppressor Proteins ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2024-03-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25063108
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Article ; Online: Tests for publication bias are unreliable in case of heteroscedasticity.

Almalik, Osama / Zhan, Zhuozhao / van den Heuvel, Edwin R

Contemporary clinical trials communications

2021 Volume 22, Page(s) 100781

Abstract: Regression based methods for the detection of publication bias in meta-analysis have been extensively evaluated in literature. When dealing with continuous outcomes, specific hidden factors (e.g., heteroscedasticity) may interfere with the test ... ...

Abstract	Regression based methods for the detection of publication bias in meta-analysis have been extensively evaluated in literature. When dealing with continuous outcomes, specific hidden factors (e.g., heteroscedasticity) may interfere with the test statistics. In this paper we investigate the influence of residual heteroscedasticity on the performance of four tests for publication bias: the Egger test, the Begg-Mazumdar test and two tests based on weighted regression. In the presence of heteroscedasticity, the Egger test and the weighted regression tests highly inflate the Type I error rate, while the Begg-Mazumdar test deflates the Type I error rate. Although all three tests already have low statistical power, heteroscedasticity typically reduces it further. Our results in combination with earlier discussions on publication bias tests lead us to conclude that application of these tests on continuous treatment effects is not warranted.
Language	English
Publishing date	2021-06-04
Publishing country	Netherlands
Document type	Journal Article
ISSN	2451-8654
ISSN (online)	2451-8654
DOI	10.1016/j.conctc.2021.100781
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Article: PLK1 and PARP positively correlate in Middle Eastern breast cancer and their combined inhibition overcomes PARP inhibitor resistance in triple negative breast cancer.

Siraj, Abdul K / Poyil, Pratheesh Kumar / Padmaja, Divya / Parvathareddy, Sandeep Kumar / Alobaisi, Khadija / Thangavel, Saravanan / Diaz, Roxanne / Begum, Rafia / Almalik, Osama / Al-Dayel, Fouad / Al-Kuraya, Khawla S

Frontiers in oncology

2024 Volume 13, Page(s) 1286585

Abstract: Background: Despite advancements in treatment approaches, patients diagnosed with aggressive breast cancer (BC) subtypes typically face an unfavorable prognosis. Globally, these cancers continue to pose a significant threat to women's health, leading to ...

Abstract	Background: Despite advancements in treatment approaches, patients diagnosed with aggressive breast cancer (BC) subtypes typically face an unfavorable prognosis. Globally, these cancers continue to pose a significant threat to women's health, leading to substantial morbidity and mortality. Consequently, there has been a significant struggle to identify viable molecular targets for therapeutic intervention in these patients. Polo-like Kinase-1 (PLK1) represents one of these molecular targets currently undergoing rigorous scrutiny for the treatment of such tumors. Yet, its role in the pathogenesis of BC in Middle Eastern ethnicity remains unexplored. Methods: We investigated the expression of PLK1 protein in a cohort of more than 1500 Middle Eastern ethnicity BC cases by immunohistochemistry. Association with clinicopathological parameters and prognosis were performed. Results: Overexpression of PLK1 was detected in 27.4% of all BC cases, and this was notably correlated with aggressive clinicopathological markers. PLK1 was enriched in the triple-negative breast cancer (TNBC) subtype and exhibited poor overall survival (p = 0.0347). Notably, there was a positive correlation between PLK1 and PARP overexpression, with co-expression of PLK1 and PARP observed in 15.7% of cases and was associated with significantly poorer overall survival (OS) compared to the overexpression of either protein alone (p = 0.0050). Conclusion: Our results shed light on the role of PLK1 in the pathogenesis and prognosis of Middle Eastern BC and support the potential clinical development of combined inhibition of PLK1 and PARP, a strategy that could potentially broaden the use of PLK1 and PARP inhibitors beyond BC cases lacking
Language	English
Publishing date	2024-01-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1286585
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Article ; Online: MicroRNA-126 expression in the peripheral white blood cells of patients with breast and ovarian cancer is a potential biomarker for the early prediction of cancer risk in the carriers of methylated

Al-Showimi, Maram / Al-Yousef, Nujoud / Alharbi, Wejdan / Alkhezayem, Sara / Almalik, Osama / Alhusaini, Hamed / Alghamdi, Amani / Al-Moghrabi, Nisreen

Oncology letters

2022 Volume 24, Issue 2, Page(s) 276

Abstract: Constitutive breast cancer type 1 gene ( ...

Abstract	Constitutive breast cancer type 1 gene (
Language	English
Publishing date	2022-06-22
Publishing country	Greece
Document type	Journal Article
ZDB-ID	2573196-8
ISSN	1792-1082 ; 1792-1074
ISSN (online)	1792-1082
ISSN	1792-1074
DOI	10.3892/ol.2022.13396
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Article ; Online: Identification and characterization of ATM founder mutation in BRCA-negative breast cancer patients of Arab ethnicity.

Bu, Rong / Siraj, Abdul K / Al-Rasheed, Maha / Iqbal, Kaleem / Azam, Saud / Qadri, Zeeshan / Haqawi, Wael / Tulbah, Asma / Al-Dayel, Fouad / Almalik, Osama / Al-Kuraya, Khawla S

Scientific reports

2023 Volume 13, Issue 1, Page(s) 20924

Abstract: Breast cancer (BC) is the most prevalent malignancy among women worldwide with germline pathogenic variants/likely pathogenic variants (PVs/LPVs) in BRCA1/2 accounting for a large portion of hereditary cases. Recently, heterozygous PVs/LPVs in the ATM ... ...

Abstract	Breast cancer (BC) is the most prevalent malignancy among women worldwide with germline pathogenic variants/likely pathogenic variants (PVs/LPVs) in BRCA1/2 accounting for a large portion of hereditary cases. Recently, heterozygous PVs/LPVs in the ATM serine/threonine kinase or Ataxia-telangiectasia mutated gene (ATM) has been identified as a moderate susceptibility factor for BC in diverse ethnicities. However, the prevalence of ATM PVs/LPVs in BC susceptibility in Arab populations remains largely unexplored. This study investigated the prevalence of ATM PVs/LPVs among BC patients from Saudi Arabia, employing capture-sequencing technology for ATM PVs/LPVs screening in a cohort of 715 unselected BC patients without BRCA1/2 PVs/LPVs. In addition, founder mutation analysis was conducted using the PHASE program. In our entire cohort, four unique PVs/LPVs in the ATM gene were identified in six cases (0.8%). Notably, one recurrent LPV, c.6115G > A:p.Glu2039Lys was identified in three cases, for which haplotype analysis confirmed as a novel putative founder mutation traced back to 13 generations on average. This founder mutation accounted for half of all identified mutant cases and 0.4% of total screened cases. This study further reveals a significant correlation between the presence of ATM mutation and family history of BC (p = 0.0127). These findings underscore an approximate 0.8% prevalence of ATM germline PVs/LPVs in Arab BC patients without BRCA1/2 PVs/LPVs and suggest a founder effect of specific recurrent ATM mutation. These insights can help in the design of a genetic testing strategy tailored to the local population in Saudi Arabia, thereby, enabling more accurate clinical management and risk prediction.
MeSH term(s)	Humans ; Female ; BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Triple Negative Breast Neoplasms ; Arabs/genetics ; Ethnicity ; Genetic Predisposition to Disease ; Germ-Line Mutation ; Ataxia Telangiectasia Mutated Proteins/genetics
Chemical Substances	BRCA1 protein, human ; BRCA1 Protein ; BRCA2 protein, human ; BRCA2 Protein ; ATM protein, human (EC 2.7.11.1) ; Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1)
Language	English
Publishing date	2023-11-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-48231-0
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Article: Lying Postures of Dairy Cows in Cubicles and on Pasture.

van Erp-van der Kooij, Elaine / Almalik, Osama / Cavestany, Daniel / Roelofs, Judith / van Eerdenburg, Frank

Animals : an open access journal from MDPI

2019 Volume 9, Issue 4

Abstract: Cows housed indoors with cubicles are probably more restricted in their choice of lying posture and orientation compared with cows housed on pasture. We therefore compared lying postures on pasture in Uruguay and the Netherlands with lying postures in ... ...

Abstract	Cows housed indoors with cubicles are probably more restricted in their choice of lying posture and orientation compared with cows housed on pasture. We therefore compared lying postures on pasture in Uruguay and the Netherlands with lying postures in cubicles in the Netherlands, also recording orientation on pasture in Uruguay and divider and bedding type in Dutch cubicles. We visited one farm with four herds in Uruguay, doing live observations, and 25 Dutch farms, taking pictures of cows. Observations of 205 cows on pasture in Uruguay showed more long postures, lying on their belly with their neck stretched. Two herds preferred lying towards north and south, while one herd preferred west and east. Pictures of 217 cows on pasture in the Netherlands showed more wide postures (lying on the side with three or four legs stretched out). Pictures of 527 cows in cubicles in the Netherlands showed more narrow postures (lying on the side with hind legs folded). More long postures (lying on the belly with a stretched neck) and less short postures (lying with the head folded back) were seen in cubicles with soft floors and English dividers; more narrow postures were seen in cubicles with concrete floors. Wide postures were seen more in cubicles with mattresses and free-hanging dividers. We conclude that since cows in cubicles show more narrow postures than on pasture and cannot choose their orientation, their choice in showing preferred behavior is restricted. More research is needed to study the consequences of restricted choice in lying behavior on the health and welfare of dairy cows.
Language	English
Publishing date	2019-04-21
Publishing country	Switzerland
Document type	Journal Article
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani9040183
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Article ; Online: Combined statistical analyses for long-term stability data with multiple storage conditions: a simulation study.

Almalik, Osama / Nijhuis, Michiel B / van den Heuvel, Edwin R

Journal of biopharmaceutical statistics

2014 Volume 24, Issue 3, Page(s) 493–506

Abstract: Shelf-life estimation usually requires that at least three registration batches are tested for stability at multiple storage conditions. The shelf-life estimates are often obtained by linear regression analysis per storage condition, an approach ... ...

Abstract	Shelf-life estimation usually requires that at least three registration batches are tested for stability at multiple storage conditions. The shelf-life estimates are often obtained by linear regression analysis per storage condition, an approach implicitly suggested by ICH guideline Q1E. A linear regression analysis combining all data from multiple storage conditions was recently proposed in the literature when variances are homogeneous across storage conditions. The combined analysis is expected to perform better than the separate analysis per storage condition, since pooling data would lead to an improved estimate of the variation and higher numbers of degrees of freedom, but this is not evident for shelf-life estimation. Indeed, the two approaches treat the observed initial batch results, the intercepts in the model, and poolability of batches differently, which may eliminate or reduce the expected advantage of the combined approach with respect to the separate approach. Therefore, a simulation study was performed to compare the distribution of simulated shelf-life estimates on several characteristics between the two approaches and to quantify the difference in shelf-life estimates. In general, the combined statistical analysis does estimate the true shelf life more consistently and precisely than the analysis per storage condition, but it did not outperform the separate analysis in all circumstances.
MeSH term(s)	Computer Simulation ; Drug Stability ; Drug Storage/standards ; Drug Storage/statistics & numerical data ; Linear Models ; Models, Statistical ; Time Factors
Language	English
Publishing date	2014
Publishing country	England
Document type	Journal Article
ZDB-ID	1131763-2
ISSN	1520-5711 ; 1054-3406
ISSN (online)	1520-5711
ISSN	1054-3406
DOI	10.1080/10543406.2014.888439
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Article ; Online: Evaluation of a virtual pet visit system with live video streaming of patient images over the Internet in a companion animal intensive care unit in the Netherlands.

Robben, Joris H / Melsen, Diede N / Almalik, Osama / Roomer, Wendy / Endenburg, Nienke

Journal of veterinary emergency and critical care (San Antonio, Tex. : 2001)

2016 Volume 26, Issue 3, Page(s) 384–392

Abstract: Objective: To evaluate the impact of a virtual pet visit system ("TelePet" System, TPS) on owners and staff of a companion animal ICU.: Design: Longitudinal interventional study (2010-2013).: Setting: Companion animal ICU at a university ... ...

Abstract	Objective: To evaluate the impact of a virtual pet visit system ("TelePet" System, TPS) on owners and staff of a companion animal ICU. Design: Longitudinal interventional study (2010-2013). Setting: Companion animal ICU at a university veterinary medical teaching hospital. Study populations: Pet owners, ICU technicians. Interventions: The introduction of the TPS, with live video streaming of patient images over the Internet, in a companion animal ICU. Measurements and main results: Pet owners experienced TPS as a valuable extra service. Most TPS users (72.4%) experienced less anxiety and felt less need (40.4% of TPS users) to visit their hospitalized pet in person. Most users (83.5%) shared TPS access with their family. The introduction of the TPS did not improve overall owner satisfaction, except for the score on "quality of medical treatment." Seven of 26 indicators of owner satisfaction were awarded higher scores by TPS users than by TPS nonusers in the survey after the introduction of the system. However, the lack of randomization of owners might have influenced findings. The enthusiasm of the ICU technicians for the system was tempered by the negative feedback from a small number of owners. Nevertheless they recognized the value of the system for owners. The system was user friendly and ICU staff and TPS users experienced few technical problems. Conclusions: As veterinary healthcare is moving toward a more client-centered approach, a virtual pet visit system, such as TPS, is a relatively simple application that may improve the well-being of most owners during the hospitalization of their pet.
MeSH term(s)	Animals ; Hospitalization ; Humans ; Intensive Care Units ; Internet ; Netherlands ; Ownership ; Pets ; Program Evaluation ; Surveys and Questionnaires ; Telemedicine/standards ; Veterinary Medicine ; Video Recording
Language	English
Publishing date	2016-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2077212-9
ISSN	1476-4431 ; 1479-3261
ISSN (online)	1476-4431
ISSN	1479-3261
DOI	10.1111/vec.12458
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