cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5063722.v1
title: Dataset for: Mixture models for undiagnosed prevalent disease and interval-censored incident disease: Applications to a cohort assembled from electronic health records

description: For cost-effectiveness and efficiency, many large-scale general-purpose cohort studies are being assembled within large health-care providers who use electronic health records. Two key features of such data are that incident disease is interval-censored between irregular visits and there can be pre-existing (prevalent) disease. Because prevalent disease is not always immediately diagnosed, some disease diagnosed at later visits are actually undiagnosed prevalent disease. We consider prevalent disease as a point mass at time zero for clinical applications where there is no interest in time of prevalent disease onset. We demonstrate that the naive Kaplan-Meier cumulative risk estimator underestimates risks at early time points and overestimates later risks. We propose a general family of mixture models for undiagnosed prevalent disease and interval-censored incident disease that we call prevalence-incidence models. Parameters for parametric prevalence-incidence models, such as the logistic regression and Weibull survival (logistic-Weibull) model, are estimated by direct likelihood maximization or by EM algorithm. Non-parametric methods are proposed to calculate cumulative risks for cases without covariates. We compare naive Kaplan-Meier, logistic-Weibull, and non-parametric estimates of cumulative risk in the cervical cancer screening program at Kaiser Permanente Northern California. Kaplan-Meier provided poor estimates while the logistic-Weibull model was a close fit to the non-parametric. Our findings support our use of logistic-Weibull models to develop the risk estimates that underlie current U.S. risk-based cervical cancer screening guidelines.
DOI: 10.6084/m9.figshare.5063617
title: Dataset for: Fungal interactions reduce carbon use efficiency

description: The efficiency by which fungi decompose organic matter contributes to the amount of carbon that is retained in biomass versus lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, including temperature and nutrient availability. Theoretically, the physiological costs of interspecific interactions should likewise alter CUE, yet the magnitude of these costs are untested. Here we conduct a microcosm experiment to quantify how interactions among wood-decay basidiomycete fungi alter growth, respiration, and CUE across a temperature and nitrogen gradient. We show that species interactions induced consistent declines in CUE, regardless of abiotic conditions. Multispecies communities exhibited reductions in CUE of up to 25% relative to individual CUE, with this biotic effect being greater than the observed variation attributable to abiotic conditions. Our results suggest that the extent to which fungal-mediated carbon fluxes respond to environmental change may be influenced strongly by species interactions.
DOI: 10.6084/m9.figshare.5063617.v1
title: Dataset for: Fungal interactions reduce carbon use efficiency

description: The efficiency by which fungi decompose organic matter contributes to the amount of carbon that is retained in biomass versus lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, including temperature and nutrient availability. Theoretically, the physiological costs of interspecific interactions should likewise alter CUE, yet the magnitude of these costs are untested. Here we conduct a microcosm experiment to quantify how interactions among wood-decay basidiomycete fungi alter growth, respiration, and CUE across a temperature and nitrogen gradient. We show that species interactions induced consistent declines in CUE, regardless of abiotic conditions. Multispecies communities exhibited reductions in CUE of up to 25% relative to individual CUE, with this biotic effect being greater than the observed variation attributable to abiotic conditions. Our results suggest that the extent to which fungal-mediated carbon fluxes respond to environmental change may be influenced strongly by species interactions.
DOI: 10.6084/m9.figshare.12906170
title: Varied Shutter Light Field Stills

description: Stills from a light field camera, Raytrix R5, taken at varied shutter speeds. Used for research into low-light enhancement. Shutter speeds vary from 0.01ms to 30ms. No ISO used.
DOI: 10.6084/m9.figshare.12906170.v1
title: Varied Shutter Light Field Stills

description: Stills from a light field camera, Raytrix R5, taken at varied shutter speeds. Used for research into low-light enhancement. Shutter speeds vary from 0.01ms to 30ms. No ISO used.
DOI: 10.6084/m9.figshare.5063332
title: plos-data.tar.gz

description: This dataset accompanies the following paper: Ferdman, Minkov, Bekkerman, and Gefen "Quantifying the Web Browser Ecosystem".
DOI: 10.6084/m9.figshare.5063332.v1
title: plos-data.tar.gz

description: This dataset accompanies the following paper: Ferdman, Minkov, Bekkerman, and Gefen "Quantifying the Web Browser Ecosystem".
DOI: 10.6084/m9.figshare.5063077
title: Depth-Based Recognition of Shape Outlying Functions

description: A major drawback of many established depth functionals is their ineffectiveness in identifying functions outlying merely in shape. Herein, a simple modification of functional depth is proposed to provide a remedy for this difficulty. The modification is versatile, widely applicable, and introduced without imposing any assumptions on the data, such as differentiability. It is shown that many favorable attributes of the original depths for functions, including consistency properties, remain preserved for the modified depths. The powerfulness of the new approach is demonstrated on a number of examples for which the known depths fail to identify the outlying functions. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5063041
title: Data from: Environmental marginality and geographic range limits: a case study with Arabidopsis lyrata ssp. lyrata

description: Data used to generate ecological niche models for Arabidopsis lyrata ssp. lyrata and to test hypotheses about niche limitation and the effects of environmental marginality on genomic diversity.<br>IMPORTANT NOTES: The locality data in these files are provided at a lower resolution than those used in the analysis in order to uphold various data release agreements. Please contact the author if you require further information (lee-yaw@zoology.ubc.ca).<br>Here you will find the estimates of nucleotide diversity for all populations used in our study. Full genomic dataset (raw reads etc.) is being published as part of separate paper and will be deposited to the appropriate archive at a later date. For more information, please contact Yvonne Willi at yvonne.willi-at-unibas.ch<br><br>
DOI: 10.6084/m9.figshare.5063041.v3
title: Data from: Environmental marginality and geographic range limits: a case study with Arabidopsis lyrata ssp. lyrata

description: Data used to generate ecological niche models for Arabidopsis lyrata ssp. lyrata and to test hypotheses about niche limitation and the effects of environmental marginality on genomic diversity.<br>IMPORTANT NOTES: The locality data in these files are provided at a lower resolution than those used in the analysis in order to uphold various data release agreements. Please contact the author if you require further information (lee-yaw@zoology.ubc.ca).<br>Here you will find the estimates of nucleotide diversity for all populations used in our study. Full genomic dataset (raw reads etc.) is being published as part of separate paper and will be deposited to the appropriate archive at a later date. For more information, please contact Yvonne Willi at yvonne.willi-at-unibas.ch<br><br>
DOI: 10.6084/m9.figshare.5063077.v2
title: Depth-Based Recognition of Shape Outlying Functions<sup>*</sup>

description: A major drawback of many established depth functionals is their ineffectiveness in identifying functions outlying merely in shape. Herein, a simple modification of functional depth is proposed to provide a remedy for this difficulty. The modification is versatile, widely applicable, and introduced without imposing any assumptions on the data, such as differentiability. It is shown that many favourable attributes of the original depths for functions, including consistency properties, remain preserved for the modified depths. The powerfulness of the new approach is demonstrated on a number of examples for which the known depths fail to identify the outlying functions.
DOI: 10.6084/m9.figshare.5063023
title: Examination of the Relationship between Students’ Attitudes towards Computer and Self-Directed Learning with Technolog

description: A lot of studies conducted in the past examined the construct of Self-Directed Learning (SDL) and attitude towards computer; however, there are not sufficient number of studies examining these constructs in terms of children and together with concept of technology. Therefore, those two constructs and the relationship between them were examined in terms of children and in the context of concept of technology using structural equation modeling (SEM). In this study, the scales of students’ attitudes towards computer (SATC) and self-directed learning with technology for young students (SDLTYS) adapted into Turkish respectively by Demir and Yurdugül (2014) and Demir and Yurdugül (2013) were administered as measurement tools. 2219 students enrolled in either a public middle or secondary school located in Bursa and Ankara constituted the sampling of the study. As a result of this study, it was found that there is a positive high level correlation (r=.74) between aforementioned two constructs. In the full manuscript of the study, discussion regarding the findings of the study is included in detail.
DOI: 10.6084/m9.figshare.5063041.v2
title: Data from: Environmental marginality and geographic range limits: a case study with Arabidopsis lyrata ssp. lyrata

description: Data used to generate ecological niche models for Arabidopsis lyrata ssp. lyrata and to test hypotheses about niche limitation and the effects of environmental marginality on genomic diversity.<br>IMPORTANT NOTES: The locality data in these files are provided at a lower resolution than those used in the analysis in order to uphold various data release agreements. Please contact the author if you require further information (lee-yaw@zoology.ubc.ca).<br>Here you will find the estimates of nucleotide diversity for all populations used in our study. Full genomic dataset (raw reads etc.) is being published as part of separate paper and will be deposited to the appropriate archive at a later date. For more information, please contact Yvonne Willi at yvonne.willi-at-unibas.ch<br><br>
DOI: 10.6084/m9.figshare.5063002
title: The Adaptation of the Scale of Attitude Towards Computer Into Turkish for Middle and Secondary School Students

description: This study aimed to develop a Turkish scale, which is reliable, valid and meets the current requirements for assessing the attitudes of students towards computers. That is why, the scale of students’ attitude towards computers (SATC), which originally belongs to Teo (2008), was adapted into Turkish. When it comes to methodology part of the study, the scale was administered to a total of 1678 students enrolled in primary or secondary school located in Ankara. After Confirmatory Factor Analysis (CFA) was performed, it was ascertained that the scale consisted of 20 items and 3 factors (computer enjoyment, computer importance and computer anxiety). The Cronbach Alpha and Omega values of the scale were found out to be 0.83 and 0.95 respectively. The findings and implications based on these findings were discussed in a more detailed way in the full paper.
DOI: 10.6084/m9.figshare.5063002.v2
title: The Adaptation of the Scale of Attitude Towards Computer Into Turkish for Middle and Secondary School Students

description: This study aimed to develop a Turkish scale, which is reliable, valid and meets the current requirements for assessing the attitudes of students towards computers. That is why, the scale of students’ attitude towards computers (SATC), which originally belongs to Teo (2008), was adapted into Turkish. When it comes to methodology part of the study, the scale was administered to a total of 1678 students enrolled in primary or secondary school located in Ankara. After Confirmatory Factor Analysis (CFA) was performed, it was ascertained that the scale consisted of 20 items and 3 factors (computer enjoyment, computer importance and computer anxiety). The Cronbach Alpha and Omega values of the scale were found out to be 0.83 and 0.95 respectively. The findings and implications based on these findings were discussed in a more detailed way in the full paper.
DOI: 10.6084/m9.figshare.5063023.v2
title: Examination of the Relationship between Students’ Attitudes towards Computer and Self-Directed Learning with Technolog

description: A lot of studies conducted in the past examined the construct of Self-Directed Learning (SDL) and attitude towards computer; however, there are not sufficient number of studies examining these constructs in terms of children and together with concept of technology. Therefore, those two constructs and the relationship between them were examined in terms of children and in the context of concept of technology using structural equation modeling (SEM). In this study, the scales of students’ attitudes towards computer (SATC) and self-directed learning with technology for young students (SDLTYS) adapted into Turkish respectively by Demir and Yurdugül (2014) and Demir and Yurdugül (2013) were administered as measurement tools. 2219 students enrolled in either a public middle or secondary school located in Bursa and Ankara constituted the sampling of the study. As a result of this study, it was found that there is a positive high level correlation (r=.74) between aforementioned two constructs. In the full manuscript of the study, discussion regarding the findings of the study is included in detail.
DOI: 10.6084/m9.figshare.5058919
title: Lobby Display with "Voting" Booth

description: Image of election-themed display in the medical library lobby. The "Voting Booth" display was set up with a laptop featuring desktop shortcuts to the two products being evaluated and a shortcut to the feedback survey link. <br><br>
DOI: 10.6084/m9.figshare.5062990.v1
title: OSO Photophysiology

description: All concentrations are scaled to brine volume
DOI: 10.6084/m9.figshare.5062990.v2
title: OSO Photophysiology

description: All concentrations are scaled to brine volume
DOI: 10.6084/m9.figshare.5058553
title: NSF GRFP Program - Giant Angstrom, NORDP 2017

description: We introduce an approach to winning NSF Graduate Research Fellowships based on narrative and plot theory. Success rates for participants at one university were 4X that of nonparticipants. To serve more students, we developed a method of training writing center consultants to support applicants. The method makes use of rhetorical concepts familiar to consultants, such that people without disciplinary knowledge can still coach effectively. We conclude with thoughts about the applicability of the method to train writing consultants to support faculty research proposals.
DOI: 10.6084/m9.figshare.5058553.v1
title: NSF GRFP Program - Giant Angstrom, NORDP 2017

description: We introduce an approach to winning NSF Graduate Research Fellowships based on narrative and plot theory. Success rates for participants at one university were 4X that of nonparticipants. To serve more students, we developed a method of training writing center consultants to support applicants. The method makes use of rhetorical concepts familiar to consultants, such that people without disciplinary knowledge can still coach effectively. We conclude with thoughts about the applicability of the method to train writing consultants to support faculty research proposals.
DOI: 10.6084/m9.figshare.5058001
title: Spectroscopic studies on <i>in vitro</i> binding of cefixime and tolcapone drugs with serum albumin

description: The interaction between cefixime (antibacterial) and tolcapone (Parkinson’s disease) drugs with bovine serum albumin (BSA) was investigated using several spectroscopic techniques viz. UV–Vis, fluorescence and circular dichroism. The thermodynamic parameters of the interactions were calculated, which indicated that the binding processes are spontaneous and H-bonding and van der Waals forces play a major role in BSA–cefixime interaction and hydrophobic interactions dominate BSA–tolcapone complexation. Cefixime quenches the intrinsic fluorescence of BSA by dynamic process while tolcapone through static process. The binding constant of the BSA–tolcapone complex (10<sup>7</sup> L mol<sup>−1</sup>) is found to be relatively higher than that of BSA–cefixime complex (10<sup>4</sup> L mol<sup>−1</sup>). The binding distance between BSA and cefixime and tolcapone is calculated to be 3.3 and 4.2 nm, respectively. Both fluorescence and circular dichrosim spectral studies confirmed conformational changes in BSA upon binding with these drugs. Molecular docking studies suggest the possible binding sites in the protein molecule.'
DOI: 10.6084/m9.figshare.5057908
title: Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity

description: Short hairpin RNAs (shRNAs) are widely used for gene silencing by the RNA interference (RNAi) mechanism. The shRNA precursor is processed by the Dicer enzyme into active small interfering RNAs (siRNAs) that subsequently target a complementary mRNA for cleavage by the Argonaute 2 (Ago2) complex. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer and are instead processed by Ago2. We termed these molecules AgoshRNAs as both processing and silencing steps are mediated by Ago2 and proposed rules for the design of effective AgoshRNA molecules. Active and non-cytotoxic AgoshRNAs against HIV-1 RNA were generated, but their silencing activity was generally reduced compared with the matching shRNAs. Thus, further optimization of the AgoshRNA design is needed. In this study, we evaluated the importance of the single-stranded loop, in particular its size and nucleotide sequence, in AgoshRNA-mediated silencing. We document that the pyrimidine/purine content is important for AgoshRNA-mediated silencing activity.
DOI: 10.6084/m9.figshare.5057908.v1
title: Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity

description: Short hairpin RNAs (shRNAs) are widely used for gene silencing by the RNA interference (RNAi) mechanism. The shRNA precursor is processed by the Dicer enzyme into active small interfering RNAs (siRNAs) that subsequently target a complementary mRNA for cleavage by the Argonaute 2 (Ago2) complex. Recent evidence indicates that shRNAs with a relatively short basepaired stem bypass Dicer and are instead processed by Ago2. We termed these molecules AgoshRNAs as both processing and silencing steps are mediated by Ago2 and proposed rules for the design of effective AgoshRNA molecules. Active and non-cytotoxic AgoshRNAs against HIV-1 RNA were generated, but their silencing activity was generally reduced compared with the matching shRNAs. Thus, further optimization of the AgoshRNA design is needed. In this study, we evaluated the importance of the single-stranded loop, in particular its size and nucleotide sequence, in AgoshRNA-mediated silencing. We document that the pyrimidine/purine content is important for AgoshRNA-mediated silencing activity.
DOI: 10.6084/m9.figshare.5057887
title: Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

description: List of bacterial isolates used in this study and assembled genomes. <br><br><br>
DOI: 10.6084/m9.figshare.5057887.v1
title: Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

description: List of bacterial isolates used in this study and assembled genomes. <br><br><br>
DOI: 10.6084/m9.figshare.5057836
title: Assessing nanomaterial exposures in aquatic ecotoxicological testing: Framework and case studies based on dispersion and dissolution

description: The unique behavior of engineered nanomaterials (ENM) in aqueous media and dynamic changes in particle settling, agglomeration and dissolution rates is a challenge to the consistency, reliability and interpretation of standard aquatic hazard bioassay results. While the toxicological endpoints (e.g., survival, growth, reproduction, etc.) in ecotoxicity bioassays are largely applicable to ENMs, the standard methods as written for dissolved substances are confounded by the dynamic settling, agglomeration and dissolution of particulate ENMs during the bioassay. A testing framework was designed to serve as a starting point to identify approaches for the consistent conduct of aquatic hazard tests that account for the behavior of ENMs in test media and suitable data collection to support representative exposure metrology. The framework was demonstrated by conducting three case studies testing ENMs with functionally distinct characteristics and behaviors. Pretests with a temporal sampling of particle concentration, agglomeration and dissolution were conducted on each ENM in test media. Results indicated that a silver nanoparticle (AgNP) powder was not dispersible, a nano-TiO<sub>2</sub> powder was dispersible but unstable, and a polyvinylpyrrolidinone-coated AgNP was relatively stable in test media. Based on these functional results, <i>Ceriodaphnia dubia</i> bioassays were conducted to compare different exposure summary methods (nominal, arithmetic average, geometric average, time-weighted average) for calculating and expressing toxicity endpoints. Results indicated that while arithmetic means were effective for expressing the toxicity of more stable materials, time-weighted averaged concentrations were appropriate for the unstable nano-TiO<sub>2</sub>.
DOI: 10.6084/m9.figshare.5057833
title: Probabilistic risk assessment of emerging materials: case study of titanium dioxide nanoparticles

description: The development and use of emerging technologies such as nanomaterials can provide both benefits and risks to society. Emerging materials may promise to bring many technological advantages but may not be well characterized in terms of their production volumes, magnitude of emissions, behaviour in the environment and effects on living organisms. This uncertainty can present challenges to scientists developing these materials and persons responsible for defining and measuring their adverse impacts. Human health risk assessment is a method of identifying the intrinsic hazard of and quantifying the dose–response relationship and exposure to a chemical, to finally determine the estimation of risk. Commonly applied deterministic approaches may not sufficiently estimate and communicate the likelihood of risks from emerging technologies whose uncertainty is large. Probabilistic approaches allow for parameters in the risk assessment process to be defined by distributions instead of single deterministic values whose uncertainty could undermine the value of the assessment. A probabilistic approach was applied to the dose–response and exposure assessment of a case study involving the production of nanoparticles of titanium dioxide in seven different exposure scenarios. Only one exposure scenario showed a statistically significant level of risk. In the latter case, this involved dumping high volumes of nano-TiO<sub>2</sub> powders into an open vessel with no personal protection equipment. The probabilistic approach not only provided the likelihood of but also the major contributing factors to the estimated risk (e.g. emission potential).