cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1583343.v1
title: The potential clinical impact of the release of two drafts of the human proteome

description: These authors have carried out an investigation of the two “draft maps of the human proteome” published in 2014 in <i>Nature</i>. The findings include an abundance of poor spectra, low-scoring peptide-spectrum matches and incorrectly identified proteins in both these studies, highlighting clear issues with the application of false discovery rates. This noise means that the claims made by the two papers – the identification of high numbers of protein coding genes, the detection of novel coding regions and the draft tissue maps themselves – should be treated with considerable caution. These authors recommend that clinicians and researchers do not use the unfiltered data from these studies. Despite this these studies will inspire further investigation into tissue-based proteomics. As long as this future work has proper quality controls, it could help produce a consensus map of the human proteome and improve our understanding of the processes that underlie health and disease.
DOI: 10.6084/m9.figshare.1583322
title: Conversion between geotropic and apogeotropic persistent direction-changing positional nystagmus

description: <i>Conclusion:</i> Clinical features in the course of conversion differed between patients with SSNHL and cupulopathy, which indicates that the pathophysiology of persistent geotropic or apogeotropic DCPN and the mechanism of the change in nystagmus direction may differ between the two groups. <i>Objective:</i> The aim of this study is to investigate clinical characteristics of 10 patients with persistent DCPN who exhibited a conversion of nystagmus direction between geotropic and apogeotropic, and discuss possible mechanisms. <i>Methods:</i> Using video-oculography, serial examinations of nystagmus in a head-roll test were performed. <i>Results:</i> Of these 10 patients, five had sudden sensorineural hearing loss (SSNHL) and the remaining five had cupulopathy. In SSNHL, direction of nystagmus changed from geotropic to apogeotropic in three patients and from apogeotropic to geotropic in two patients. In cupulopathy, persistent apogeotropic DCPN always preceded persistent geotropic DCPN. The change in nystagmus direction occurred earlier in patients with cupulopathy (1 or 2 days after vertigo onset) than in patients with SSNHL (4–23 days after vertigo onset). While the null plane was consistently identified on one side, regardless of the nystagmus direction in cupulopathy, it was not always identified on the side of hearing loss in SSNHL.
DOI: 10.6084/m9.figshare.1583315
title: Dynamic image of convection

description: dynamic process of convection
DOI: 10.6084/m9.figshare.1583343.v3
title: The potential clinical impact of the release of two drafts of the human proteome

description: The authors have carried out an investigation of the two “draft maps of the human proteome” published in 2014 in <i>Nature</i>. The findings include an abundance of poor spectra, low-scoring peptide-spectrum matches and incorrectly identified proteins in both these studies, highlighting clear issues with the application of false discovery rates. This noise means that the claims made by the two papers – the identification of high numbers of protein coding genes, the detection of novel coding regions and the draft tissue maps themselves – should be treated with considerable caution. The authors recommend that clinicians and researchers do not use the unfiltered data from these studies. Despite this these studies will inspire further investigation into tissue-based proteomics. As long as this future work has proper quality controls, it could help produce a consensus map of the human proteome and improve our understanding of the processes that underlie health and disease.
DOI: 10.6084/m9.figshare.1583314
title: Determine the refractive index profile

description: To find out the horizontal refractive index distribution and verify our theory, we repeated the experiment in Figure 3 of the main text. The He-Ne probe beam is weakly focused in to solution using a 250 mm lens to get a finer probe beam (diameter &lt;0.5 mm). Thus the measured horizontal deflection can be more accurate. Then, we changed the distance between the focused probe beam and the boundary of the pump beam, and the deflection of the probe beam was recorded. Finally, after a serial procedure of data processing, we get the refractive index profile along the x direction from the center of the pumped area to 4 mm outside the pumped area.
DOI: 10.6084/m9.figshare.1583343.v2
title: The potential clinical impact of the release of two drafts of the human proteome

description: The authors have carried out an investigation of the two “draft maps of the human proteome” published in 2014 in <i>Nature</i>. The findings include an abundance of poor spectra, low-scoring peptide-spectrum matches and incorrectly identified proteins in both these studies, highlighting clear issues with the application of false discovery rates. This noise means that the claims made by the two papers – the identification of high numbers of protein coding genes, the detection of novel coding regions and the draft tissue maps themselves – should be treated with considerable caution. The authors recommend that clinicians and researchers do not use the unfiltered data from these studies. Despite this these studies will inspire further investigation into tissue-based proteomics. As long as this future work has proper quality controls, it could help produce a consensus map of the human proteome and improve our understanding of the processes that underlie health and disease.
DOI: 10.6084/m9.figshare.1583315.v1
title: Dynamic image of convection

description: dynamic process of convection
DOI: 10.6084/m9.figshare.1583322.v1
title: Conversion between geotropic and apogeotropic persistent direction-changing positional nystagmus

description: <i>Conclusion:</i> Clinical features in the course of conversion differed between patients with SSNHL and cupulopathy, which indicates that the pathophysiology of persistent geotropic or apogeotropic DCPN and the mechanism of the change in nystagmus direction may differ between the two groups. <i>Objective:</i> The aim of this study is to investigate clinical characteristics of 10 patients with persistent DCPN who exhibited a conversion of nystagmus direction between geotropic and apogeotropic, and discuss possible mechanisms. <i>Methods:</i> Using video-oculography, serial examinations of nystagmus in a head-roll test were performed. <i>Results:</i> Of these 10 patients, five had sudden sensorineural hearing loss (SSNHL) and the remaining five had cupulopathy. In SSNHL, direction of nystagmus changed from geotropic to apogeotropic in three patients and from apogeotropic to geotropic in two patients. In cupulopathy, persistent apogeotropic DCPN always preceded persistent geotropic DCPN. The change in nystagmus direction occurred earlier in patients with cupulopathy (1 or 2 days after vertigo onset) than in patients with SSNHL (4–23 days after vertigo onset). While the null plane was consistently identified on one side, regardless of the nystagmus direction in cupulopathy, it was not always identified on the side of hearing loss in SSNHL.
DOI: 10.6084/m9.figshare.1583314.v4
title: Determine the refractive index profile

description: To find out the horizontal refractive index distribution and verify our theory, we repeated the experiment in Figure 3 of the main text. The He-Ne probe beam is weakly focused in to solution using a 250 mm lens to get a finer probe beam (diameter &lt;0.5 mm). Thus the measured horizontal deflection can be more accurate. Then, we changed the distance between the focused probe beam and the boundary of the pump beam, and the deflection of the probe beam was recorded. Finally, after a serial procedure of data processing, we get the refractive index profile along the x direction from the center of the pumped area to 4 mm outside the pumped area.
DOI: 10.6084/m9.figshare.1583314.v3
title: Determine the refractive index profile

description: To find out the horizontal refractive index distribution and verify our theory, we repeated the experiment in Figure 3 of the main text. The He-Ne probe beam is weakly focused in to solution using a 250 mm lens to get a finer probe beam (diameter &lt;0.5 mm). Thus the measured horizontal deflection can be more accurate. Then, we changed the distance between the focused probe beam and the boundary of the pump beam, and the deflection of the probe beam was recorded. Finally, after a serial procedure of data processing, we get the refractive index profile along the x direction from the center of the pumped area to 4 mm outside the pumped area.
DOI: 10.6084/m9.figshare.1583299
title: THE ANALYSIS OF GENE SEQUENCING INDUSTRIES IN 2015

description: The year is a challenging year for sequencing industry. The improvement of technology makes it gradually plays a more important role in all kinds of research, especially the medical research.
DOI: 10.6084/m9.figshare.1583226
title: A Brief Introduction of Immunoprecipitation

description: Protein is always the focus of research for global scientists for it is the most important molecule in living forms. Immunoprecipitation is a classical method to researching interaction different proteins on the basis of specificity between antibody and antigen and it is also regarded as an effective way to recognize the mutual physiological action between two kinds of proteins in cells.
DOI: 10.6084/m9.figshare.1583299.v1
title: THE ANALYSIS OF GENE SEQUENCING INDUSTRIES IN 2015

description: The year is a challenging year for sequencing industry. The improvement of technology makes it gradually plays a more important role in all kinds of research, especially the medical research.
DOI: 10.6084/m9.figshare.1582730
title: Nonparametric Conditional Density Estimation in a High-Dimensional Regression Setting

description: In some applications (e.g., in cosmology and economics), the regression E[Z|x] is not adequate to represent the association between a predictor <b>x</b> and a response <i>Z</i> because of multi-modality and asymmetry of <i>f</i>(<i>z</i>|<b>x</b>); using the full density instead of a single-point estimate can then lead to less bias in subsequent analysis. As of now, there are no effective ways of estimating <i>f</i>(<i>z</i>|<b>x</b>) when <b>x</b> represents high-dimensional, complex data. In this article, we propose a new nonparametric estimator of <i>f</i>(<i>z</i>|<b>x</b>) that adapts to sparse (low-dimensional) structure in <b>x</b>. By directly expanding <i>f</i>(<i>z</i>|<b>x</b>) in the eigenfunctions of a kernel-based operator, we avoid tensor products in high dimensions as well as ratios of estimated densities. Our basis functions are orthogonal with respect to the underlying data distribution, allowing fast implementation and tuning of parameters. We derive rates of convergence and show that the method adapts to the intrinsic dimension of the data. We also demonstrate the effectiveness of the series method on images, spectra, and an application to photometric redshift estimation of galaxies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1582732
title: Particle Approximations of the Score and Observed Information Matrix for Parameter Estimation in State–Space Models With Linear Computational Cost

description: Poyiadjis, Doucet, and Singh showed how particle methods can be used to estimate both the score and the observed information matrix for state–space models. These methods either suffer from a computational cost that is quadratic in the number of particles, or produce estimates whose variance increases quadratically with the amount of data. This article introduces an alternative approach for estimating these terms at a computational cost that is linear in the number of particles. The method is derived using a combination of kernel density estimation, to avoid the particle degeneracy that causes the quadratically increasing variance, and Rao–Blackwellization. Crucially, we show the method is robust to the choice of bandwidth within the kernel density estimation, as it has good asymptotic properties regardless of this choice. Our estimates of the score and observed information matrix can be used within both online and batch procedures for estimating parameters for state–space models. Empirical results show improved parameter estimates compared to existing methods at a significantly reduced computational cost. Supplementary materials including code are available.
DOI: 10.6084/m9.figshare.1582732.v2
title: Particle Approximations of the Score and Observed Information Matrix for Parameter Estimation in State–Space Models With Linear Computational Cost

description: Poyiadjis, Doucet, and Singh showed how particle methods can be used to estimate both the score and the observed information matrix for state–space models. These methods either suffer from a computational cost that is quadratic in the number of particles, or produce estimates whose variance increases quadratically with the amount of data. This article introduces an alternative approach for estimating these terms at a computational cost that is linear in the number of particles. The method is derived using a combination of kernel density estimation, to avoid the particle degeneracy that causes the quadratically increasing variance, and Rao–Blackwellization. Crucially, we show the method is robust to the choice of bandwidth within the kernel density estimation, as it has good asymptotic properties regardless of this choice. Our estimates of the score and observed information matrix can be used within both online and batch procedures for estimating parameters for state–space models. Empirical results show improved parameter estimates compared to existing methods at a significantly reduced computational cost. Supplementary materials including code are available.
DOI: 10.6084/m9.figshare.1582732.v1
title: Particle Approximations of the Score and Observed Information Matrix for Parameter Estimation in State Space Models With Linear Computational Cost

description: Poyiadjis et al. (2011) show how particle methods can be used to estimate both the score and the observed information matrix for state space models. These methods either suffer from a computational cost that is quadratic in the number of particles, or produce estimates whose variance increases quadratically with the amount of data. This paper introduces an alternative approach for estimating these terms at a computational cost that is linear in the number of particles. The method is derived using a combination of kernel density estimation, to avoid the particle degeneracy that causes the quadratically increasing variance, and Rao-Blackwellisation. Crucially, we show the method is robust to the choice of bandwidth within the kernel density estimation, as it has good asymptotic properties regardless of this choice. Our estimates of the score and observed information matrix can be used within both online and batch procedures for estimating parameters for state space models. Empirical results show improved parameter estimates compared to existing methods at a significantly reduced computational cost. Supplementary materials including code are available.
DOI: 10.6084/m9.figshare.1582724
title: Insect Abundance as a result for Plant Abundance and Location

description: This dataset observes how plant abundance and location affect insect abundance. This experiment was completed by myself, Adamo, Ava, Ashley and Katherine. The project ran on two separate days from approximately 3:00 to 5:00 pm, at York University in Toronto, Canada. The two days were October 13th and October 20th. The data was collected in two different locations. On day 1, 30 quadrats were placed in the Danby woodlot, and 30 quadrats were placed in the Danby grassland adjacent to the woodlot. The first day had clear weather, no rain and a temperature of 19⁰C. The second day, a week after day 1, the same process was repeated providing a total of 60 quadrats of data per location. On day 2, there was light rain during data collection, and a temperature of 18⁰C. To place the quadrat, a random number generator was used to determine how many steps should be taken. The steps were measured by the same person each time to ensure consistency. The plant abundance was rated on a scale excluding grass and dead plants, and then the insects were counted by all members of the group. In the grassland, insect abundance ranged from 0- 18 insects counted per quadrat. The most common number of bugs to be observed was around 5-7. In the woodlot, insect abundance ranged from 0-30 insects per quadrat. The most common number of bugs to be observed was 4.
DOI: 10.6084/m9.figshare.1582724.v1
title: Insect Abundance as a result for Plant Abundance and Location

description: This dataset observes how plant abundance and location affect insect abundance. This experiment was completed by myself, Adamo, Ava, Ashley and Katherine. The project ran on two separate days from approximately 3:00 to 5:00 pm, at York University in Toronto, Canada. The two days were October 13th and October 20th. The data was collected in two different locations. On day 1, 30 quadrats were placed in the Danby woodlot, and 30 quadrats were placed in the Danby grassland adjacent to the woodlot. The first day had clear weather, no rain and a temperature of 19⁰C. The second day, a week after day 1, the same process was repeated providing a total of 60 quadrats of data per location. On day 2, there was light rain during data collection, and a temperature of 18⁰C. To place the quadrat, a random number generator was used to determine how many steps should be taken. The steps were measured by the same person each time to ensure consistency. The plant abundance was rated on a scale excluding grass and dead plants, and then the insects were counted by all members of the group. In the grassland, insect abundance ranged from 0- 18 insects counted per quadrat. The most common number of bugs to be observed was around 5-7. In the woodlot, insect abundance ranged from 0-30 insects per quadrat. The most common number of bugs to be observed was 4.
DOI: 10.6084/m9.figshare.1582725.v2
title: FGFR3/fibroblast growth factor receptor 3 inhibits autophagy through decreasing the ATG12–ATG5 conjugate, leading to the delay of cartilage development in achondroplasia

description: FGFR3 (fibroblast growth factor receptor 3) is a negative regulator of endochondral ossification. Gain-of-function mutations in <i>FGFR3</i> are responsible for achondroplasia, the most common genetic form of dwarfism in humans. Autophagy, an evolutionarily conserved catabolic process, maintains chondrocyte viability in the growth plate under stress conditions, such as hypoxia and nutritional deficiencies. However, the role of autophagy and its underlying molecular mechanisms in achondroplasia remain elusive. In this study, we found activated FGFR3 signaling inhibited autophagic activity in chondrocytes, both in vivo and in vitro. By employing an embryonic bone culture system, we demonstrated that treatment with autophagy inhibitor 3-MA or chloroquine led to cartilage growth retardation, which mimics the effect of activated-FGFR3 signaling on chondrogenesis. Furthermore, we found that FGFR3 interacted with ATG12–ATG5 conjugate by binding to ATG5. More intriguingly, FGFR3 signaling was found to decrease the protein level of ATG12–ATG5 conjugate. Consistently, using in vitro chondrogenic differentiation assay system, we showed that the ATG12–ATG5 conjugate was essential for the viability and differentiation of chondrocytes. Transient transfection of ATG5 partially rescued FGFR3-mediated inhibition on chondrocyte viability and differentiation. Our findings reveal that FGFR3 inhibits the autophagic activity by decreasing the ATG12–ATG5 conjugate level, which may play an essential role in the pathogenesis of achondroplasia.
DOI: 10.6084/m9.figshare.1582725.v1
title: FGFR3/Fibroblast Growth Factor Receptor 3 Inhibits Autophagy through Decreasing the ATG12–ATG5 Conjugate, Leading to the Delay of Cartilage Development in Achondroplasia

description: FGFR3 (fibroblast growth factor receptor 3) is a negative regulator of endochondral ossification. Gain-of-function mutations in <i>FGFR3</i> are responsible for achondroplasia, the most common genetic form of dwarfism in humans. Autophagy, an evolutionarily conserved catabolic process, maintains chondrocyte viability in the growth plate under stress conditions, such as hypoxia and nutritional deficiencies. However, the role of autophagy and its underlying molecular mechanisms in achondroplasia remain elusive. In this study, we found activated FGFR3 signaling inhibited autophagic activity in chondrocytes, both <i>in vivo</i> and <i>in vitro</i>. By employing an embryonic bone culture system, we demonstrated that treatment with autophagy inhibitor 3-MA or chloroquine led to cartilage growth retardation, which mimics the effect of activated-FGFR3 signaling on chondrogenesis. Furthermore, we found that FGFR3 interacted with ATG12–ATG5 conjugate by binding to ATG5. More intriguingly, FGFR3 signaling was found to decrease the protein level of ATG12–ATG5 conjugate. Consistently, using <i>in vitro</i> chondrogenic differentiation assay system, we showed that the ATG12–ATG5 conjugate was essential for the viability and differentiation of chondrocytes. Transient transfection of ATG5 partially rescued FGFR3-mediated inhibition on chondrocyte viability and differentiation. Our findings reveal that FGFR3 inhibits the autophagic activity by decreasing the ATG12–ATG5 conjugate level, which may play an essential role in the pathogenesis of achondroplasia.
DOI: 10.6084/m9.figshare.1582717
title: Recent progress in urinary proteome analysis for prostate cancer diagnosis and management

description: Prostate cancer (PCa) is fifth leading cause of cancer-associated deaths in men worldwide. Although the application of the serum prostate-specific antigen (PSA) screening test resulted in an increase in the PCa diagnosed cases, it demonstrated a negligible benefit regarding the associated mortality. Treatment options vary, with active surveillance to be preferable for patients with low-risk PCa and therapy of advanced castration-resistant PCa to rely on α-emitters and cytotoxic chemotherapy. Although recent developments have led to the approval of novel drugs for the treatment of castration-resistant PCa, the optimal sequence and timing of medication have not been yet determined. New screening modalities could improve the discriminatory accuracy between tumors with favorable clinical prognosis. Implementation of proteomic-based biomarkers appears to be a promising improvement, which could enable a more accurate diagnosis, guide treatment and improve patient outcome. Reviewed here are urinary proteome-based approaches for detection of PCa and patient management.
DOI: 10.6084/m9.figshare.1582717.v1
title: Recent progress in urinary proteome analysis for prostate cancer diagnosis and management

description: Prostate cancer (PCa) is fifth leading cause of cancer-associated deaths in men worldwide. Although the application of the serum prostate-specific antigen (PSA) screening test resulted in an increase in the PCa diagnosed cases, it demonstrated a negligible benefit regarding the associated mortality. Treatment options vary, with active surveillance to be preferable for patients with low-risk PCa and therapy of advanced castration-resistant PCa to rely on α-emitters and cytotoxic chemotherapy. Although recent developments have led to the approval of novel drugs for the treatment of castration-resistant PCa, the optimal sequence and timing of medication have not been yet determined. New screening modalities could improve the discriminatory accuracy between tumors with favorable clinical prognosis. Implementation of proteomic-based biomarkers appears to be a promising improvement, which could enable a more accurate diagnosis, guide treatment and improve patient outcome. Reviewed here are urinary proteome-based approaches for detection of PCa and patient management.