cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21517215.v1
title: Transcriptomic reprogramming of diatom <i>Minutocellus polymorphus</i> grown on urea

description: <i>Minutocellus polymorphus</i> MMDL5290, a minute diatom, can efficiently utilize organic nitrogen (N) urea as the sole N source and achieve equivalent growth rate and photosynthesis capacity as it does with nitrate. Interestingly, <i>M</i>. <i>polymorphus</i> MMDL5290 growing on urea-replete (400 µM) medium yields a similar growth rate to that on nitrate-replete (882 µM). So far, very few reports are available on the molecular regulation mechanisms of microalgae with similar growth potential under different N sources. To address this gap, our study aimed to characterize the differences in transcriptome-level responses of <i>M</i>. <i>polymorphus</i> MMDL5290 between nitrate-replete and urea-replete conditions. We identified 4075 differentially expressed genes between these two groups. Interestingly, gene expression in light-harvesting, electron transport chain, ATP synthesis, and chlorophyll and carotenoid synthesis was up-regulated under urea, while the expression of carbon fixation genes did not change significantly. Meanwhile, transcriptome profiling indicated that under the urea-replete condition, <i>M</i>. <i>polymorphus</i> MMDL5290 triggered massive gene expression reconfiguration, inducing cells to increase investment in protein synthesis and antioxidative stress. This may explain why higher photosynthetic capacity in urea-grown cells does not lead to higher growth. Furthermore, down-regulation of PT (signal peptide) genes was observed under the urea-replete condition, suggesting a repressed capacity of phosphate transport. In addition, we identified 139 stably and highly expressed genes, which have the potential to be used as candidate reference genes in future gene expression studies on <i>M</i>. <i>polymorphus</i> MMDL5290.
DOI: 10.6084/m9.figshare.11555751
title: A Stochastic Second-Order Generalized Estimating Equations Approach for Estimating Association Parameters

description: Design and analysis of cluster randomized trials (CRTs) must take into account the intraclass correlation coefficient (ICC), which quantifies the correlation among outcomes from the same cluster. Second-order generalized estimating equations (GEE2) provide a statistically robust way in estimating this quantity and other association parameters. However, GEE2 becomes computationally infeasible as cluster sizes grow. This article proposes a stochastic variant to fitting GEE2 which alleviates reliance on parameter starting values and provides substantially faster speeds and higher convergence rates than the widely used deterministic Newton–Raphson method. We also propose new estimators for the ICC which account for informative missing outcome data through the use of GEE2, for which we incorporate a “second-order” inverse probability weighting scheme and “second-order” doubly robust estimating equations that guard against partial model misspecification. Our proposed methods are evaluated through simulations and applied to data from a CRT in Bangladesh evaluating the effect of different marketing interventions on the use of hygienic latrines. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.11555751.v1
title: A stochastic second-order generalized estimating equations approach for estimating association parameters

description: Design and analysis of cluster randomized trials must take into account the intraclass correlation coefficient, which quantifies the correlation among outcomes from the same cluster. Second-order generalized estimating equations (GEE2) provides a statistically robust way in estimating this quantity and other association parameters. However, GEE2 becomes computationally infeasible as cluster sizes grow. This paper proposes a stochastic variant to fitting GEE2 which alleviates reliance on parameter starting values and provides substantially faster speeds and higher convergence rates than the widely used deterministic Newton-Raphson method. We also propose new estimators for the ICC which account for informative missing outcome data through the use of GEE2, for which we incorporate a “second-order” inverse probability weighting scheme and “second-order” doubly robust (DR) estimating equations that guard against partial model misspecification. Our proposed methods are evaluated through simulations and applied to data from a cluster randomized trial in Bangladesh evaluating the effect of different marketing interventions on the use of hygienic latrines.
DOI: 10.6084/m9.figshare.11555751.v3
title: A Stochastic Second-Order Generalized Estimating Equations Approach for Estimating Association Parameters

description: Design and analysis of cluster randomized trials (CRTs) must take into account the intraclass correlation coefficient (ICC), which quantifies the correlation among outcomes from the same cluster. Second-order generalized estimating equations (GEE2) provide a statistically robust way in estimating this quantity and other association parameters. However, GEE2 becomes computationally infeasible as cluster sizes grow. This article proposes a stochastic variant to fitting GEE2 which alleviates reliance on parameter starting values and provides substantially faster speeds and higher convergence rates than the widely used deterministic Newton–Raphson method. We also propose new estimators for the ICC which account for informative missing outcome data through the use of GEE2, for which we incorporate a “second-order” inverse probability weighting scheme and “second-order” doubly robust estimating equations that guard against partial model misspecification. Our proposed methods are evaluated through simulations and applied to data from a CRT in Bangladesh evaluating the effect of different marketing interventions on the use of hygienic latrines. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19944375
title: Correlation of gemcitabine sensitization by Chk1 inhibition with p53 status

description: Chk1 inhibition can selectively improve gemcitabine sensitivity in p53-deficient cells by checkpoints abrogation throughout the cell cycle. However, the dependency of p53 status is still controversial for predicting the priority of such synergy. This study aimed at expounding the differential therapeutic properties of gemcitabine sensitization by Chk1 inhibition potentially affected by p53 status. We introduced wild-type and hotspot mutant p53 in p53-null H1299 cells, and quantified combination of gemcitabine with two Chk1 inhibitors using Chou–Talalay method. As a result, depletion of p53 preferentially produced synergistic effects. Wild-type and mutant p53 also conferred drug synergy but gradually showed compromised potency of growth inhibition. These data provide increased evidence that p53 status is a weak predictor for identifying an effective synergy, but genetic loss of p53 is relatively favorable for combination treatment. Further efforts on validation in more cell lines and clinical models could improve the predictive validity in this study.
DOI: 10.6084/m9.figshare.19944375.v1
title: Correlation of gemcitabine sensitization by Chk1 inhibition with p53 status

description: Chk1 inhibition can selectively improve gemcitabine sensitivity in p53-deficient cells by checkpoints abrogation throughout the cell cycle. However, the dependency of p53 status is still controversial for predicting the priority of such synergy. This study aimed at expounding the differential therapeutic properties of gemcitabine sensitization by Chk1 inhibition potentially affected by p53 status. We introduced wild-type and hotspot mutant p53 in p53-null H1299 cells, and quantified combination of gemcitabine with two Chk1 inhibitors using Chou–Talalay method. As a result, depletion of p53 preferentially produced synergistic effects. Wild-type and mutant p53 also conferred drug synergy but gradually showed compromised potency of growth inhibition. These data provide increased evidence that p53 status is a weak predictor for identifying an effective synergy, but genetic loss of p53 is relatively favorable for combination treatment. Further efforts on validation in more cell lines and clinical models could improve the predictive validity in this study.
DOI: 10.6084/m9.figshare.19944490
title: On-farm evaluation of regenerative land-use practices in a semi-arid pasture agroecosystem in West Texas, USA

description: ABSTRACT Continually rising scarcity in water and nutrient resources, especially in semi-arid agricultural systems, combined with increased frequency of extreme weather events such as drought, contribute to a growing need for resilient and regenerative agricultural ecosystems. However, evaluating a myriad of combinations of producer-led sustainable management practices in on-farm research remains challenging. Few studies have elucidated spatial variability in measured soil properties across the study area due to logistical and economic constraints. As such, this study aimed to: 1) establish soil health assessment and landscape variability data immediately after land-use change to a sustainable pasture management system, and 2) delineate relationships and predictive capability between measured soil health parameters. Soil samples were collected on May 23, 2018 in a grid pattern across two adjacent pastures on a farm in the semi-arid Southern High Plains (Texas, USA) that had recently been converted from long-term continuous cotton production to grazed pasture. Significant differences were found in soil chemical and biological properties between pastures (e.g., ~37 % reduction in microbial community size and 36 and 178 % greater electrical conductivity (EC) and Na contents, respectively, in the East pasture) that likely resulted from recent tillage and receiving irrigation compared to similar soil types and management history in the West pasture. Spatial diagrams of measured parameters revealed localization of measured properties, such as higher clay content and soil organic matter in the southeastern portion of the study area, and clear boundaries between pastures in terms of arbuscular mycorrhizal fungi (AMF) distribution. Soil physical and chemical properties were sufficiently correlated with biological measurements to predict soil microbial community size based on routine soil test analyses. The patterns of distributed elements evaluated in this study can provide a basis for management decisions on soil health and potential contaminant monitoring across the study area. These findings provide insight as to how novel, producer-designed soil health management practices in small semi-arid production systems impact soil properties, as well as help develop cost-effective predictive modeling solutions that aid long-term monitoring efforts. Such strategies will be critical tools in resource-scarce semi-arid regions such as those found in the current study region of Texas, as well as similar semi-arid regions such as northern China and northeastern Brazil. Overall, the results of this study provide direction for long-term soil health monitoring at this site, as well as a critical evaluation of relationships between soil health indicator measurements that aids interpretation and management planning.
DOI: 10.6084/m9.figshare.19944490.v1
title: On-farm evaluation of regenerative land-use practices in a semi-arid pasture agroecosystem in West Texas, USA

description: ABSTRACT Continually rising scarcity in water and nutrient resources, especially in semi-arid agricultural systems, combined with increased frequency of extreme weather events such as drought, contribute to a growing need for resilient and regenerative agricultural ecosystems. However, evaluating a myriad of combinations of producer-led sustainable management practices in on-farm research remains challenging. Few studies have elucidated spatial variability in measured soil properties across the study area due to logistical and economic constraints. As such, this study aimed to: 1) establish soil health assessment and landscape variability data immediately after land-use change to a sustainable pasture management system, and 2) delineate relationships and predictive capability between measured soil health parameters. Soil samples were collected on May 23, 2018 in a grid pattern across two adjacent pastures on a farm in the semi-arid Southern High Plains (Texas, USA) that had recently been converted from long-term continuous cotton production to grazed pasture. Significant differences were found in soil chemical and biological properties between pastures (e.g., ~37 % reduction in microbial community size and 36 and 178 % greater electrical conductivity (EC) and Na contents, respectively, in the East pasture) that likely resulted from recent tillage and receiving irrigation compared to similar soil types and management history in the West pasture. Spatial diagrams of measured parameters revealed localization of measured properties, such as higher clay content and soil organic matter in the southeastern portion of the study area, and clear boundaries between pastures in terms of arbuscular mycorrhizal fungi (AMF) distribution. Soil physical and chemical properties were sufficiently correlated with biological measurements to predict soil microbial community size based on routine soil test analyses. The patterns of distributed elements evaluated in this study can provide a basis for management decisions on soil health and potential contaminant monitoring across the study area. These findings provide insight as to how novel, producer-designed soil health management practices in small semi-arid production systems impact soil properties, as well as help develop cost-effective predictive modeling solutions that aid long-term monitoring efforts. Such strategies will be critical tools in resource-scarce semi-arid regions such as those found in the current study region of Texas, as well as similar semi-arid regions such as northern China and northeastern Brazil. Overall, the results of this study provide direction for long-term soil health monitoring at this site, as well as a critical evaluation of relationships between soil health indicator measurements that aids interpretation and management planning.
DOI: 10.6084/m9.figshare.14701659
title: Risk stratification and outcomes of intracranial hemorrhage in patients with immune thrombocytopenia under 60 years of age

description: Intracranial hemorrhage (ICH) is a devastating complication of immune thrombocytopenia (ITP). However, information on ICH in ITP patients under the age of 60 years is limited, and no predictive tools are available in clinical practice. A total of 93 adult patients with ITP who developed ICH before 60 years of age were retrospectively identified from 2005 to 2019 by 27 centers in China. For each case, 2 controls matched by the time of ITP diagnosis and the duration of ITP were provided by the same center. Multivariate analysis identified head trauma (OR = 3.216, 95%CI 1.296–7.979, <i>P</i> =.012), a platelet count ≤ 15,000/μL at the time of ITP diagnosis (OR = 1.679, 95%CI 1.044–2.698, <i>P</i> =.032) and severe/life-threatening bleeding (severe bleeding <i>vs</i>. mild bleeding, OR = 1.910, 95%CI 1.088–3.353, <i>P</i> =.024; life-threatening bleeding <i>vs</i>. mild bleeding, OR = 2.620, 95%CI 1.360–5.051, <i>P</i> =.004) as independent risk factors for ICH. Intraparenchymal hemorrhage (OR = 5.191, 95%CI 1.717–15.692, <i>P</i> =.004) and a history of severe bleeding (OR = 4.322, 95%CI 1.532–12.198, <i>P</i> =.006) were associated with the 30-day outcome of ICH. These findings may facilitate ICH risk stratification and outcome prediction in patients with ITP.
DOI: 10.6084/m9.figshare.14701659.v1
title: Risk stratification and outcomes of intracranial hemorrhage in patients with immune thrombocytopenia under 60 years of age

description: Intracranial hemorrhage (ICH) is a devastating complication of immune thrombocytopenia (ITP). However, information on ICH in ITP patients under the age of 60 years is limited, and no predictive tools are available in clinical practice. A total of 93 adult patients with ITP who developed ICH before 60 years of age were retrospectively identified from 2005 to 2019 by 27 centers in China. For each case, 2 controls matched by the time of ITP diagnosis and the duration of ITP were provided by the same center. Multivariate analysis identified head trauma (OR = 3.216, 95%CI 1.296–7.979, <i>P</i> =.012), a platelet count ≤ 15,000/μL at the time of ITP diagnosis (OR = 1.679, 95%CI 1.044–2.698, <i>P</i> =.032) and severe/life-threatening bleeding (severe bleeding <i>vs</i>. mild bleeding, OR = 1.910, 95%CI 1.088–3.353, <i>P</i> =.024; life-threatening bleeding <i>vs</i>. mild bleeding, OR = 2.620, 95%CI 1.360–5.051, <i>P</i> =.004) as independent risk factors for ICH. Intraparenchymal hemorrhage (OR = 5.191, 95%CI 1.717–15.692, <i>P</i> =.004) and a history of severe bleeding (OR = 4.322, 95%CI 1.532–12.198, <i>P</i> =.006) were associated with the 30-day outcome of ICH. These findings may facilitate ICH risk stratification and outcome prediction in patients with ITP.
DOI: 10.6084/m9.figshare.19944543
title: Effects of Meloidogyne incognita on the fungal community in tobacco rhizosphere

description: ABSTRACT The often widespread and serious Root-Knot Nematode (RKN) disease is an important soil-borne disease affecting tobacco production. This study aimed to understand micro-ecological changes caused by RKN disease and interactions between disease and rhizosphere soil fungal communities. The 18S rRNA gene sequencing was used to study changes in rhizosphere fungal community of tobacco plants having RKN disease. In June 2018, a paired comparison was performed between rhizosphere fungal community structures of healthy tobacco plants and those with RKN disease in Yuxi and Jiuxiang, Yunnan Province, China. Compared with uninfested soil, the OTU abundance, Shannon, ACE and Chao1 indexes of infested soil in the two tobacco areas showed a decreasing trend. Principal Coordinate Analysis showed fungal communities of infested soil and uninfested soil in the two tobacco areas were clustered in different areas, and the community composition was significantly different. Moreover, the dominant fungi community and relative abundance are significantly different at phylum, genus and species levels. More beneficial fungi, such as Penicillium and Aspergillus, were found in soil samples of healthy plants, whereas more pathogenic fungi, such as Phoma and Alternaria, were found in soil samples of diseased plants. In conclusion, changes in fungal community structure and decreases in species diversity and richness were important characteristics of rhizosphere soils from diseased tobacco plants. Disequilibrium in the tobacco rhizosphere micro-ecosystem may allow the development of RKN disease and other more complex diseases.
DOI: 10.6084/m9.figshare.19944543.v1
title: Effects of Meloidogyne incognita on the fungal community in tobacco rhizosphere

description: ABSTRACT The often widespread and serious Root-Knot Nematode (RKN) disease is an important soil-borne disease affecting tobacco production. This study aimed to understand micro-ecological changes caused by RKN disease and interactions between disease and rhizosphere soil fungal communities. The 18S rRNA gene sequencing was used to study changes in rhizosphere fungal community of tobacco plants having RKN disease. In June 2018, a paired comparison was performed between rhizosphere fungal community structures of healthy tobacco plants and those with RKN disease in Yuxi and Jiuxiang, Yunnan Province, China. Compared with uninfested soil, the OTU abundance, Shannon, ACE and Chao1 indexes of infested soil in the two tobacco areas showed a decreasing trend. Principal Coordinate Analysis showed fungal communities of infested soil and uninfested soil in the two tobacco areas were clustered in different areas, and the community composition was significantly different. Moreover, the dominant fungi community and relative abundance are significantly different at phylum, genus and species levels. More beneficial fungi, such as Penicillium and Aspergillus, were found in soil samples of healthy plants, whereas more pathogenic fungi, such as Phoma and Alternaria, were found in soil samples of diseased plants. In conclusion, changes in fungal community structure and decreases in species diversity and richness were important characteristics of rhizosphere soils from diseased tobacco plants. Disequilibrium in the tobacco rhizosphere micro-ecosystem may allow the development of RKN disease and other more complex diseases.
DOI: 10.6084/m9.figshare.19944546
title: Microbial rhizosphere communities in response to chlorimuron-ethyl herbicide in soils under alfafa crop

description: ABSTRACT Biolog Eco technology was used to investigate the effects of different chemical herbicide application methods, such as pre-emergence after sowing and post-emergence (stem and leaf spraying), on the characteristics of carbon source utilization by microbial communities in alfalfa rhizosphere soil. The averages of well color development (AWCD) and microbial metabolism diversity indices of post-emergence herbicide spraying on stems and leaves were significantly lower than those of pre-emergence herbicide and without herbicide treatments. Furthermore, pre-emergence after sowing herbicide treatment did not affect soil microorganisms. The principal component analysis (PCA) revealed that the microbial community diversities of the rhizosphere soils differed significantly between herbicide treatments. Carbohydrate was the carbon source type that was most sensitive to herbicide treatment changes, followed by amino acids and carboxylic acids. The herbicide application method significantly reduced the capacities of the microbial community to utilize the carbon sources, as mainly manifested in the ability to use polymers. As shown by a comprehensive analysis on the growth of alfalfa and the physiological and biochemical indices of its root system, the application of herbicide chlorimuron-ethyl reduced the alfalfa yield, and the two different application methods tested showed no significant difference. Herbicide application and different application methods showed significant impacts on alfalfa root activity and membrane permeability, suggesting that the application of herbicide damaged the membrane permeability and the activity of the alfalfa root system. Impacts of herbicide residues in the soil after stem and leaf post-emergence treatment on alfalfa growth and soil microorganisms should not be ignored.