cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2624664
title: Transcription Profiling of NOD-like Receptors in the Human Cornea with Disease

description: <i>Purpose</i>: To investigate the expression of nucleotide-binding oligomerization domain-like receptors (NLRs) in human corneas with disease and corneal cells. <i>Methods</i>: The expression of NOD1, NOD2, NLRP1, and NLRP3 was analyzed using real-time RT-PCR in (1) corneas with active infection, history of herpetic stromal keratitis (HSK), chronic allograft rejection, and limbal stem cell deficiency (LSCD), and (2) human corneal cells after lipopolysaccharide (LPS) stimulation. Healthy corneas and cells without LPS served as controls. <i>Results</i>: The mRNA levels of <i>NOD2</i> and <i>NLRP3</i> were increased in corneas with infection and HSK. Conversely, the levels of <i>NOD1, NOD2, NLRP1</i>, and <i>NLRP3</i> transcripts were decreased in corneas with LSCD. In corneas with rejection, the expression of <i>NOD1</i> and <i>NLRP1</i> was downregulated. Corneal endothelial cells upregulated the expression of <i>NOD2</i> and <i>NLRP3</i> upon LPS. <i>Conclusions</i>: The changes in the NLR expression may reflect different susceptibility to infectious and non-infectious injuries in corneas with various diseases.
DOI: 10.6084/m9.figshare.2626050.v1
title: Design and Cognitive Evaluation of Six Dynamic Lane Departure Warning Symbols

description: <b>Objective</b>: Lane departure, caused by inattention, distraction, drowsiness, or any unusual driver behavior is a typical risk threatening the driver as well as other road users. Accurate perception of such situations through effective warnings would help drivers to avoid serious consequences. With regard to critical functions of warning symbols for risk communication, the present study focused on providing effective and easily perceivable symbols, compatible with human cognitive capabilities. Thus, the main purpose of the present study was to design and cognitively appraise six newly designed dynamic symbols, candidates for a new type of lane departure warning system. <b>Methods</b>: Simplicity, familiarity, concreteness, meaningfulness, and semantic closeness were the major assessment criteria, defining cognitive features by the earlier researchers in the field. A total number of 187 driving license applicants, with the mean age of 20.58 years (SD = 3.20), participated in the present survey. The participants rated cognitive features of the six dynamic symbols along a 0–100 scale. <b>Results</b>: Significant main effect of the element factor type of the designed symbols on rating cognitive features, revealed that the existence of car element was the best predictor for illustrating lane departure. Interaction of both element factor and location of element factor significantly affected the ratings. However, the location of element factor did not solely have any strong effect on the ratings. The results also demonstrated that semantic closeness received the highest overall mean score across symbols (Mean = 61.80), specially within the symbols that include the car element (Mean = 75.67). Moreover, a significant difference was observed between the average ratings of the cognitive features, despite the fact that a significant correlation was found between cognitive features. <b>Conclusion</b>: The most considerable result of the current study was the match between the symbol with the highest ratings and the ISO related icon in appearance. Since previous studies demonstrated a strong correlation between comprehension scores of the symbol and both semantic closeness and meaningfulness, high level comprehensibility of the best ranked symbol is expected.
DOI: 10.6084/m9.figshare.2624664.v1
title: Transcription Profiling of NOD-like Receptors in the Human Cornea with Disease

description: <i>Purpose</i>: To investigate the expression of nucleotide-binding oligomerization domain-like receptors (NLRs) in human corneas with disease and corneal cells. <i>Methods</i>: The expression of NOD1, NOD2, NLRP1, and NLRP3 was analyzed using real-time RT-PCR in (1) corneas with active infection, history of herpetic stromal keratitis (HSK), chronic allograft rejection, and limbal stem cell deficiency (LSCD), and (2) human corneal cells after lipopolysaccharide (LPS) stimulation. Healthy corneas and cells without LPS served as controls. <i>Results</i>: The mRNA levels of <i>NOD2</i> and <i>NLRP3</i> were increased in corneas with infection and HSK. Conversely, the levels of <i>NOD1, NOD2, NLRP1</i>, and <i>NLRP3</i> transcripts were decreased in corneas with LSCD. In corneas with rejection, the expression of <i>NOD1</i> and <i>NLRP1</i> was downregulated. Corneal endothelial cells upregulated the expression of <i>NOD2</i> and <i>NLRP3</i> upon LPS. <i>Conclusions</i>: The changes in the NLR expression may reflect different susceptibility to infectious and non-infectious injuries in corneas with various diseases.
DOI: 10.6084/m9.figshare.2885308.v115
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v122
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2624604
title: Chronic Non-infectious Uveitis in Patients with Juvenile Idiopathic Arthritis

description: <i>Purpose</i>: To describe clinical findings and analyze treatment evolution of chronic, non-infectious uveitis in patients with juvenile idiopathic arthritis (JIA). <i>Methods</i>: A total of 82 patients (147 eyes) with JIA-related uveitis treated for ≥2 months were included (78% females; 79% bilateral uveitis; 74% anterior uveitis). Outcome measures were visual acuity (VA), inflammation control, side-effects, and surgical procedures. <i>Results</i>: Mean ± SD age at diagnosis was 4.9 ± 3.8 years; mean ± SD follow-up time was 8.7 ± 7.8 years. Mean VA did not significantly change throughout the study. Three (2%) eyes resulted in no light perception (NLP) vision. Thirty (37%) patients underwent 69 procedures. In total, 41 (50%) patients achieved inflammation control. TNF-α inhibitors were significantly associated with inflammation control. Seven (8.5%) patients stopped treatment due to side-effects. <i>Conclusions</i>: JIA is a cause of significant ocular morbidity. TNF-α inhibitor use was associated with inflammation control. Prospective, randomized, double blind clinical trials in this regard are warranted.
DOI: 10.6084/m9.figshare.2624604.v1
title: Chronic Non-infectious Uveitis in Patients with Juvenile Idiopathic Arthritis

description: <i>Purpose</i>: To describe clinical findings and analyze treatment evolution of chronic, non-infectious uveitis in patients with juvenile idiopathic arthritis (JIA). <i>Methods</i>: A total of 82 patients (147 eyes) with JIA-related uveitis treated for ≥2 months were included (78% females; 79% bilateral uveitis; 74% anterior uveitis). Outcome measures were visual acuity (VA), inflammation control, side-effects, and surgical procedures. <i>Results</i>: Mean ± SD age at diagnosis was 4.9 ± 3.8 years; mean ± SD follow-up time was 8.7 ± 7.8 years. Mean VA did not significantly change throughout the study. Three (2%) eyes resulted in no light perception (NLP) vision. Thirty (37%) patients underwent 69 procedures. In total, 41 (50%) patients achieved inflammation control. TNF-α inhibitors were significantly associated with inflammation control. Seven (8.5%) patients stopped treatment due to side-effects. <i>Conclusions</i>: JIA is a cause of significant ocular morbidity. TNF-α inhibitor use was associated with inflammation control. Prospective, randomized, double blind clinical trials in this regard are warranted.
DOI: 10.6084/m9.figshare.2885308.v116
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v123
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2599966
title: Bayesian and Maximum Likelihood Estimation for Gaussian Processes on an Incomplete Lattice

description: This article proposes a new approach for Bayesian and maximum likelihood parameter estimation for stationary Gaussian processes observed on a large lattice with missing values. We propose a Markov chain Monte Carlo approach for Bayesian inference, and a Monte Carlo expectation-maximization algorithm for maximum likelihood inference. Our approach uses data augmentation and circulant embedding of the covariance matrix, and provides likelihood-based inference for the parameters and the missing data. Using simulated data and an application to satellite sea surface temperatures in the Pacific Ocean, we show that our method provides accurate inference on lattices of sizes up to 512 × 512, and is competitive with two popular methods: composite likelihood and spectral approximations.
DOI: 10.6084/m9.figshare.2599927
title: Imposing Minimax and Quantile Constraints on Optimal Matching in Observational Studies

description: Modern methods construct a matched sample by minimizing the total cost of a flow in a network, finding a pairing of treated and control individuals that minimizes the sum of within-pair covariate distances subject to constraints that ensure distributions of covariates are balanced. In aggregate, these methods work well; however, they can exhibit a lack of interest in a small number of pairs with large covariate distances. Here, a new method is proposed for imposing a minimax constraint on a minimum total distance matching. Such a match minimizes the total within-pair distance subject to various constraints including the constraint that the maximum pair difference is as small as possible. In an example with 1391 matched pairs, this constraint eliminates dozens of pairs with moderately large differences in age, but otherwise exhibits the same excellent covariate balance found without this additional constraint. A minimax constraint eliminates edges in the network, and can improve the worst-case time bound for the performance of the minimum cost flow algorithm, that is, a better match from a practical perspective may take less time to construct. The technique adapts ideas for a different problem, the bottleneck assignment problem, whose sole objective is to minimize the maximum within-pair difference; however, here, that objective becomes a constraint on the minimum cost flow problem. The method generalizes. Rather than constrain the maximum distance, it can constrain an order statistic. Alternatively, the method can minimize the maximum difference in propensity scores, and subject to doing that, minimize the maximum robust Mahalanobis distance. An example from labor economics is used to illustrate. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2599966.v1
title: Bayesian and Maximum Likelihood Estimation for Gaussian Processes on an Incomplete Lattice

description: This article proposes a new approach for Bayesian and maximum likelihood parameter estimation for stationary Gaussian processes observed on a large lattice with missing values. We propose a Markov chain Monte Carlo approach for Bayesian inference, and a Monte Carlo expectation-maximization algorithm for maximum likelihood inference. Our approach uses data augmentation and circulant embedding of the covariance matrix, and provides likelihood-based inference for the parameters and the missing data. Using simulated data and an application to satellite sea surface temperatures in the Pacific Ocean, we show that our method provides accurate inference on lattices of sizes up to 512 × 512, and is competitive with two popular methods: composite likelihood and spectral approximations.
DOI: 10.6084/m9.figshare.2600599
title: Reassessment and reassignment of the early Maastrichtian mosasaur <i>Hainosaurus bernardi</i> Dollo, 1885, to <i>Tylosaurus</i> Marsh, 1872

description: Redescription of <i>Hainosaurus bernardi</i> Dollo, 1885a, from the early Maastrichtian of the Ciply Phosphatic Chalk of Belgium, results in a reassignment of the taxon to the genus <i>Tylosaurus</i> Marsh, 1872, because the genus <i>Hainosaurus</i> cannot be diagnosed independent of <i>Tylosaurus</i>. The diagnosis of <i>Hainosaurus bernardi</i> by Dollo, 1885a, is reviewed, and the two incomplete and poorly preserved specimens assigned to the taxon are compared with recognized species of <i>Tylosaurus</i>. <i>Hainosaurus</i> was originally diagnosed from characters of the jugal, quadrate, maxilla, premaxilla, frontal, parietal, and teeth. Here, we show that most of the characters of these elements are shared with the genus <i>Tylosaurus</i>, and that those that are not shared, but that are purported key diagnostic characters for <i>Hainosaurus</i>, are simply not preserved, or are too poorly preserved to support a differential diagnosis of <i>H. bernardi</i> at the generic level. The available data support the conclusion that <i>Hainosaurus</i> is a junior synonym of <i>Tylosaurus</i> because no anatomical features distinguish the former from the latter. The genus <i>Tylosaurus</i> occupied a wider geographic and temporal distribution than has been previously suggested, inhabiting the North Atlantic Circle Basin from the Turonian to the Maastrichtian. There are species-level features that support <i>T. bernardi</i> as distinct from other described species of <i>Tylosaurus</i>. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Jimenez-Huidobro, P., and M. W. Caldwell. 2016. Reassessment and reassignment of the early Maastrichtian mosasaur <i>Hainosaurus bernardi</i> Dollo, 1885, to <i>Tylosaurus</i> Marsh, 1872. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1096275.
DOI: 10.6084/m9.figshare.2600599.v1
title: Reassessment and reassignment of the early Maastrichtian mosasaur <i>Hainosaurus bernardi</i> Dollo, 1885, to <i>Tylosaurus</i> Marsh, 1872

description: Redescription of <i>Hainosaurus bernardi</i> Dollo, 1885a, from the early Maastrichtian of the Ciply Phosphatic Chalk of Belgium, results in a reassignment of the taxon to the genus <i>Tylosaurus</i> Marsh, 1872, because the genus <i>Hainosaurus</i> cannot be diagnosed independent of <i>Tylosaurus</i>. The diagnosis of <i>Hainosaurus bernardi</i> by Dollo, 1885a, is reviewed, and the two incomplete and poorly preserved specimens assigned to the taxon are compared with recognized species of <i>Tylosaurus</i>. <i>Hainosaurus</i> was originally diagnosed from characters of the jugal, quadrate, maxilla, premaxilla, frontal, parietal, and teeth. Here, we show that most of the characters of these elements are shared with the genus <i>Tylosaurus</i>, and that those that are not shared, but that are purported key diagnostic characters for <i>Hainosaurus</i>, are simply not preserved, or are too poorly preserved to support a differential diagnosis of <i>H. bernardi</i> at the generic level. The available data support the conclusion that <i>Hainosaurus</i> is a junior synonym of <i>Tylosaurus</i> because no anatomical features distinguish the former from the latter. The genus <i>Tylosaurus</i> occupied a wider geographic and temporal distribution than has been previously suggested, inhabiting the North Atlantic Circle Basin from the Turonian to the Maastrichtian. There are species-level features that support <i>T. bernardi</i> as distinct from other described species of <i>Tylosaurus</i>. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Jimenez-Huidobro, P., and M. W. Caldwell. 2016. Reassessment and reassignment of the early Maastrichtian mosasaur <i>Hainosaurus bernardi</i> Dollo, 1885, to <i>Tylosaurus</i> Marsh, 1872. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1096275.
DOI: 10.6084/m9.figshare.2951263.v124
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2599927.v2
title: Imposing Minimax and Quantile Constraints on Optimal Matching in Observational Studies

description: Modern methods construct a matched sample by minimizing the total cost of a flow in a network, finding a pairing of treated and control individuals that minimizes the sum of within-pair covariate distances subject to constraints that ensure distributions of covariates are balanced. In aggregate, these methods work well; however, they can exhibit a lack of interest in a small number of pairs with large covariate distances. Here, a new method is proposed for imposing a minimax constraint on a minimum total distance matching. Such a match minimizes the total within-pair distance subject to various constraints including the constraint that the maximum pair difference is as small as possible. In an example with 1391 matched pairs, this constraint eliminates dozens of pairs with moderately large differences in age, but otherwise exhibits the same excellent covariate balance found without this additional constraint. A minimax constraint eliminates edges in the network, and can improve the worst-case time bound for the performance of the minimum cost flow algorithm, that is, a better match from a practical perspective may take less time to construct. The technique adapts ideas for a different problem, the bottleneck assignment problem, whose sole objective is to minimize the maximum within-pair difference; however, here, that objective becomes a constraint on the minimum cost flow problem. The method generalizes. Rather than constrain the maximum distance, it can constrain an order statistic. Alternatively, the method can minimize the maximum difference in propensity scores, and subject to doing that, minimize the maximum robust Mahalanobis distance. An example from labor economics is used to illustrate. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2885308.v117
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2599927.v1
title: Imposing minimax and quantile constraints on optimal matching in observational studies

description: Modern methods construct a matched sample by minimizing the total cost of a flow in a network, finding a pairing of treated and control individuals that minimizes the sum of within-pair covariate distances subject to constraints that ensure distributions of covariates are balanced. In aggregate, these methods work well; however, they can exhibit a lack of interest in a small number of pairs with large covariate distances. Here, a new method is proposed for imposing a minimax constraint on a minimum total distance matching. Such a match minimizes the total within-pair distance subject to various constraints including the constraint that the maximum pair difference is as small as possible. In an example with 1391 matched pairs, this constraint eliminates dozens of pairs with moderately large differences in age, but otherwise exhibits the same excellent covariate balance found without this additional constraint. A minimax constraint eliminates edges in the network, and can improve the worst-case time bound for the performance of the minimum cost flow algorithm; that is, a better match from a practical perspective may take less time to construct. The technique adapts ideas for a different problem, the bottleneck assignment problem, whose sole objective is to minimize the maximum within-pair difference; however, here, that objective becomes a constraint on the minimum cost flow problem. The method generalizes. Rather than constrain the maximum distance, it can constrain an order statistic. Alternatively, the method can minimize the maximum difference in propensity scores, and subject to doing that, minimize the maximum robust Mahalanobis distance. An example from labor economics is used to illustrate.
DOI: 10.6084/m9.figshare.2885308.v118
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v125
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v119
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2598997.v2
title: Various checkpoints prevent the synthesis of <i>Staphylococcus aureus</i> peptidoglycan hydrolase LytM in the stationary growth phase

description: In <i>Staphylococcus aureus</i>, peptidoglycan metabolism plays a role in the host inflammatory response and pathogenesis. Transcription of the peptidoglycan hydrolases is activated by the essential 2-component system WalKR at low cell density. During stationary growth phase, WalKR is not active and transcription of the peptidoglycan hydrolase genes is repressed. In this work, we studied regulation of expression of the glycylglycine endopeptidase LytM. We show that, in addition to the transcriptional regulation mediated by WalKR, the synthesis of LytM is negatively controlled by a unique mechanism at the stationary growth phase. We have identified 2 different mRNAs encoding <i>lytM</i>, which vary in the length of their 5′ untranslated (5′UTR) regions. LytM is predominantly produced from the WalKR-regulated mRNA transcript carrying a short 5′UTR. The <i>lytM</i> mRNA is also transcribed as part of a polycistronic operon with the upstream SA0264 gene and is constitutively expressed. Although SA0264 protein can be synthesized from the longer operon transcript, <i>lytM</i> cannot be translated because its ribosome-binding site is sequestered into a translationally inactive secondary structure. In addition, the effector of the <i>agr</i> system, RNAIII, can inhibit translation of <i>lytM</i> present on the operon without altering the transcript level but does not have an effect on the translation of the upstream gene. We propose that this dual regulation of <i>lytM</i> expression, at the transcriptional and post-transcriptional levels, contributes to prevent cell wall damage during the stationary phase of growth.