cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8363823
title: Data underlying the publication Development and implementation of a risk assessment tool for broiler farm biosecurity and a health intervention plan in the Netherlands, Greece, and Cyprus

description: Introduction Preventing pathogens from entering and spreading on farms is the first step in reducing health problems.<br> For this study a BiosEcurity Assessment Tool was developed to identify strengths and weaknesses in biosecurity on broiler farms,<br> which was used as a starting point to formulate tailor-made health plans to improve broiler health and reduce antimicrobial use. Measurements and data collection Farms were divided into 3 separate areas according to associated biosecurity risk; high disease risk external areas (red zone), medium risk service areas (orange zone),<br> and the clean and highly secure access-restricted green zone. In the Netherlands, Cyprus, and Greece, 13, 15, and 7 broiler houses were monitored for 4 production cycles (2 preintervention and 2 postintervention cycles).<br> At the start of the study the BiosEcurity Assessment Tool assessment was performed and a health plan was made in consultation with the veterinarian.<br> After the second cycle a start was made with the implementation of the health plan.
DOI: 10.5281/zenodo.8363822
title: Data underlying the publication Development and implementation of a risk assessment tool for broiler farm biosecurity and a health intervention plan in the Netherlands, Greece, and Cyprus

description: Introduction Preventing pathogens from entering and spreading on farms is the first step in reducing health problems.<br> For this study a BiosEcurity Assessment Tool was developed to identify strengths and weaknesses in biosecurity on broiler farms,<br> which was used as a starting point to formulate tailor-made health plans to improve broiler health and reduce antimicrobial use. Measurements and data collection Farms were divided into 3 separate areas according to associated biosecurity risk; high disease risk external areas (red zone), medium risk service areas (orange zone),<br> and the clean and highly secure access-restricted green zone. In the Netherlands, Cyprus, and Greece, 13, 15, and 7 broiler houses were monitored for 4 production cycles (2 preintervention and 2 postintervention cycles).<br> At the start of the study the BiosEcurity Assessment Tool assessment was performed and a health plan was made in consultation with the veterinarian.<br> After the second cycle a start was made with the implementation of the health plan.
DOI: 10.5281/zenodo.8367011
title: Wykaz 36. Wykaz stanowisk Orsillus depressus wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 36. Wykaz stanowisk Orsillus depressus wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.5281/zenodo.8367010
title: Wykaz 36. Wykaz stanowisk Orsillus depressus wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 36. Wykaz stanowisk Orsillus depressus wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.6084/m9.figshare.24174507
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.6084/m9.figshare.24174507.v1
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.6084/m9.figshare.24174510
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.6084/m9.figshare.24174510.v1
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.5281/zenodo.8367021
title: Wykaz 37. Wykaz stanowisk Oxycarenus lavaterae wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 37. Wykaz stanowisk Oxycarenus lavaterae wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.5281/zenodo.8367020
title: Wykaz 37. Wykaz stanowisk Oxycarenus lavaterae wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 37. Wykaz stanowisk Oxycarenus lavaterae wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.6084/m9.figshare.23866866
title: An LM Test for the Conditional Independence between Regressors and Factor Loadings in Panel Data Models with Interactive Effects

description: A huge literature on modeling cross-sectional dependence in panels has been developed using interactive effects (IE). One area of contention is the hypothesis concerned with whether the regressors and factor loadings are correlated or not. Under the null hypothesis that they are conditionally independent, we can still apply the consistent and robust two-way fixed effects estimator. As an important specification test we develop an LM test for both static and dynamic panels with IE. Simulation results confirm the satisfactory performance of the LM test in small samples. We demonstrate its usefulness with an application to a total of 22 datasets, including static panels with a small <i>T</i> and dynamic panels with serially correlated factors, providing convincing evidence that the null hypothesis is not rejected in
DOI: 10.6084/m9.figshare.23866880
title: A Design-Based Perspective on Synthetic Control Methods

description: Since their introduction by Abadie and Gardeazabal, Synthetic Control (SC) methods have quickly become one of the leading methods for estimating causal effects in observational studies in settings with panel data. Formal discussions often motivate SC methods by the assumption that the potential outcomes were generated by a factor model. Here we study SC methods from a design-based perspective, assuming a model for the selection of the treated unit(s) and period(s). We show that the standard SC estimator is generally biased under random assignment. We propose a Modified Unbiased Synthetic Control (MUSC) estimator that guarantees unbiasedness under random assignment and derive its exact, randomization-based, finite-sample variance. We also propose an unbiased estimator for this variance. We document in settings with real data that under random assignment, SC-type estimators can have root mean-squared errors that are substantially lower than that of other common estimators. We show that such an improvement is weakly guaranteed if the treated period is similar to the other periods, for example, if the treated period was randomly selected. While our results only directly apply in settings where treatment is assigned randomly, we believe that they can complement model-based approaches even for observational studies.
DOI: 10.6084/m9.figshare.23866880.v1
title: A Design-Based Perspective on Synthetic Control Methods

description: Since their introduction by Abadie and Gardeazabal, Synthetic Control (SC) methods have quickly become one of the leading methods for estimating causal effects in observational studies in settings with panel data. Formal discussions often motivate SC methods by the assumption that the potential outcomes were generated by a factor model. Here we study SC methods from a design-based perspective, assuming a model for the selection of the treated unit(s) and period(s). We show that the standard SC estimator is generally biased under random assignment. We propose a Modified Unbiased Synthetic Control (MUSC) estimator that guarantees unbiasedness under random assignment and derive its exact, randomization-based, finite-sample variance. We also propose an unbiased estimator for this variance. We document in settings with real data that under random assignment, SC-type estimators can have root mean-squared errors that are substantially lower than that of other common estimators. We show that such an improvement is weakly guaranteed if the treated period is similar to the other periods, for example, if the treated period was randomly selected. While our results only directly apply in settings where treatment is assigned randomly, we believe that they can complement model-based approaches even for observational studies.
DOI: 10.6084/m9.figshare.23744123
title: Generalized Autoregressive Positive-valued Processes

description: We introduce generalized autoregressive positive-valued (GARP) processes, a class of autoregressive and moving-average processes that extends the class of existing autoregressive positive-valued (ARP) processes in one important dimension: each conditional moment dynamic is driven by a different and identifiable moving average of the variable of interest. The article provides ergodicity conditions for GARP processes and derives closed-form conditional and unconditional moments. The article also presents estimation and inference methods, illustrated by an application to European option pricing where the daily realized variance follows a GARP dynamic. Our results show that using GARP processes reduces pricing errors by substantially more than using ARP processes.
DOI: 10.6084/m9.figshare.23744123.v2
title: Generalized Autoregressive Positive-valued Processes

description: We introduce generalized autoregressive positive-valued (GARP) processes, a class of autoregressive and moving-average processes that extends the class of existing autoregressive positive-valued (ARP) processes in one important dimension: each conditional moment dynamic is driven by a different and identifiable moving average of the variable of interest. The article provides ergodicity conditions for GARP processes and derives closed-form conditional and unconditional moments. The article also presents estimation and inference methods, illustrated by an application to European option pricing where the daily realized variance follows a GARP dynamic. Our results show that using GARP processes reduces pricing errors by substantially more than using ARP processes.
DOI: 10.6084/m9.figshare.23744123.v1
title: Generalized Autoregressive Gamma Processes

description: We introduce generalized autoregressive gamma (GARG) processes, a class of autoregressive and moving-average processes that extends the class of existing Autoregressive Gamma (ARG) processes in one important dimension: each conditional moment dynamic is driven by a different and identifiable moving average of the variable of interest. The paper provides ergodicity conditions for GARG processes and derives closed-form conditional and unconditional moments. The paper also presents estimation and inference methods, illustrated by an application to European option pricing where the daily realized variance follows a GARG dynamic. Our results show that using GARG processes reduces pricing errors by substantially more than using ARG processes.
DOI: 10.5281/zenodo.8367031
title: Wykaz 38. Wykaz stanowisk Halyomorpha halys wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 38. Wykaz stanowisk Halyomorpha halys wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.5281/zenodo.8367030
title: Wykaz 38. Wykaz stanowisk Halyomorpha halys wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 38. Wykaz stanowisk Halyomorpha halys wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.5281/zenodo.8367037
title: Wykaz 39. Wykaz stanowisk Nezara viridula wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 39. Wykaz stanowisk Nezara viridula wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.5281/zenodo.8367036
title: Wykaz 39. Wykaz stanowisk Nezara viridula wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 39. Wykaz stanowisk Nezara viridula wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 26.02.2023).
DOI: 10.26106/rdhm-fz33
title: A bi-partion of seven leading journals in bioethics and philosophy of medicine

description: Data set for the study "Half a century of bioethics and philosophy of medicine: A topic-modeling study" published in Bioethics.
DOI: 10.5281/zenodo.8367049
title: Wykaz 40. Wykaz stanowisk Perillus bioculatus wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 40. Wykaz stanowisk Perillus bioculatus wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 28.09.2022).
DOI: 10.5281/zenodo.8367048
title: Wykaz 40. Wykaz stanowisk Perillus bioculatus wykorzystanych podczas modelowania niszy ekologicznej

description: Zielińska, Anna. Ocena warunków siedliskowych dla inwazyjnych gatunków pluskwiaków różnoskrzydłych (Hemiptera: Heteroptera) na terenie Europy, ze szczególnym uwzględnieniem Polski (praca doktorska). Wykaz 40. Wykaz stanowisk Perillus bioculatus wykorzystanych podczas modelowania niszy ekologicznej (dane na dzień: 28.09.2022).
DOI: 10.5281/zenodo.8272790
title: Identifying GPCRs involved in adipose tissue function using the innovative RNA-seq database FATTLAS

description: G protein-coupled receptors (GPCRs) modulate the function of adipose tissue (AT) in general and of adipocytes, specifically. Although it is well-established that GPCRs are widely expressed in AT, their repertoire as well as their regulation and function in (patho)physiological conditions (e.g., obesity) is not fully resolved. Here, we established FATTLAS, an interactive public database, for improved access and analysis of RNA-seq data of mouse and human AT. After extracting the GPCRome of non-obese and obese individuals, highly expressed and regulated GPCRs were identified. Exemplarily, we describe four receptors (MRGPRF, GPR146, FZD5, PTGER2) and analyzed their functions in a (pre)adipocyte cell model. Besides all receptors being involved in adipogenesis, MRGPRF is essential for adipocyte viability and regulates cAMP levels, while GPR146 modulates adipocyte lipolysis via constitutive activation of Gi proteins. Taken together, by implementing and using FATTLAS we describe four hitherto unrecognized GPCRs associated with AT function and adipogenesis.