cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1582709
title: Early lethality and neuronal proteinopathy in mice expressing cytoplasm-targeted FUS that lacks the RNA recognition motif

description: Mutations to the RNA binding protein, fused in sarcoma (FUS) occur in ∼5% of familial ALS and FUS-positive cytoplasmic inclusions are commonly observed in these patients. Altered RNA metabolism is increasingly implicated in ALS, yet it is not understood how the specificity with which FUS interacts with RNA in the cytoplasm can affect its aggregation in vivo. To further understand this, we expressed, in mice, a form of FUS (FUS ΔRRMcyt) that lacked the RNA recognition motif (RRM), thought to impart specificity to FUS-RNA interactions, and carried an ALS-associated point mutation, R522G, retaining the protein in the cytoplasm. Here we report the phenotype and results of histological assessment of the brain of transgenic mice expressing this isoform of FUS. Results demonstrated that neuronal expression of FUS ΔRRMcyt caused early lethality often preceded by severe tremor. Large FUS-positive cytoplasmic inclusions were found in many brain neurons; however, neither neuronal loss nor neuroinflammatory response was observed. In conclusion, the extensive FUS proteinopathy and severe phenotype of these mice suggests that affecting the interactions of FUS with RNA in vivo may augment its aggregation in the neuronal cytoplasm and the severity of disease processes.
DOI: 10.6084/m9.figshare.1582675
title: Comparison of Equivalence Between Two Commercially Available S499-phosphorylated FMRP Antibodies in Mice

description: Antibody densitization data for western blots.
DOI: 10.6084/m9.figshare.1582675.v1
title: Comparison of Equivalence Between Two Commercially Available S499-phosphorylated FMRP Antibodies in Mice

description: Antibody densitization data for western blots.
DOI: 10.6084/m9.figshare.1582668
title: DataBase_NeuralCorrelates_ToMPD

description: DataBase_NeuralCorrelates_ToMPD
DOI: 10.6084/m9.figshare.1582668.v1
title: DataBase_NeuralCorrelates_ToMPD

description: DataBase_NeuralCorrelates_ToMPD
DOI: 10.6084/m9.figshare.1582639
title: Raw data for Kuntz and Eisen, 2015 ‘Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis’

description: Time-lapse imaging of developing Drosophila melanogaster embryos. Please see README.txt for a summary and specific details of the files contained in the compressed folder.
DOI: 10.6084/m9.figshare.1582635
title: Ecology BIOL 2050 - Lab 5 & 6 Insect diversity near pond environment

description: The lab experiment consisted of a group of five members that setup pan traps over two trials. One trial was done per week for two weeks at the York University pond area. The experiment location was primarily non-mowed grassland with a small patch of mowed grassland between 20 and 25 meters from the pond. The temperature for trial 1 and 2 were 13 and 10 degrees Celsius respectively. The equipments used included 36 pan traps, 12 of each colour including white, yellow, and blue, two transect tapes, and soapy water. The group travelled to the east side of the pond and marked the edge of the pond as 0 meters. A transect of 25 meters were measured east of the starting location towards the University campus. A set of traps were placed starting at 0 meters and subsequent traps were set every 5 meters from the starting position. The traps were divided into two of each colour per transect, with a total of six traps per location. A second lateral transect of 5 meters were measured that bisected the original transect at each trap location. The six traps were randomly chosen and placed along the 5 meters lateral transect 1 meter apart from each other. There were a total of six transect trap locations with six traps each at 0, 5, 10, 15, 20, and 25 meters from the pond. The total number of different plant species were counted along each 5 meters lateral transect, the species was not identified it was only acknowledged that they were different species. The traps were left to stand for one hour and thirty minutes after which the group counted the insects that were captured starting from the earliest traps set. Although this experiment was focused on insects, all invertebrates that were captured by the traps were also included in the.
DOI: 10.6084/m9.figshare.1581981
title: Microbial community succession driven by different nutrients in tailings: effects of different nutrients on microbial community and remediation efficiency of tailing

description: Carbon source and nitrogen source
DOI: 10.6084/m9.figshare.1581680
title: Supplemental Data

description: fasta file of amino acid sequences used as MASCOT database for protein identification
DOI: 10.6084/m9.figshare.1582635.v1
title: Ecology BIOL 2050 - Lab 5 & 6 Insect diversity near pond environment

description: The lab experiment consisted of a group of five members that setup pan traps over two trials. One trial was done per week for two weeks at the York University pond area. The experiment location was primarily non-mowed grassland with a small patch of mowed grassland between 20 and 25 meters from the pond. The temperature for trial 1 and 2 were 13 and 10 degrees Celsius respectively. The equipments used included 36 pan traps, 12 of each colour including white, yellow, and blue, two transect tapes, and soapy water. The group travelled to the east side of the pond and marked the edge of the pond as 0 meters. A transect of 25 meters were measured east of the starting location towards the University campus. A set of traps were placed starting at 0 meters and subsequent traps were set every 5 meters from the starting position. The traps were divided into two of each colour per transect, with a total of six traps per location. A second lateral transect of 5 meters were measured that bisected the original transect at each trap location. The six traps were randomly chosen and placed along the 5 meters lateral transect 1 meter apart from each other. There were a total of six transect trap locations with six traps each at 0, 5, 10, 15, 20, and 25 meters from the pond. The total number of different plant species were counted along each 5 meters lateral transect, the species was not identified it was only acknowledged that they were different species. The traps were left to stand for one hour and thirty minutes after which the group counted the insects that were captured starting from the earliest traps set. Although this experiment was focused on insects, all invertebrates that were captured by the traps were also included in the.
DOI: 10.6084/m9.figshare.1581633
title: How Much Information Does Dependence Between Wavelet Coefficients Contain?

description: This article is motivated by several articles that propose statistical inference where the independence of wavelet coefficients for both short- as well as long-range dependent time series is assumed. We focus on the sample variance and investigate the influence of the dependence between wavelet coefficients and this statistic. To this end, we derive asymptotic distributional properties of the sample variance for a time series that is synthesized, ignoring some or all dependence between wavelet coefficients. We show that the second-order properties differ from the those of the true time series whose wavelet coefficients have the same marginal distribution except in the independent Gaussian case. This holds true even if the dependency is correct within each level and only the dependence between levels is ignored. In the case of sample autocovariances and sample autocorrelations at lag one, we indicate that first-order properties are erroneous. In a second step, we investigate several nonparametric bootstrap schemes in the wavelet domain, which take more and more dependence into account until finally the full dependency is mimicked. We obtain very similar results, where only a bootstrap mimicking the full covariance structure correctly can be valid asymptotically. A simulation study supports our theoretical findings for the wavelet domain bootstraps. For long-range-dependent time series with long-memory parameter <i>d</i> &gt; 1/4, we show that some additional problems occur, which cannot be solved easily without using additional information for the bootstrap. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581636
title: Expression of histone methyltransferases as novel biomarkers for renal cell tumor diagnosis and prognostication

description: Renal cell tumors (RCTs) are the most lethal of the common urological cancers. The widespread use of imaging entailed an increased detection of small renal masses, emphasizing the need for accurate distinction between benign and malignant RCTs, which is critical for adequate therapeutic management. Histone methylation has been implicated in renal tumorigenesis, but its potential clinical value as RCT biomarker remains mostly unexplored. Hence, the main goal of this study was to identify differentially expressed histone methyltransferases (HMTs) and histone demethylases (HDMs) that might prove useful for RCT diagnosis and prognostication, emphasizing the discrimination between oncocytoma (a benign tumor) and renal cell carcinoma (RCC), especially the chromophobe subtype (chRCC). We found that the expression levels of 3 genes—<i>SMYD2, SETD3</i>, and <i>NO66</i>—was significantly altered in a set of RCTs, which was further validated in a large independent cohort. Higher expression levels were found in RCTs compared to normal renal tissues (RNTs) and in chRCCs comparatively to oncocytomas. <i>SMYD2</i> and <i>SETD3</i> mRNA levels correlated with protein expression assessed by immunohistochemistry. <i>SMYD2</i> transcript levels discriminated RCTs from RNT, with 82.1% sensitivity and 100% specificity [area under curve (AUC) = 0.959], and distinguished chRCCs from oncocytomas, with 71.0% sensitivity and 73.3% specificity (AUC = 0.784). Low expression levels of <i>SMYD2, SETD3</i>, and <i>NO66</i> were significantly associated with shorter disease-specific and disease-free survival, especially in patients with non-organ confined tumors. We conclude that expression of selected HMTs and HDMs might constitute novel biomarkers to assist in RCT diagnosis and assessment of tumor aggressiveness.
DOI: 10.6084/m9.figshare.1581636.v1
title: Expression of histone methyltransferases as novel biomarkers for renal cell tumor diagnosis and prognostication

description: Renal cell tumors (RCTs) are the most lethal of the common urological cancers. The widespread use of imaging entailed an increased detection of small renal masses, emphasizing the need for accurate distinction between benign and malignant RCTs, which is critical for adequate therapeutic management. Histone methylation has been implicated in renal tumorigenesis, but its potential clinical value as RCT biomarker remains mostly unexplored. Hence, the main goal of this study was to identify differentially expressed histone methyltransferases (HMTs) and histone demethylases (HDMs) that might prove useful for RCT diagnosis and prognostication, emphasizing the discrimination between oncocytoma (a benign tumor) and renal cell carcinoma (RCC), especially the chromophobe subtype (chRCC). We found that the expression levels of 3 genes—<i>SMYD2, SETD3</i>, and <i>NO66</i>—was significantly altered in a set of RCTs, which was further validated in a large independent cohort. Higher expression levels were found in RCTs compared to normal renal tissues (RNTs) and in chRCCs comparatively to oncocytomas. <i>SMYD2</i> and <i>SETD3</i> mRNA levels correlated with protein expression assessed by immunohistochemistry. <i>SMYD2</i> transcript levels discriminated RCTs from RNT, with 82.1% sensitivity and 100% specificity [area under curve (AUC) = 0.959], and distinguished chRCCs from oncocytomas, with 71.0% sensitivity and 73.3% specificity (AUC = 0.784). Low expression levels of <i>SMYD2, SETD3</i>, and <i>NO66</i> were significantly associated with shorter disease-specific and disease-free survival, especially in patients with non-organ confined tumors. We conclude that expression of selected HMTs and HDMs might constitute novel biomarkers to assist in RCT diagnosis and assessment of tumor aggressiveness.
DOI: 10.6084/m9.figshare.1581677
title: The Bipolar Diffusion Charging of Nanoparticles: A Review and Development of Approaches for Non-Spherical Particles

description: Theoretical and experimental analyses of the steady state, bipolar diffusion charge distribution on nanoparticles are reviewed. This charge distribution plays a critical role in electrical mobility measurements of nanoparticle size distribution functions, where it is approximated via empirical regression equations. While the regression approach has been broadly successful, there remain several unresolved issues related to charge distribution calculations. Specifically, research to date has not revealed a method to reliably calculate nanoparticle-ion collision rates in the presence of strong attractive potentials, charge distribution predictions do not routinely consider the mass and (electrical) mobility distributions of the charging ions, and calculation approaches applicable to both spherical and nonspherical particles have not been compared to experimental data. In light of these issues, we examine the steady-state bipolar charge distribution on gold nanospheres and gold nanorods via tandem differential mobility analysis (TDMA). We compare measurements to regression equations as well as to Brownian Dynamics (BD) simulations, which take ion mobility and mass distributions as inputs. These distributions were measured using a DMA coupled to a mass spectrometer. Both regression equations and BD simulations are found to agree reasonably well with measurements in air, and we find that particle mobility diameter has a much greater influence on charging than particle morphology. Results support the use of BD calculations to predict bipolar charge distributions when ion properties are known. Nevertheless, our work supports continued use of regression equations when such information is not available. Copyright © 2015 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.1581677.v1
title: The Bipolar Diffusion Charging of Nanoparticles: A Review and Development of Approaches for Non-Spherical Particles

description: ABSTRACTTheoretical and experimental analyses of the steady state, bipolar diffusion charge distribution on nanoparticles are reviewed. This charge distribution plays a critical role in electrical mobility measurements of nanoparticle size distribution functions, where it is approximated via empirical regression equations. While the regression approach has been broadly successful, there remain several unresolved issues related to charge distribution calculations. Specifically, research to date has not revealed a method to reliably calculate nanoparticle-ion collision rates in the presence of strong attractive potentials, charge distribution predictions do not routinely consider the mass and (electrical) mobility distributions of the charging ions, and calculation approaches applicable to both spherical and non-spherical particles have not been compared to experimental data. In light of these issues, we examine the steady-state bipolar charge distribution on gold nanospheres and gold nanorods via tandem differential mobility analysis (TDMA). We compare measurements to regression equations as well as to Brownian Dynamics (BD) simulations, which take ion mobility and mass distributions as inputs. These distributions were measured using a DMA coupled to a mass spectrometer. Both regression equations and BD simulations are found to agree reasonably well with measurements in air, and we find that particle mobility diameter has a much greater influence on charging than particle morphology. Results support the use of BD calculations to predict bipolar charge distributions when ion properties are known. Nevertheless, our work supports continued use of regression equations when such information is not available.
DOI: 10.6084/m9.figshare.1581632.v1
title: Inference for Monotone Functions Under Short and Long Range Dependence: Confidence Intervals and New Universal Limits

description: We introduce new point-wise confidence interval estimates for monotone functions observed with additive, dependent noise. Our methodology applies to both short- and long-range dependence regimes for the errors. The interval estimates are obtained via the method of inversion of certain discrepancy statistics. This approach avoids the estimation of nuisance parameters such as the derivative of the unknown function, which previous methods are forced to deal with. The resulting estimates are therefore more accurate, stable, and widely applicable in practice under minimal assumptions on the trend and error structure. The dependence of the errors especially long-range dependence leads to new phenomena, where new universal limits based on convex minorant functionals of drifted fractional Brownian motion emerge. Some extensions to uniform confidence bands are also developed.
DOI: 10.6084/m9.figshare.1581633.v2
title: How Much Information Does Dependence Between Wavelet Coefficients Contain?

description: This article is motivated by several articles that propose statistical inference where the independence of wavelet coefficients for both short- as well as long-range dependent time series is assumed. We focus on the sample variance and investigate the influence of the dependence between wavelet coefficients and this statistic. To this end, we derive asymptotic distributional properties of the sample variance for a time series that is synthesized, ignoring some or all dependence between wavelet coefficients. We show that the second-order properties differ from the those of the true time series whose wavelet coefficients have the same marginal distribution except in the independent Gaussian case. This holds true even if the dependency is correct within each level and only the dependence between levels is ignored. In the case of sample autocovariances and sample autocorrelations at lag one, we indicate that first-order properties are erroneous. In a second step, we investigate several nonparametric bootstrap schemes in the wavelet domain, which take more and more dependence into account until finally the full dependency is mimicked. We obtain very similar results, where only a bootstrap mimicking the full covariance structure correctly can be valid asymptotically. A simulation study supports our theoretical findings for the wavelet domain bootstraps. For long-range-dependent time series with long-memory parameter <i>d</i> &gt; 1/4, we show that some additional problems occur, which cannot be solved easily without using additional information for the bootstrap. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1581677.v3
title: The Bipolar Diffusion Charging of Nanoparticles: A Review and Development of Approaches for Non-Spherical Particles

description: Theoretical and experimental analyses of the steady state, bipolar diffusion charge distribution on nanoparticles are reviewed. This charge distribution plays a critical role in electrical mobility measurements of nanoparticle size distribution functions, where it is approximated via empirical regression equations. While the regression approach has been broadly successful, there remain several unresolved issues related to charge distribution calculations. Specifically, research to date has not revealed a method to reliably calculate nanoparticle-ion collision rates in the presence of strong attractive potentials, charge distribution predictions do not routinely consider the mass and (electrical) mobility distributions of the charging ions, and calculation approaches applicable to both spherical and nonspherical particles have not been compared to experimental data. In light of these issues, we examine the steady-state bipolar charge distribution on gold nanospheres and gold nanorods via tandem differential mobility analysis (TDMA). We compare measurements to regression equations as well as to Brownian Dynamics (BD) simulations, which take ion mobility and mass distributions as inputs. These distributions were measured using a DMA coupled to a mass spectrometer. Both regression equations and BD simulations are found to agree reasonably well with measurements in air, and we find that particle mobility diameter has a much greater influence on charging than particle morphology. Results support the use of BD calculations to predict bipolar charge distributions when ion properties are known. Nevertheless, our work supports continued use of regression equations when such information is not available. Copyright © 2015 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.1581677.v2
title: The Bipolar Diffusion Charging of Nanoparticles: A Review and Development of Approaches for Non-Spherical Particles

description: Theoretical and experimental analyses of the steady state, bipolar diffusion charge distribution on nanoparticles are reviewed. This charge distribution plays a critical role in electrical mobility measurements of nanoparticle size distribution functions, where it is approximated via empirical regression equations. While the regression approach has been broadly successful, there remain several unresolved issues related to charge distribution calculations. Specifically, research to date has not revealed a method to reliably calculate nanoparticle-ion collision rates in the presence of strong attractive potentials, charge distribution predictions do not routinely consider the mass and (electrical) mobility distributions of the charging ions, and calculation approaches applicable to both spherical and nonspherical particles have not been compared to experimental data. In light of these issues, we examine the steady-state bipolar charge distribution on gold nanospheres and gold nanorods via tandem differential mobility analysis (TDMA). We compare measurements to regression equations as well as to Brownian Dynamics (BD) simulations, which take ion mobility and mass distributions as inputs. These distributions were measured using a DMA coupled to a mass spectrometer. Both regression equations and BD simulations are found to agree reasonably well with measurements in air, and we find that particle mobility diameter has a much greater influence on charging than particle morphology. Results support the use of BD calculations to predict bipolar charge distributions when ion properties are known. Nevertheless, our work supports continued use of regression equations when such information is not available.Copyright 2015 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.1581632
title: Inference for Monotone Functions Under Short- and Long-Range Dependence: Confidence Intervals and New Universal Limits

description: We introduce new point-wise confidence interval estimates for monotone functions observed with additive, dependent noise. Our methodology applies to both short- and long-range dependence regimes for the errors. The interval estimates are obtained via the method of inversion of certain discrepancy statistics. This approach avoids the estimation of nuisance parameters such as the derivative of the unknown function, which previous methods are forced to deal with. The resulting estimates are therefore more accurate, stable, and widely applicable in practice under minimal assumptions on the trend and error structure. The dependence of the errors especially long-range dependence leads to new phenomena, where new universal limits based on convex minorant functionals of drifted fractional Brownian motion emerge. Some extensions to uniform confidence bands are also developed. Supplementary materials for this article are available online.