cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1629348.v2
title: The Local Brewery: A Project for Use in Differential Equations Courses

description: We describe a modeling project designed for an ordinary differential equations (ODEs) course using first-order and systems of first-order differential equations to model the fermentation process in beer. The project aims to expose the students to the modeling process by creating and solving a mathematical model and effectively communicating their findings in a technical report. The students are required to produce a simple first-order differential equation and find the solution, given varying initial conditions. The students are also required to analyze a more complex, nonlinear ODE system model of the fermentation process. In dealing with the nonlinear system of equations, we provide the students a <i>Mathematica</i> file to reduce the time spent developing the model, but allow for more time to interpret the model. We also share some perspectives on the implementation of the project, provide alternative implementations, and possible extensions to the project.
DOI: 10.6084/m9.figshare.1629344
title: Seeing Things From Others’ Points of View: Collaboration in Undergraduate Mathematics

description: We report on three approaches taken to incorporate collaborative activities into undergraduate mathematics classes. There is strong evidence from research in K-12 classrooms that these, and similar, approaches support a range of positive learning outcomes for students. Despite the potential benefits the cited studies have shown, research into the use of such methods at the tertiary level is limited. We describe the ways in which we have implemented research projects, collaborative tutorials, and team-based learning in a range of undergraduate mathematics classes in two countries. We present quantitative and qualitative evidence from these teaching experiences to support our claim that there is a definite mandate for significant opportunities within our courses for students to work cooperatively, talk together, and argue about mathematics.
DOI: 10.6084/m9.figshare.1629348.v1
title: The Local Brewery. A Project for Use in Differential Equations Courses

description: We describe a modeling project designed for an ordinary differential equations course using first order and systems of first order differential equations to model the fermentation process in beer. The project aims to expose the students to the modeling process by creating and solving a mathematical model and effectively communicating their findings in a technical report. The students are required to produce a simple first order differential equation and find the solution, given varying initial conditions. The students are also required to analyze a more complex, non-linear ODE system model of the fermentation process. In dealing with the non-linear system of equations, we provide the students a <i>Mathematica</i> file to reduce the time spent developing the model, but allow for more time to interpret the model. We also share some perspectives on the implementation of the project, provide alternative implementations, and possible extensions to the project.
DOI: 10.6084/m9.figshare.1629344.v2
title: Seeing Things From Others’ Points of View: Collaboration in Undergraduate Mathematics

description: We report on three approaches taken to incorporate collaborative activities into undergraduate mathematics classes. There is strong evidence from research in K-12 classrooms that these, and similar, approaches support a range of positive learning outcomes for students. Despite the potential benefits the cited studies have shown, research into the use of such methods at the tertiary level is limited. We describe the ways in which we have implemented research projects, collaborative tutorials, and team-based learning in a range of undergraduate mathematics classes in two countries. We present quantitative and qualitative evidence from these teaching experiences to support our claim that there is a definite mandate for significant opportunities within our courses for students to work cooperatively, talk together, and argue about mathematics.
DOI: 10.6084/m9.figshare.1629344.v1
title: Seeing Things from Others’ Points of View: Collaboration in Undergraduate Mathematics

description: We report on three approaches taken to incorporate collaborative activities into undergraduate mathematics classes. There is strong evidence from research in K-12 classrooms that these, and similar, approaches support a range of positive learning outcomes for students. Despite the potential benefits the cited studies have shown, research into the use of such methods at the tertiary level is limited. We describe the ways in which we have implemented research projects, collaborative tutorials and team-based learning in a range of undergraduate mathematics classes in two countries. We present quantitative and qualitative evidence from these teaching experiences to support our claim that there is a definite mandate for significant opportunities within our courses for students to work cooperatively, talk together and argue about mathematics.
DOI: 10.6084/m9.figshare.1629338
title: Mere Renovation is Too Little Too Late: We Need to Rethink our Undergraduate Curriculum from the Ground Up

description: The last half-dozen years have seen <i>The American Statistician</i> publish well-argued and provocative calls to change our thinking about statistics and how we teach it, among them Brown and Kass, Nolan and Temple-Lang, and Legler et al. Within this past year, the ASA has issued a new and comprehensive set of guidelines for undergraduate programs (ASA, <i>Curriculum Guidelines for Undergraduate Programs in Statistical Science</i>). Accepting (and applauding) all this as background, the current article argues the need to rethink our curriculum from the ground up, and offers five principles and two caveats intended to help us along the path toward a new synthesis. These principles and caveats rest on my sense of three parallel evolutions: the convergence of trends in the roles of mathematics, computation, and context within statistics education. These ongoing changes, together with the articles cited above and the seminal provocation by Leo Breiman call for a deep rethinking of what we teach to undergraduates. In particular, following Brown and Kass, we should put priority on two goals, to make “fundamental concepts accessible” and to “minimize prerequisites to research.” [Received December 2014. Revised July 2015]
DOI: 10.6084/m9.figshare.1629338.v1
title: Mere Renovation is Too Little Too Late: We Need to Rethink our Undergraduate Curriculum from the Ground Up

description: The last half-dozen years have seen <i>The American Statistician</i> publish well-argued and provocative calls to change our thinking about statistics and how we teach it, among them Brown and Kass, Nolan and Temple-Lang, and Legler et al. Within this past year, the ASA has issued a new and comprehensive set of guidelines for undergraduate programs (ASA, <i>Curriculum Guidelines for Undergraduate Programs in Statistical Science</i>). Accepting (and applauding) all this as background, the current article argues the need to rethink our curriculum from the ground up, and offers five principles and two caveats intended to help us along the path toward a new synthesis. These principles and caveats rest on my sense of three parallel evolutions: the convergence of trends in the roles of mathematics, computation, and context within statistics education. These ongoing changes, together with the articles cited above and the seminal provocation by Leo Breiman call for a deep rethinking of what we teach to undergraduates. In particular, following Brown and Kass, we should put priority on two goals, to make “fundamental concepts accessible” and to “minimize prerequisites to research.” [Received December 2014. Revised July 2015]
DOI: 10.6084/m9.figshare.1628815.v1
title: Distribution of sound pressure around a singing cricket: radiation pattern and asymmetry in the sound field

description: Male field crickets generate calls to attract distant females through tegminal stridulation: the rubbing together of the overlying right wing which bears a file of cuticular teeth against the underlying left wing which carries a sclerotized scraper. During stridulation, specialized areas of membrane on both wings are set into oscillating vibrations to produce acoustic radiation. The location of females is unknown to the calling males and thus increasing effective signal range in all directions will maximize transmission effectiveness. However, producing an omnidirectional sound field of high sound pressure levels may be problematic due to the mechanical asymmetry found in this sound generation system. Mechanical asymmetry occurs by the right wing coming to partially cover the left wing during the closing stroke phase of stridulation. As such, it is hypothesized that the sound field on the left-wing side of the animal will contain lower sound pressure components than on the right-wing side as a result of this coverage. This hypothesis was tested using a novel method to accurately record a high-resolution, three dimensional mapping of sound pressure levels around restrained <i>Gryllus bimaculatus</i> field crickets singing under pharmacological stimulation. The results indicate that a bilateral asymmetry is present across individuals, with greater amplitude components present in the right-wing side of the animal. Individual variation in sound pressure to either the right- or left-wing side is also observed. However, statistically significant differences in bilateral sound field asymmetry as presented here may not affect signalling in the field.
DOI: 10.6084/m9.figshare.1627982
title: Association of plasmacytoid dendritic cells with B cell infiltration in minor salivary glands in patients with Sjögren's syndrome

description: <i>Objectives</i>: Sjogren’s syndrome (SS) is an autoimmune disease with features of both over-production of specific autoantibodies and organ-specific disorders, mainly sialadenitis and dacryoadenitis. However, little is known about the factors that contribute to lymphocytic infiltration of SS. <i>Methods</i>: Minor salivary gland (MSG) tissue was obtained from 83 patients with primary SS (pSS) and 95 patients with secondary SS and examined pathologically, and correlation between infiltrated immune cells and histological features was evaluated. <i>Results</i>: Plasmacytoid dendritic cells (pDCs) were increased in MSG of SS compared to Sicca syndrome. The density of pDCs was characteristically correlated with the accumulation of CXCL13<sup>+</sup>CD68<sup>+</sup> macrophages and CXCR5<sup>+</sup>CD19<sup>+</sup> B in the MSG of pSS. <i>In vitro</i> analysis indicated that Type I interferon (IFN) enhanced CXCL13 production by macrophages. Type I IFN was mainly expressed in pDCs and its expression was correlated with the accumulation of CXCL13<sup>+</sup> macrophages in the MSG of pSS. <i>Conclusions</i>: Our histological findings suggest the possible mechanism of type I IFN-CXCL13 axis during the pathological processes of acute/chronic salivary inflammation in SS; local production of type I IFN by pDCs, induction of CXCL13 production in macrophages by type I IFN, induction of accumulation of CXCR5<sup>+</sup>CD19<sup>+</sup> B cells by CXCL13 in the MSG.
DOI: 10.6084/m9.figshare.1627981
title: Mycophenolate mofetil therapy for two cases of antiphospholipid antibody-associated chorea

description: Chorea is associated with involuntary movement and may occur via an autoimmune mechanism. Until now, we treated immune-mediated chorea with glucocorticoids and cyclophosphamide as the efficacy of mycophenolate mofetil (MMF) therapy for this condition was unknown. Here, we report two cases of antiphospholipid antibody (aPL)-associated chorea that were cured by MMF. Measurement of aPL could help for future management of chorea patients. This report provides new insight into the beneficial effects of MMF on aPL-associated chorea.
DOI: 10.6084/m9.figshare.1627981.v1
title: Mycophenolate mofetil therapy for two cases of antiphospholipid antibody-associated chorea

description: Chorea is associated with involuntary movement and may occur via an autoimmune mechanism. Until now, we treated immune-mediated chorea with glucocorticoids and cyclophosphamide as the efficacy of mycophenolate mofetil (MMF) therapy for this condition was unknown. Here, we report two cases of antiphospholipid antibody (aPL)-associated chorea that were cured by MMF. Measurement of aPL could help for future management of chorea patients. This report provides new insight into the beneficial effects of MMF on aPL-associated chorea.
DOI: 10.6084/m9.figshare.1627982.v2
title: Association of plasmacytoid dendritic cells with B cell infiltration in minor salivary glands in patients with Sjögren's syndrome

description: <i>Objectives</i>: Sjogren’s syndrome (SS) is an autoimmune disease with features of both over-production of specific autoantibodies and organ-specific disorders, mainly sialadenitis and dacryoadenitis. However, little is known about the factors that contribute to lymphocytic infiltration of SS. <i>Methods</i>: Minor salivary gland (MSG) tissue was obtained from 83 patients with primary SS (pSS) and 95 patients with secondary SS and examined pathologically, and correlation between infiltrated immune cells and histological features was evaluated. <i>Results</i>: Plasmacytoid dendritic cells (pDCs) were increased in MSG of SS compared to Sicca syndrome. The density of pDCs was characteristically correlated with the accumulation of CXCL13<sup>+</sup>CD68<sup>+</sup> macrophages and CXCR5<sup>+</sup>CD19<sup>+</sup> B in the MSG of pSS. <i>In vitro</i> analysis indicated that Type I interferon (IFN) enhanced CXCL13 production by macrophages. Type I IFN was mainly expressed in pDCs and its expression was correlated with the accumulation of CXCL13<sup>+</sup> macrophages in the MSG of pSS. <i>Conclusions</i>: Our histological findings suggest the possible mechanism of type I IFN-CXCL13 axis during the pathological processes of acute/chronic salivary inflammation in SS; local production of type I IFN by pDCs, induction of CXCL13 production in macrophages by type I IFN, induction of accumulation of CXCR5<sup>+</sup>CD19<sup>+</sup> B cells by CXCL13 in the MSG.
DOI: 10.6084/m9.figshare.1627982.v1
title: Association of Plasmacytoid Dendritic Cells with B Cell Infiltration in Minor Salivary Glands in Patients with Sjögren's Syndrome

description: <b><i>Objectives:</i></b>Sjogren’s syndrome (SS) is an autoimmune disease with features of both over-production of specific autoantibodies and organ-specific disorders, mainly sialadenitis and dacryoadenitis. However, little is known about the factors that contribute to lymphocytic infiltration of SS.<b><i>Methods:</i></b>Minor salivary gland (MSG) tissue was obtained from 83 patients with primary SS (pSS) and 95 patients with secondary SS and examined pathologically, and correlation between infiltrated immune cells and histological features was evaluated.<b><i>Results:</i></b> Plasmacytoid dendritic cells (pDCs) were increased in MSG of SS compared to Sicca syndrome. The density of pDCs was characteristically correlated with the accumulation of CXCL13<sup>+</sup>CD68<sup>+</sup> macrophages and CXCR5<sup>+</sup>CD19<sup>+</sup> B in the MSG of pSS. In vitro analysis indicated that Type I interferon (IFN) enhanced CXCL13 production by macrophages. Type I IFN was mainly expressed in pDCs and its expression was correlated with the accumulation of CXCL13<sup>+</sup> macrophages in the MSG of pSS.<b><i>Conclusions:</i></b>Our histological findings suggest the possible mechanism of type I IFN-CXCL13 axis during the pathological processes of acute/chronic salivary inflammation in SS; local production of type I IFN by pDCs, induction of CXCL13 production in macrophages by type I IFN, induction of accumulation of CXCR5<sup>+</sup>CD19<sup>+</sup> B cells by CXCL13 in the MSG.
DOI: 10.6084/m9.figshare.1627973.v1
title: Gamma-actin is involved in regulating centrosome function and mitotic progression in cancer cells

description: Reorganization of the actin cytoskeleton during mitosis is crucial for regulating cell division. A functional role for γ-actin in mitotic arrest induced by the microtubule-targeted agent, paclitaxel, has recently been demonstrated. We hypothesized that γ-actin plays a role in mitosis. Herein, we investigated the effect of γ-actin in mitosis and demonstrated that γ-actin is important in the distribution of β-actin and formation of actin-rich retraction fibers during mitosis. The reduced ability of paclitaxel to induce mitotic arrest as a result of γ-actin depletion was replicated with a range of mitotic inhibitors, suggesting that γ-actin loss reduces the ability of broad classes of anti-mitotic agents to induce mitotic arrest. In addition, partial depletion of γ-actin enhanced centrosome amplification in cancer cells and caused a significant delay in prometaphase/metaphase. This prolonged prometaphase/metaphase arrest was due to mitotic defects such as uncongressed and missegregated chromosomes, and correlated with an increased presence of mitotic spindle abnormalities in the γ-actin depleted cells. Collectively, these results demonstrate a previously unknown role for γ-actin in regulating centrosome function, chromosome alignment and maintenance of mitotic spindle integrity.
DOI: 10.6084/m9.figshare.1627971
title: Deregulated expression of Cdc6 in the skin facilitates papilloma formation and affects the hair growth cycle

description: Cdc6 encodes a key protein for DNA replication, responsible for the recruitment of the MCM helicase to replication origins during the G1 phase of the cell division cycle. The oncogenic potential of deregulated Cdc6 expression has been inferred from cellular studies, but no mouse models have been described to study its effects in mammalian tissues. Here we report the generation of K5-Cdc6, a transgenic mouse strain in which Cdc6 expression is deregulated in tissues with stratified epithelia. Higher levels of CDC6 protein enhanced the loading of MCM complexes to DNA in epidermal keratinocytes, without affecting their proliferation rate or inducing DNA damage. While Cdc6 overexpression did not promote skin tumors, it facilitated the formation of papillomas in cooperation with mutagenic agents such as DMBA. In addition, the elevated levels of CDC6 protein in the skin extended the resting stage of the hair growth cycle, leading to better fur preservation in older mice.
DOI: 10.6084/m9.figshare.1627970
title: Erk5 contributes to maintaining the balance of cellular nucleotide levels and erythropoiesis

description: An adequate supply of nucleotides is essential for accurate DNA replication, and inappropriate deoxyribonucleotide triphosphate (dNTP) concentrations can lead to replication stress, a common source of DNA damage, genomic instability and tumourigenesis. Here, we provide evidence that Erk5 is necessary for correct nucleotide supply during erythroid development. Mice with Erk5 knockout in the haematopoietic lineage showed impaired erythroid development in bone marrow, accompanied by altered dNTP levels and increased DNA mutagenesis in erythroid progenitors as detected by exome sequencing. Moreover, Erk5-depleted leukemic Jurkat cells presented a marked sensitivity to thymidine-induced S phase stalling, as evidenced by increased H2AX phosphorylation and apoptosis. The increase in thymidine sensitivity correlated with a higher dTTP/dCTP ratio. These results indicate that Erk5 is necessary to maintain the balance of nucleotide levels, thus preventing dNTP misincorporation and DNA damage in proliferative erythroid progenitors and leukemic Jurkat T cells.
DOI: 10.6084/m9.figshare.1627971.v1
title: Deregulated expression of Cdc6 in the skin facilitates papilloma formation and affects the hair growth cycle

description: Cdc6 encodes a key protein for DNA replication, responsible for the recruitment of the MCM helicase to replication origins during the G1 phase of the cell division cycle. The oncogenic potential of deregulated Cdc6 expression has been inferred from cellular studies, but no mouse models have been described to study its effects in mammalian tissues. Here we report the generation of K5-Cdc6, a transgenic mouse strain in which Cdc6 expression is deregulated in tissues with stratified epithelia. Higher levels of CDC6 protein enhanced the loading of MCM complexes to DNA in epidermal keratinocytes, without affecting their proliferation rate or inducing DNA damage. While Cdc6 overexpression did not promote skin tumors, it facilitated the formation of papillomas in cooperation with mutagenic agents such as DMBA. In addition, the elevated levels of CDC6 protein in the skin extended the resting stage of the hair growth cycle, leading to better fur preservation in older mice.
DOI: 10.6084/m9.figshare.1627970.v1
title: Erk5 contributes to maintaining the balance of cellular nucleotide levels and erythropoiesis

description: An adequate supply of nucleotides is essential for accurate DNA replication, and inappropriate deoxyribonucleotide triphosphate (dNTP) concentrations can lead to replication stress, a common source of DNA damage, genomic instability and tumourigenesis. Here, we provide evidence that Erk5 is necessary for correct nucleotide supply during erythroid development. Mice with Erk5 knockout in the haematopoietic lineage showed impaired erythroid development in bone marrow, accompanied by altered dNTP levels and increased DNA mutagenesis in erythroid progenitors as detected by exome sequencing. Moreover, Erk5-depleted leukemic Jurkat cells presented a marked sensitivity to thymidine-induced S phase stalling, as evidenced by increased H2AX phosphorylation and apoptosis. The increase in thymidine sensitivity correlated with a higher dTTP/dCTP ratio. These results indicate that Erk5 is necessary to maintain the balance of nucleotide levels, thus preventing dNTP misincorporation and DNA damage in proliferative erythroid progenitors and leukemic Jurkat T cells.
DOI: 10.6084/m9.figshare.1627969.v1
title: A DDB2 mutant protein unable to interact with PCNA promotes cell cycle progression of human transformed embryonic kidney cells

description: DNA damage binding protein 2 (DDB2) is a protein involved in the early step of DNA damage recognition of the nucleotide excision repair (NER) process. Recently, it has been suggested that DDB2 may play a role in DNA replication, based on its ability to promote cell proliferation. We have previously shown that DDB2 binds PCNA during NER, but also in the absence of DNA damage; however, whether and how this interaction influences cell proliferation is not known. In this study, we have addressed this question by using HEK293 cell clones stably expressing DDB2<sup>Wt</sup> protein, or a mutant form (DDB2<sup>Mut</sup>) unable to interact with PCNA. We report that overexpression of the DDB2<sup>Mut</sup> protein provides a proliferative advantage over the wild type form, by influencing cell cycle progression. In particular, an increase in the number of S-phase cells, together with a reduction in p21<sup>CDKN1A</sup> protein level, and a shorter cell cycle length, has been observed in the DDB2<sup>Mut</sup> cells. These results suggest that DDB2 influences cell cycle progression thanks to its interaction with PCNA.