cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1623129.v1
title: Miocene andesitic lavas of Sierra de Angangueo: a petrological, geochemical, and geochronological approach to arc magmatism in Central Mexico

description: ABSTRACTThe early and middle Miocene andesitic lavas of the Sierra de Angangueo (MALSA) represent one of the most prominent landforms of intermediate magmatism in Central Mexico. In this paper, we present new petrological, geochemical, thermobarometric, and geochronological data in order to discuss the conditions of MALSA’s emplacement in the lithosphere.MALSA comprises a voluminous eroded early Miocene andesitic structure, emplaced on a Mesozoic basement. MALSA shows a wide variety of textures, from glassy and aphanitic to porphyritic, mainly composed of plagioclase (An<sub>10-55</sub>), clinopyroxene (Wo<sub>60-65</sub>; En<sub>35-40</sub>), amphibole (Mg-hornblende/edenite), and rarely olivine (Fo<sub>75–86</sub>) or orthopyroxene (En<sub>72-80</sub>). Major and trace elements plots follow a typical calc-alkaline trend with relatively increasing fractionation.The <sup>87</sup>Sr/<sup>86</sup>Sr isotopic signatures range between 0.703343 and 0.704459 and εNd values from +1.37 to +4.84; apparently without a significant contribution of an old, thick, or highly radiogenic continental crust. Lead isotope values <sup>206</sup>Pb/<sup>204</sup>Pb vary between 18.68 and 18.83, <sup>207</sup>Pb/<sup>204</sup>Pb from 15.57 to 15.65, and <sup>208</sup>Pb/<sup>204</sup>Pb from 38.39 to 38.67, suggesting contamination of magmas by juvenile crust. Thermodynamic calculations indicate equilibrium conditions at ≤900°C and ~2 kbar and an average log ƒO<sub>2</sub> ≈ −10.Ar–Ar and K–Ar dating carried out on whole rock, matrix, amphibole, and plagioclase phenocrysts yielded ages between 13.0 ± 0.5 and 23.9 ± 0.3 Ma. These dates indicate a series of pulses with maximum magmatic activity between 24 and 18 Ma.The geochemical and petrologic data suggest partial melting processes in the lower or middle crust associated with possible magma mixing during its ascent; such a mechanism could explain a hybrid mantle-lower crust origin of this large volume of andesites. The MALSA, as well as the early to middle Miocene magmatism from Western Mexico, could represent two coeval and independent magmatic arcs prior to the present Trans-Mexican Volcanic Belt (TMVB) in Central Mexico.
DOI: 10.6084/m9.figshare.1623111
title: Influence of MRI-based bone outline definition errors on external radiotherapy dose calculation accuracy in heterogeneous pseudo-CT images of prostate cancer patients

description: <b>Background.</b> This work evaluates influences of susceptibility-induced bone outline shift and perturbations, and bone segmentation errors on external radiotherapy dose calculation accuracy in magnetic resonance imaging (MRI)-based pseudo-computed tomography (CT) images of the male pelvis.<b>Material and methods.</b> T<sub>1</sub>/T<sub>2</sub>*-weighted fast gradient echo, T<sub>1</sub>-weighted spin echo and T<sub>2</sub>-weighted fast spin echo images were used in bone detection investigation. Bone edge location and bone diameter in MRI were evaluated by comparing those in the images with actual physical measurements of fresh deer bones positioned in a gelatine phantom. Dose calculation accuracy in pseudo-CT images was investigated for 15 prostate cancer patients. Bone outlines in T<sub>1</sub>/T<sub>2</sub>*-weighted images were contoured and additional segmentation errors were simulated by expanding and contracting the bone contours with 1 mm spacing. Heterogeneous pseudo-CT images were constructed by adopting a technique transforming the MRI intensity values into Hounsfield units with separate conversion models within and outside of bone segment.<b>Results.</b> Bone edges and diameter in the phantom were illustrated correctly within a 1 mm-pixel size in MRI. Each 1 mm-sized systematic error in bone segment resulted in roughly 0.4% change to the prostate dose level in the pseudo-CT images. The prostate average (range) dose levels in pseudo-CT images with additional systematic bone segmentation errors of −2 mm, 0 mm and 2 mm were 0.5% (−0.5–1.4%), −0.2% (−1.0–0.7%), and −0.9% (−1.8–0.0%) compared to those in CT images, respectively, in volumetric modulated arc therapy treatment plans calculated by Monte Carlo algorithm.<b>Conclusions.</b> Susceptibility-induced bone outline shift and perturbations do not result in substantial uncertainty for MRI-based dose calculation. Dose consistency of 2% can be achieved reliably for the prostate if heterogeneous pseudo-CT images are constructed with ≤± 2 mm systematic error in bone segment.
DOI: 10.6084/m9.figshare.1623067
title: A comparison of morbidity following conformal versus intensity-modulated radiotherapy for urinary bladder cancer

description: <b>Background.</b> In radiotherapy (RT) of urinary bladder cancer, the use of intensity-modulated RT (IMRT) opens for sparing of considerable intestinal volumes. The purpose of the present study was to investigate the acute and late toxicities following either conformal RT (CRT) or IMRT for bladder cancer, and to correlate the toxicities to dose-volume parameters.<b>Material and methods.</b> The study included 116 consecutively treated patients with muscle-invasive bladder cancer who received either CRT (n = 66) or IMRT (n = 50) during 2007–2010. Acute side effects were retrospectively collected whereas late effects were assessed by a cross-sectional evaluation by telephone interview of 44 recurrence-free patients. Acute and late toxicities were scored according to the Common Terminology Criteria for Adverse Event (CTCAE) version 3.0.<b>Results.</b> Acute diarrhoea grade ≥ 2 was more frequent in patients treated by CRT (56%) compared to IMRT (30%) (p = 0.008). Logistic regression analysis showed a correlation between acute diarrhoea and bowel cavity dose-volume parameters in the 10–50 Gy range. Severe late toxicity (grade ≥ 3) was recorded in 10% of the total cohort, with no statistical difference between the IMRT and CRT groups.<b>Conclusion.</b> Patients treated with IMRT for bladder cancer had significantly less acute diarrhoea compared to those treated with CRT, but there was no significant difference in late morbidity between the groups. The risk of acute diarrhoea was related to the volume of bowel irradiated.
DOI: 10.6084/m9.figshare.1623067.v1
title: A comparison of morbidity following conformal versus intensity-modulated radiotherapy for urinary bladder cancer

description: <b>Background.</b> In radiotherapy (RT) of urinary bladder cancer, the use of intensity-modulated RT (IMRT) opens for sparing of considerable intestinal volumes. The purpose of the present study was to investigate the acute and late toxicities following either conformal RT (CRT) or IMRT for bladder cancer, and to correlate the toxicities to dose-volume parameters.<b>Material and methods.</b> The study included 116 consecutively treated patients with muscle-invasive bladder cancer who received either CRT (n = 66) or IMRT (n = 50) during 2007–2010. Acute side effects were retrospectively collected whereas late effects were assessed by a cross-sectional evaluation by telephone interview of 44 recurrence-free patients. Acute and late toxicities were scored according to the Common Terminology Criteria for Adverse Event (CTCAE) version 3.0.<b>Results.</b> Acute diarrhoea grade ≥ 2 was more frequent in patients treated by CRT (56%) compared to IMRT (30%) (p = 0.008). Logistic regression analysis showed a correlation between acute diarrhoea and bowel cavity dose-volume parameters in the 10–50 Gy range. Severe late toxicity (grade ≥ 3) was recorded in 10% of the total cohort, with no statistical difference between the IMRT and CRT groups.<b>Conclusion.</b> Patients treated with IMRT for bladder cancer had significantly less acute diarrhoea compared to those treated with CRT, but there was no significant difference in late morbidity between the groups. The risk of acute diarrhoea was related to the volume of bowel irradiated.
DOI: 10.6084/m9.figshare.1621931
title: Mitotic phosphatase activity is required for MCC maintenance during the spindle checkpoint

description: The spindle checkpoint prevents activation of the anaphase-promoting complex (APC/C) until all chromosomes are correctly attached to the mitotic spindle. Early in mitosis, the mitotic checkpoint complex (MCC) inactivates the APC/C by binding the APC/C activating protein CDC20 until the chromosomes are properly aligned and attached to the mitotic spindle, at which point MCC disassembly releases CDC20 to activate the APC/C. Once the APC/C is activated, it targets cyclin B and securin for degradation, and the cell progresses into anaphase. While phosphorylation is known to drive many of the events during the checkpoint, the precise molecular mechanisms regulating spindle checkpoint maintenance and inactivation are still poorly understood. We sought to determine the role of mitotic phosphatases during the spindle checkpoint. To address this question, we treated spindle checkpoint-arrested cells with various phosphatase inhibitors and examined the effect on the MCC and APC/C activation. Using this approach we found that two phosphatase inhibitors, calyculin A and okadaic acid (1 µM), caused MCC dissociation and APC/C activation leading to cyclin A and B degradation in spindle checkpoint-arrested cells. Although the cells were able to degrade cyclin B, they did not exit mitosis as evidenced by high levels of Cdk1 substrate phosphorylation and chromosome condensation. Our results provide the first evidence that phosphatases are essential for maintenance of the MCC during operation of the spindle checkpoint.
DOI: 10.6084/m9.figshare.1621932
title: Calibration of stochastic computer simulators using likelihood emulation

description: We calibrate a stochastic computer simulation model of ‘moderate’ computational expense. The simulator is an imperfect representation of reality, and we recognise this discrepancy to ensure a reliable calibration. The calibration model combines a Gaussian process emulator of the likelihood surface with importance sampling. Changing the discrepancy specification changes only the importance weights, which lets us investigate sensitivity to different discrepancy specifications at little computational cost. We present a case study of a natural history model that has been used to characterise UK bowel cancer incidence. Data sets and computer code are provided as supplementary material.
DOI: 10.6084/m9.figshare.1621931.v1
title: Mitotic phosphatase activity is required for MCC maintenance during the spindle checkpoint

description: The spindle checkpoint prevents activation of the anaphase-promoting complex (APC/C) until all chromosomes are correctly attached to the mitotic spindle. Early in mitosis, the mitotic checkpoint complex (MCC) inactivates the APC/C by binding the APC/C activating protein CDC20 until the chromosomes are properly aligned and attached to the mitotic spindle, at which point MCC disassembly releases CDC20 to activate the APC/C. Once the APC/C is activated, it targets cyclin B and securin for degradation, and the cell progresses into anaphase. While phosphorylation is known to drive many of the events during the checkpoint, the precise molecular mechanisms regulating spindle checkpoint maintenance and inactivation are still poorly understood. We sought to determine the role of mitotic phosphatases during the spindle checkpoint. To address this question, we treated spindle checkpoint-arrested cells with various phosphatase inhibitors and examined the effect on the MCC and APC/C activation. Using this approach we found that two phosphatase inhibitors, calyculin A and okadaic acid (1 µM), caused MCC dissociation and APC/C activation leading to cyclin A and B degradation in spindle checkpoint-arrested cells. Although the cells were able to degrade cyclin B, they did not exit mitosis as evidenced by high levels of Cdk1 substrate phosphorylation and chromosome condensation. Our results provide the first evidence that phosphatases are essential for maintenance of the MCC during operation of the spindle checkpoint.
DOI: 10.6084/m9.figshare.1621928
title: A new role for PGRP-S (Tag7) in immune defense: lymphocyte migration is induced by a chemoattractant complex of Tag7 with Mts1

description: PGRP-S (Tag7) is an innate immunity protein involved in the antimicrobial defense systems, both in insects and in mammals. We have previously shown that Tag7 specifically interacts with several proteins, including Hsp70 and the calcium binding protein S100A4 (Mts1), providing a number of novel cellular functions. Here we show that Tag7–Mts1 complex causes chemotactic migration of lymphocytes, with NK cells being a preferred target. Cells of either innate immunity (neutrophils and monocytes) or acquired immunity (CD4<sup>+</sup> and CD8<sup>+</sup> lymphocytes) can produce this complex, which confirms the close connection between components of the 2 branches of immune response.
DOI: 10.6084/m9.figshare.1621932.v1
title: Calibration of stochastic computer simulators using likelihood emulation

description: We calibrate a stochastic computer simulation model of ‘moderate’ computational expense. The simulator is an imperfect representation of reality, and we recognise this discrepancy to ensure a reliable calibration. The calibration model combines a Gaussian process emulator of the likelihood surface with importance sampling. Changing the discrepancy specification changes only the importance weights, which lets us investigate sensitivity to different discrepancy specifications at little computational cost. We present a case study of a natural history model that has been used to characterise UK bowel cancer incidence. Data sets and computer code are provided as supplementary material.
DOI: 10.6084/m9.figshare.1621928.v1
title: A new role for PGRP-S (Tag7) in immune defense: lymphocyte migration is induced by a chemoattractant complex of Tag7 with Mts1

description: PGRP-S (Tag7) is an innate immunity protein involved in the antimicrobial defense systems, both in insects and in mammals. We have previously shown that Tag7 specifically interacts with several proteins, including Hsp70 and the calcium binding protein S100A4 (Mts1), providing a number of novel cellular functions. Here we show that Tag7–Mts1 complex causes chemotactic migration of lymphocytes, with NK cells being a preferred target. Cells of either innate immunity (neutrophils and monocytes) or acquired immunity (CD4<sup>+</sup> and CD8<sup>+</sup> lymphocytes) can produce this complex, which confirms the close connection between components of the 2 branches of immune response.
DOI: 10.6084/m9.figshare.1621923
title: Cell surface heparan sulfate proteoglycans are involved in the binding of Hsp90α and Hsp90β to the cell plasma membrane

description: Extracellular membrane-bound and secreted heat shock protein 90 (Hsp90) is known to be involved in cell motility and invasion. The mechanism of Hsp90 anchoring to the plasma membrane remains obscure. We showed that treatment of human glioblastoma A-172 and fibrosarcoma HT1080 cells with sodium chlorate, heparinase, and heparin causes a prominent loss of 2 Hsp90 cytosolic isoforms, Hsp90α and Hsp90β, from the cell surface and strongly inhibits the binding of exogenous Hsp90 to cells. We revealed that Hsp90α and Hsp90β are partly colocalized with heparan sulfate proteoglycans (HSPGs) on the cell surface and that this colocalization was sensitive to heparin. The results demonstrate that cell surface HSPGs are involved in the binding/anchoring of Hsp90α and Hsp90β to the plasma membrane.
DOI: 10.6084/m9.figshare.1621922
title: Inhibition of cell adhesion by phosphorylated Ezrin/Radixin/Moesin

description: Altered phosphorylation status of the C-terminal Thr residues of Ezrin/Radixin/Moesin (ERM) is often linked to cell shape change. To determine the role of phophorylated ERM, we modified phosphorylation status of ERM and investigated changes in cell adhesion and morphology. Treatment with Calyculin-A (Cal-A), a protein phosphatase inhibitor, dramatically augmented phosphorylated ERM (phospho-ERM). Cal-A-treatment or expression of phospho-mimetic Moesin mutant (Moesin-TD) induced cell rounding in adherent cells. Moreover, reattachment of detached cells to substrate was inhibited by either treatment. Phospho-ERM, Moesin-TD and actin cytoskeleton were observed at the plasma membrane of such round cells. Augmented cell surface rigidity was also observed in both cases.Meanwhile, non-adherent KG-1 cells were rather rich in phospho-ERM. Treatment with Staurosporine, a protein kinase inhibitor that dephosphorylates phospho-ERM, up-regulated the integrin-dependent adhesion of KG-1 cells to substrate.These findings strongly suggest the followings: (1) Phospho-ERM inhibit cell adhesion, and therefore, dephosphorylation of ERM proteins is essential for cell adhesion. (2) Phospho-ERM induce formation and/or maintenance of spherical cell shape. (3) ERM are constitutively both phosphorylated and dephosphorylated in cultured adherent and non-adherent cells.
DOI: 10.6084/m9.figshare.1621923.v1
title: Cell surface heparan sulfate proteoglycans are involved in the binding of Hsp90α and Hsp90β to the cell plasma membrane

description: Extracellular membrane-bound and secreted heat shock protein 90 (Hsp90) is known to be involved in cell motility and invasion. The mechanism of Hsp90 anchoring to the plasma membrane remains obscure. We showed that treatment of human glioblastoma A-172 and fibrosarcoma HT1080 cells with sodium chlorate, heparinase, and heparin causes a prominent loss of 2 Hsp90 cytosolic isoforms, Hsp90α and Hsp90β, from the cell surface and strongly inhibits the binding of exogenous Hsp90 to cells. We revealed that Hsp90α and Hsp90β are partly colocalized with heparan sulfate proteoglycans (HSPGs) on the cell surface and that this colocalization was sensitive to heparin. The results demonstrate that cell surface HSPGs are involved in the binding/anchoring of Hsp90α and Hsp90β to the plasma membrane.
DOI: 10.6084/m9.figshare.1621921
title: Long-term wheel-running and acute 6-h advances alter glucose tolerance and insulin levels in TALLYHO/JngJ mice

description: ABSTRACTStudies have shown a relationship between circadian rhythm disruptions and type-2 diabetes. This investigation examined the effects of circadian disruption (6-h phase advances) on the progression of diabetes in a type-2 diabetic mouse model –TALLYHO/JngJ – and whether wheel-running can alleviate the effects of the phase advances. 6-h advances alter fasting glucose, glucose tolerance and insulin production. Wheel-running reduced body mass, improved glucose tolerance and reduced insulin in TALLYHO/JngJ and alleviated some of the changes in diabetic symptoms due to 6-h advances. These results indicate that individuals with type-2 diabetes can benefit from physical activity and exercise can be a countermeasure to offset the effects of an acute phase advance.
DOI: 10.6084/m9.figshare.1621921.v1
title: Long-term wheel-running and acute 6-h advances alter glucose tolerance and insulin levels in TALLYHO/JngJ mice

description: ABSTRACTStudies have shown a relationship between circadian rhythm disruptions and type-2 diabetes. This investigation examined the effects of circadian disruption (6-h phase advances) on the progression of diabetes in a type-2 diabetic mouse model –TALLYHO/JngJ – and whether wheel-running can alleviate the effects of the phase advances. 6-h advances alter fasting glucose, glucose tolerance and insulin production. Wheel-running reduced body mass, improved glucose tolerance and reduced insulin in TALLYHO/JngJ and alleviated some of the changes in diabetic symptoms due to 6-h advances. These results indicate that individuals with type-2 diabetes can benefit from physical activity and exercise can be a countermeasure to offset the effects of an acute phase advance.
DOI: 10.6084/m9.figshare.1621922.v1
title: Inhibition of cell adhesion by phosphorylated Ezrin/Radixin/Moesin

description: Altered phosphorylation status of the C-terminal Thr residues of Ezrin/Radixin/Moesin (ERM) is often linked to cell shape change. To determine the role of phophorylated ERM, we modified phosphorylation status of ERM and investigated changes in cell adhesion and morphology. Treatment with Calyculin-A (Cal-A), a protein phosphatase inhibitor, dramatically augmented phosphorylated ERM (phospho-ERM). Cal-A-treatment or expression of phospho-mimetic Moesin mutant (Moesin-TD) induced cell rounding in adherent cells. Moreover, reattachment of detached cells to substrate was inhibited by either treatment. Phospho-ERM, Moesin-TD and actin cytoskeleton were observed at the plasma membrane of such round cells. Augmented cell surface rigidity was also observed in both cases.Meanwhile, non-adherent KG-1 cells were rather rich in phospho-ERM. Treatment with Staurosporine, a protein kinase inhibitor that dephosphorylates phospho-ERM, up-regulated the integrin-dependent adhesion of KG-1 cells to substrate.These findings strongly suggest the followings: (1) Phospho-ERM inhibit cell adhesion, and therefore, dephosphorylation of ERM proteins is essential for cell adhesion. (2) Phospho-ERM induce formation and/or maintenance of spherical cell shape. (3) ERM are constitutively both phosphorylated and dephosphorylated in cultured adherent and non-adherent cells.
DOI: 10.6084/m9.figshare.1621917
title: Synthesis and Structure of Aminophosphonates Containing 3,5-Di-Tert-Butyl-4-Hydroxyphenyl and Acetal Groups

description: The reactions of <b>dialkyl</b> [(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadienyl)methyl]phosphonates with N-nucleophiles (aminoacetaldehyde dimethyl acetal and diethyl [(2,2-dimethoxyethyl)aminomethyl]phosphonate give new aminophosphonates containing the 3,5-di-tert-butyl-4-hydroxyphenyl substituent, in addition to the acetal group. The crystal structure of diethyl {(3,5-di-tert-butyl-4-hydroxyphenyl)[(2,2-dimethoxyethyl)amino]methyl}phosphonate is elucidated. The presence of a chiral carbon atom and prochiral phosphorus atom in the aminophosphonate products is responsible for the complicated pattern in the <sup>1</sup>H NMR spectra, the features of which are discussed.
DOI: 10.6084/m9.figshare.1621917.v1
title: Synthesis and Structure of Aminophosphonates Containing 3,5-Di-Tert-Butyl-4-Hydroxyphenyl and Acetal Groups

description: The reactions of <b>dialkyl</b> [(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadienyl)methyl]phosphonates with N-nucleophiles (aminoacetaldehyde dimethyl acetal and diethyl [(2,2-dimethoxyethyl)aminomethyl]phosphonate give new aminophosphonates containing the 3,5-di-tert-butyl-4-hydroxyphenyl substituent, in addition to the acetal group. The crystal structure of diethyl {(3,5-di-tert-butyl-4-hydroxyphenyl)[(2,2-dimethoxyethyl)amino]methyl}phosphonate is elucidated. The presence of a chiral carbon atom and prochiral phosphorus atom in the aminophosphonate products is responsible for the complicated pattern in the <sup>1</sup>H NMR spectra, the features of which are discussed.