cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568429
title: Constructed Second Control Groups and Attenuation of Unmeasured Biases

description: The informal folklore of observational studies claims that if an irrelevant observed covariate is left uncontrolled, say unmatched, then it will influence treatment assignment in haphazard ways, thereby diminishing the biases from unmeasured covariates. We prove a result along these lines: it is true, in a certain sense, to a limited degree, under certain conditions. Alas, the conditions are neither inconsequential nor easy to check in empirical work; indeed, they are often dubious, more often implausible. We suggest the result is most useful in the computerized construction of a second control group, where the investigator can see more in available data without necessarily believing the required conditions. One of the two control groups controls for the possibly irrelevant observed covariate, the other control group either leaves it uncontrolled or forces separation; therefore, the investigator views one situation from two angles under different assumptions. A pair of sensitivity analyses for the two control groups is coordinated by a weighted Holm or recycling procedure built around the possibility of slight attenuation of bias in one control group. Issues are illustrated using an observational study of the possible effects of cigarette smoking as a cause of increased homocysteine levels, a risk factor for cardiovascular disease. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568429.v2
title: Constructed Second Control Groups and Attenuation of Unmeasured Biases

description: The informal folklore of observational studies claims that if an irrelevant observed covariate is left uncontrolled, say unmatched, then it will influence treatment assignment in haphazard ways, thereby diminishing the biases from unmeasured covariates. We prove a result along these lines: it is true, in a certain sense, to a limited degree, under certain conditions. Alas, the conditions are neither inconsequential nor easy to check in empirical work; indeed, they are often dubious, more often implausible. We suggest the result is most useful in the computerized construction of a second control group, where the investigator can see more in available data without necessarily believing the required conditions. One of the two control groups controls for the possibly irrelevant observed covariate, the other control group either leaves it uncontrolled or forces separation; therefore, the investigator views one situation from two angles under different assumptions. A pair of sensitivity analyses for the two control groups is coordinated by a weighted Holm or recycling procedure built around the possibility of slight attenuation of bias in one control group. Issues are illustrated using an observational study of the possible effects of cigarette smoking as a cause of increased homocysteine levels, a risk factor for cardiovascular disease. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568429.v1
title: Constructed second control groups and attenuation of unmeasured biases

description: The informal folklore of observational studies claims that if an irrelevant observed covariate is left uncontrolled, say unmatched, then it will influence treatment assignment in haphazard ways, thereby diminishing the biases from unmeasured covariates. We prove a result along these lines: it is true, in a certain sense, to a limited degree, under certain conditions. Alas, the conditions are neither inconsequential nor easy to check in empirical work; indeed, they are often dubious, more often implausible. We suggest the result is most useful in the computerized construction of a second control group, where the investigator can see more in available data without necessarily believing the required conditions. One of the two control groups controls for the possibly irrelevant observed covariate, the other control group either leaves it uncontrolled or forces separation; therefore, the investigator views one situation from two angles under different assumptions. A pair of sensitivity analyses for the two control groups is coordinated by a weighted Holm or recycling procedure built around the possibility of slight attenuation of bias in one control group. Issues are illustrated using an observational study of the possible effects of cigarette smoking as a cause of increased homocysteine levels, a risk factor for cardiovascular disease.
DOI: 10.6084/m9.figshare.1568424
title: Characterization of <i>Arabidopsis</i> sterol glycosyltransferase <i>TTG15/UGT80B1</i> role during freeze and heat stress

description: Sterol glycosyltransferases regulate the properties of sterols by catalyzing the transfer of carbohydrate molecules to the sterol moiety for the synthesis of steryl glycosides and acyl steryl glycosides. We have analyzed the functional role of <i>TTG15/UGT80B1</i> gene of <i>Arabidopsis thaliana</i> in freeze/thaw and heat shock stress using T-DNA insertional <i>sgt</i> knockout mutants. Quantitative study of spatial as well as temporal gene expression showed tissue-specific and dynamic expression patterns throughout the growth stages. Comparative responses of Col-0, <i>TTG15/UGT80B1</i> knockout mutant and <i>p</i>35<i>S</i>:<i>TTG15/UGT80B1</i> restored lines were analyzed under heat and freeze stress conditions. Heat tolerance was determined by survival of plants at 42°C for 3 h, MDA analysis and chlorophyll fluorescence image (CFI) analysis. Freezing tolerance was determined by survival of the plants at -1°C temperature in non-acclimatized (NA) and cold acclimatized (CA) conditions and also by CFI analysis, which revealed that, <i>p</i>35S:<i>TTG15/UGT80B1</i> restored plants were more adapted to freeze stress than <i>TTG15/UGT80B1</i> knockout mutant under CA condition. HPLC analysis of the plants showed reduced sterol glycoside in mutant seedlings as compared to other genotypes. Following CA condition, both β-sitosterol and sitosterol glycoside quantity was more in Col-0 and <i>p</i>35<i>S</i>:<i>TTG15/UGT80B1</i> restored lines, whereas it was significantly less in <i>TTG15/UGT80B1</i> knockout mutants. From these results, it may be concluded that due to low content of free sterols and sterol glycosides, the physiology of mutant plants was more affected during both, the chilling and heat stress.
DOI: 10.6084/m9.figshare.1568424.v1
title: Characterization of <i>Arabidopsis</i> sterol glycosyltransferase <i>TTG15/UGT80B1</i> role during freeze and heat stress

description: Sterol glycosyltransferases regulate the properties of sterols by catalyzing the transfer of carbohydrate molecules to the sterol moiety for the synthesis of steryl glycosides and acyl steryl glycosides. We have analyzed the functional role of <i>TTG15/UGT80B1</i> gene of <i>Arabidopsis thaliana</i> in freeze/thaw and heat shock stress using T-DNA insertional <i>sgt</i> knockout mutants. Quantitative study of spatial as well as temporal gene expression showed tissue-specific and dynamic expression patterns throughout the growth stages. Comparative responses of Col-0, <i>TTG15/UGT80B1</i> knockout mutant and <i>p</i>35<i>S</i>:<i>TTG15/UGT80B1</i> restored lines were analyzed under heat and freeze stress conditions. Heat tolerance was determined by survival of plants at 42°C for 3 h, MDA analysis and chlorophyll fluorescence image (CFI) analysis. Freezing tolerance was determined by survival of the plants at -1°C temperature in non-acclimatized (NA) and cold acclimatized (CA) conditions and also by CFI analysis, which revealed that, <i>p</i>35S:<i>TTG15/UGT80B1</i> restored plants were more adapted to freeze stress than <i>TTG15/UGT80B1</i> knockout mutant under CA condition. HPLC analysis of the plants showed reduced sterol glycoside in mutant seedlings as compared to other genotypes. Following CA condition, both β-sitosterol and sitosterol glycoside quantity was more in Col-0 and <i>p</i>35<i>S</i>:<i>TTG15/UGT80B1</i> restored lines, whereas it was significantly less in <i>TTG15/UGT80B1</i> knockout mutants. From these results, it may be concluded that due to low content of free sterols and sterol glycosides, the physiology of mutant plants was more affected during both, the chilling and heat stress.
DOI: 10.6084/m9.figshare.1568421
title: A palaeontological case study for species delimitation in diverging fossil lineages

description: A general lineage concept is widely adopted in studies of species delimitation for extant taxa with DNA sequence data. In the general lineage concept, species are separately evolving metapopulations that acquire sets of properties during the process of speciation. Murine rodents from the Miocene Siwalik Group of Pakistan have an excellent fossil record showing temporal trends of morphological change, and are therefore ideal to observe the process of lineage divergence as fossil evidence. Here, we review the evolution of Siwalik murine rodents in the sense of the general lineage concept and draw lines of evidence for lineage separation. For currently available datasets, we applied the initial split criterion as well as three operational criteria (phenetic, diagnosable and ecological properties). In early Siwalik murine rodents, the acquisition of distinct phenetic properties emerges subsequent to the event of the evolutionary split. The phenetic evidence occurs closer in time to ‘true’ divergence, while distinct diagnosable and ecological properties fully arise later. Within a sequence of time-controlled samples, these observations explicitly show that phenetic properties (here, shape data and a combination of linear measurements) more precisely delimit the divergence of fossil species than does the fixation of diagnostic properties.
DOI: 10.6084/m9.figshare.1568419
title: Elevated levels of Th17 cells in children with central obesity

description: <b><i>Background</i>.</b> It is believed that the recently discovered interleukin 17-producing Th17 cells play a role in the pathogenesis of chronic inflammation in the course of obesity and diabetes. <b><i>Objectives</i>.</b> The purpose of our study was to complete data on this subject in children. <b><i>Methods</i>.</b> We assessed Th17 cell levels in the peripheral blood of children diagnosed with central obesity (<i>n</i> = 14) and compared the results with data obtained in patients with newly diagnosed (<i>n</i> = 11) and long-term type 1 diabetes mellitus (<i>n</i> = 18), and in a control group as well (<i>n</i> = 24). <b><i>Results</i>.</b> (i) Children with central obesity were characterized by higher percentages of Th17 cells as compared to children from the control group; (ii) in the peripheral blood of patients with long-term type 1 diabetes the Th17 cell counts were higher compared to the control group; (iii) total plasma cholesterol concentration correlated positively with Th17/Treg cells ratio; and (iv) among patients with long-term diabetes, disease duration correlated positively with Th17 cell count and Th17/Th1 cell ratio. <b><i>Conclusion</i>.</b> The results of our study indicate that Th17 cells may be involved in chronic inflammation accompanying obesity and type 1 diabetes mellitus in children.
DOI: 10.6084/m9.figshare.1568419.v1
title: Elevated levels of Th17 cells in children with central obesity

description: <b><i>Background</i>.</b> It is believed that the recently discovered interleukin 17-producing Th17 cells play a role in the pathogenesis of chronic inflammation in the course of obesity and diabetes. <b><i>Objectives</i>.</b> The purpose of our study was to complete data on this subject in children. <b><i>Methods</i>.</b> We assessed Th17 cell levels in the peripheral blood of children diagnosed with central obesity (<i>n</i> = 14) and compared the results with data obtained in patients with newly diagnosed (<i>n</i> = 11) and long-term type 1 diabetes mellitus (<i>n</i> = 18), and in a control group as well (<i>n</i> = 24). <b><i>Results</i>.</b> (i) Children with central obesity were characterized by higher percentages of Th17 cells as compared to children from the control group; (ii) in the peripheral blood of patients with long-term type 1 diabetes the Th17 cell counts were higher compared to the control group; (iii) total plasma cholesterol concentration correlated positively with Th17/Treg cells ratio; and (iv) among patients with long-term diabetes, disease duration correlated positively with Th17 cell count and Th17/Th1 cell ratio. <b><i>Conclusion</i>.</b> The results of our study indicate that Th17 cells may be involved in chronic inflammation accompanying obesity and type 1 diabetes mellitus in children.
DOI: 10.6084/m9.figshare.1568421.v1
title: A palaeontological case study for species delimitation in diverging fossil lineages

description: A general lineage concept is widely adopted in studies of species delimitation for extant taxa with DNA sequence data. In the general lineage concept, species are separately evolving metapopulations that acquire sets of properties during the process of speciation. Murine rodents from the Miocene Siwalik Group of Pakistan have an excellent fossil record showing temporal trends of morphological change, and are therefore ideal to observe the process of lineage divergence as fossil evidence. Here, we review the evolution of Siwalik murine rodents in the sense of the general lineage concept and draw lines of evidence for lineage separation. For currently available datasets, we applied the initial split criterion as well as three operational criteria (phenetic, diagnosable and ecological properties). In early Siwalik murine rodents, the acquisition of distinct phenetic properties emerges subsequent to the event of the evolutionary split. The phenetic evidence occurs closer in time to ‘true’ divergence, while distinct diagnosable and ecological properties fully arise later. Within a sequence of time-controlled samples, these observations explicitly show that phenetic properties (here, shape data and a combination of linear measurements) more precisely delimit the divergence of fossil species than does the fixation of diagnostic properties.
DOI: 10.6084/m9.figshare.1568421.v3
title: A palaeontological case study for species delimitation in diverging fossil lineages

description: A general lineage concept is widely adopted in studies of species delimitation for extant taxa with DNA sequence data. In the general lineage concept, species are separately evolving metapopulations that acquire sets of properties during the process of speciation. Murine rodents from the Miocene Siwalik Group of Pakistan have an excellent fossil record showing temporal trends of morphological change, and are therefore ideal to observe the process of lineage divergence as fossil evidence. Here, we review the evolution of Siwalik murine rodents in the sense of the general lineage concept and draw lines of evidence for lineage separation. For currently available datasets, we applied the initial split criterion as well as three operational criteria (phenetic, diagnosable and ecological properties). In early Siwalik murine rodents, the acquisition of distinct phenetic properties emerges subsequent to the event of the evolutionary split. The phenetic evidence occurs closer in time to ‘true’ divergence, while distinct diagnosable and ecological properties fully arise later. Within a sequence of time-controlled samples, these observations explicitly show that phenetic properties (here, shape data and a combination of linear measurements) more precisely delimit the divergence of fossil species than does the fixation of diagnostic properties.
DOI: 10.6084/m9.figshare.1568421.v2
title: A palaeontological case study for species delimitation in diverging fossil lineages

description: A general lineage concept is widely adopted in studies of species delimitation for extant taxa with DNA sequence data. In the general lineage concept, species are separately evolving metapopulations that acquire sets of properties during the process of speciation. Murine rodents from the Miocene Siwalik Group of Pakistan have an excellent fossil record showing temporal trends of morphological change, and are therefore ideal to observe the process of lineage divergence as fossil evidence. Here, we review the evolution of Siwalik murine rodents in the sense of the general lineage concept and draw lines of evidence for lineage separation. For currently available datasets, we applied the initial split criterion as well as three operational criteria (phenetic, diagnosable and ecological properties). In early Siwalik murine rodents, the acquisition of distinct phenetic properties emerges subsequent to the event of the evolutionary split. The phenetic evidence occurs closer in time to ‘true’ divergence, while distinct diagnosable and ecological properties fully arise later. Within a sequence of time-controlled samples, these observations explicitly show that phenetic properties (here, shape data and a combination of linear measurements) more precisely delimit the divergence of fossil species than does the fixation of diagnostic properties.
DOI: 10.6084/m9.figshare.1568409
title: Heterogeneous Condensation of Water Vapor on Nanoparticles in a Membrane-Based High-Flow Process Monitored by a New <i>In Situ</i> Measuring Cell

description: This article presents a membrane-based process to improve separation efficiency of airborne particles by heterogeneous condensation of water vapor. A plant was set up in laboratory scale to control the supersaturated state of water vapor in air accurately. Droplet growth due to heterogeneous condensation is investigated experimentally and supersaturation is calculated by solving the differential equations for heat and mass transfer in a laminar gas flow. The apparatus is based on a water condensation particle counter (WCPC). It operates with several growth tubes in parallel thereby allowing higher aerosol throughput. The increase of particle size based on heterogeneous condensation is detected by an <i>in situ</i> measuring system. Therefore a new measuring cell was operated with well-defined test aerosols differing in wetting abilities and initial nuclei size. First results of particle activation and condensational droplet growth are presented.Copyright 2015 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.1568405
title: Molecular dynamics simulations of the free and inhibitor-bound cruzain systems in aqueous solvent: insights on the inhibition mechanism in acidic pH

description: The major cysteine protease of <i>Trypanosoma cruzi</i>, cruzain (CRZ), has been described as a therapeutic target for Chagas’ disease, which affects millions of people worldwide. Thus, a series of CRZ inhibitors has been studied, including a new competitive inhibitor, Nequimed176 (NEQ176). Nevertheless, the structural and dynamic basis for CRZ inhibition remains unclear. Hoping to contribute to this ever-growing understanding of timescale dynamics in the CRZ inhibition mechanism, we have performed the first study using 100 ns of molecular dynamics (MD) simulations of two CRZ systems in an aqueous solvent under pH 5.5: CRZ in the apo form (ligand free) and CRZ complexed to NEQ176. According to the MD simulations, the enzyme adopts an open conformation in the apo form and a closed conformation in the NEQ176–CRZ complex. We also suggest that this closed conformation is related to the hydrogen-bonding interactions between NEQ176 and CRZ, which occurs through key residues, mainly Gly66, Met68, Asn69, and Leu160. In addition, the cross-correlation analysis shows evidence of the correlated motions among Ala110–Asp140, Leu160–Gly189, and Glu190–Gly215 subdomains, as well as, the movements related to Ala1–Thr59 and Asp60–Pro90 regions seem to be crucial for CRZ activity.
DOI: 10.6084/m9.figshare.1568405.v2
title: Molecular dynamics simulations of the free and inhibitor-bound cruzain systems in aqueous solvent: insights on the inhibition mechanism in acidic pH

description: The major cysteine protease of <i>Trypanosoma cruzi</i>, cruzain (CRZ), has been described as a therapeutic target for Chagas’ disease, which affects millions of people worldwide. Thus, a series of CRZ inhibitors has been studied, including a new competitive inhibitor, Nequimed176 (NEQ176). Nevertheless, the structural and dynamic basis for CRZ inhibition remains unclear. Hoping to contribute to this ever-growing understanding of timescale dynamics in the CRZ inhibition mechanism, we have performed the first study using 100 ns of molecular dynamics (MD) simulations of two CRZ systems in an aqueous solvent under pH 5.5: CRZ in the apo form (ligand free) and CRZ complexed to NEQ176. According to the MD simulations, the enzyme adopts an open conformation in the apo form and a closed conformation in the NEQ176–CRZ complex. We also suggest that this closed conformation is related to the hydrogen-bonding interactions between NEQ176 and CRZ, which occurs through key residues, mainly Gly66, Met68, Asn69, and Leu160. In addition, the cross-correlation analysis shows evidence of the correlated motions among Ala110–Asp140, Leu160–Gly189, and Glu190–Gly215 subdomains, as well as, the movements related to Ala1–Thr59 and Asp60–Pro90 regions seem to be crucial for CRZ activity.
DOI: 10.6084/m9.figshare.1568405.v1
title: Molecular Dynamics Simulations of the Free and Inhibitor-Bound Cruzain Systems in Aqueous Solvent: Insights on the Inhibition Mechanism in Acidic pH

description: The major cysteine protease of <i>Trypanosoma cruzi</i>, cruzain (CRZ), has been described as a therapeutic target for Chagas’ disease, which affects millions of people worldwide. Thus, a series of CRZ inhibitors has been studied, including a new competitive inhibitor, Nequimed176 (NEQ176). Nevertheless, the structural and dynamic basis for CRZ inhibition remains unclear. Hoping to contribute to this ever-growing understanding of timescale dynamics in the CRZ inhibition mechanism, we have performed the first study using 100 ns molecular dynamics (MD) simulations of two CRZ systems in an aqueous solvent under pH 5.5: CRZ in the apo form (ligand free) and CRZ complexed to NEQ176. According to the MD simulations, the enzyme adopts an open conformation in the apo form and a closed conformation in the NEQ176-CRZ complex. We also suggest that this closed conformation is related to the hydrogen-bonding interactions between NEQ176 and CRZ, which occurs through key residues, mainly Gly66, Met68, Asn69, and Leu160. In addition, the cross-correlation analysis shows evidence of the correlated motions among Ala110-Asp140, Leu160-Gly189, and Glu190-Gly215 sub-domains, as well as, the movements related to Ala1-Thr59 and Asp60-Pro90 regions seem to be crucial for CRZ activity.
DOI: 10.6084/m9.figshare.1568409.v7
title: Heterogeneous Condensation of Water Vapor on Nanoparticles in a Membrane-Based High-Flow Process Monitored by a New <i>In Situ</i> Measuring Cell

description: This article presents a membrane-based process to improve separation efficiency of airborne particles by heterogeneous condensation of water vapor. A plant was set up in laboratory scale to control the supersaturated state of water vapor in air accurately. Droplet growth due to heterogeneous condensation is investigated experimentally and supersaturation is calculated by solving the differential equations for heat and mass transfer in a laminar gas flow. The apparatus is based on a water condensation particle counter (WCPC). It operates with several growth tubes in parallel thereby allowing higher aerosol throughput. The increase of particle size based on heterogeneous condensation is detected by an <i>in situ</i> measuring system. Therefore a new measuring cell was operated with well-defined test aerosols differing in wetting abilities and initial nuclei size. First results of particle activation and condensational droplet growth are presented.Copyright 2015 American Association for Aerosol Research