cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3996970
title: Ultimate strength assessment of stiffened panel using non-linear mechanical behavior of an equivalent single layer: grillage FE model used for analysis

description: This example shows how the ESL can be applied in the ultimate strength structural analysis in Abaqus finite element software. In other words, ESL methodology is applied only in some parts of the structure while larger structural supporting components like girders and webframes are still modeled explicitly. Dataset includes following files: 1. ESL_nonlinear_grillage.inp - this is Abaqus input file for running the ESL nonlinear grillage model. 2. UGENS.for - this defines the nonlinear stiffness or ABD matrix. This is called by input file.
DOI: 10.5281/zenodo.3997054
title: Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 144 POPC lipids, 51 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Frames are saved in every 100 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. <strong>Please note that</strong> the trajectories might need to be reimaged.
DOI: 10.5281/zenodo.3997050
title: Ultimate strength assessment of stiffened panel using non-linear mechanical behavior of an equivalent single layer: grillage FE model used for analysis

description: This example shows how the ESL can be applied in the ultimate strength structural analysis in Abaqus finite element software. In other words, ESL methodology is applied only in some parts of the structure while larger structural supporting components like girders and webframes are still modeled explicitly. FIles include also the Full_3D_FEM model used for validating the ESL model. Dataset includes following files: 1. ESL_nonlinear_grillage.inp - this is Abaqus input file for running the ESL nonlinear grillage model. 2. ugensFINALv_master.for - this defines the nonlinear stiffness or ABD matrix. This is called by input file (ESL_nonlinear_grillage.inp ). 3. Full_3D_FEM.inp - Full_3D_FEM model used for validating the ESL model.
DOI: 10.5281/zenodo.3996969
title: Ultimate strength assessment of stiffened panel using non-linear mechanical behavior of an equivalent single layer: grillage FE model used for analysis

description: This example shows how the ESL can be applied in the ultimate strength structural analysis in Abaqus finite element software. In other words, ESL methodology is applied only in some parts of the structure while larger structural supporting components like girders and webframes are still modeled explicitly. FIles include also the Full_3D_FEM model used for validating the ESL model. Dataset includes following files: 1. ESL_nonlinear_grillage.inp - this is Abaqus input file for running the ESL nonlinear grillage model. 2. ugensFINALv_master.for - this defines the nonlinear stiffness or ABD matrix. This is called by input file (ESL_nonlinear_grillage.inp ). 3. Full_3D_FEM.inp - Full_3D_FEM model used for validating the ESL model.
DOI: 10.6084/m9.figshare.12849740
title: Reliable Real-Time Output Gap Estimates Based on a Modified Hamilton Filter

description: We propose a simple modification of Hamilton’s time series filter that yields reliable and economically meaningful real-time output gap estimates. The original filter relies on 8 quarter ahead forecast errors of a simple autoregression of real GDP. While this approach yields a cyclical component that is hardly revised with new incoming data due to the one-sided filtering approach, it does not cover typical business cycle frequencies evenly, but mutes short and amplifies medium length cycles. Further, as the estimated trend contains high-frequency noise, it can hardly be interpreted as potential GDP. A simple modification based on the mean of 4 to 12 quarter ahead forecast errors shares the favorable real-time properties of the Hamilton filter, but leads to a much better coverage of typical business cycle frequencies and a smooth estimated trend. Based on output growth and inflation forecasts and a comparison to revised output gap estimates from policy institutions, we find that real-time output gaps based on the modified and the original Hamilton filter are economically much more meaningful measures of the business cycle than those based on other simple statistical trend-cycle decomposition techniques, such as the HP or bandpass filter, and should thus be used preferably.
DOI: 10.6084/m9.figshare.12849740.v2
title: Reliable Real-Time Output Gap Estimates Based on a Modified Hamilton Filter

description: We propose a simple modification of Hamilton’s time series filter that yields reliable and economically meaningful real-time output gap estimates. The original filter relies on 8 quarter ahead forecast errors of a simple autoregression of real GDP. While this approach yields a cyclical component that is hardly revised with new incoming data due to the one-sided filtering approach, it does not cover typical business cycle frequencies evenly, but mutes short and amplifies medium length cycles. Further, as the estimated trend contains high-frequency noise, it can hardly be interpreted as potential GDP. A simple modification based on the mean of 4 to 12 quarter ahead forecast errors shares the favorable real-time properties of the Hamilton filter, but leads to a much better coverage of typical business cycle frequencies and a smooth estimated trend. Based on output growth and inflation forecasts and a comparison to revised output gap estimates from policy institutions, we find that real-time output gaps based on the modified and the original Hamilton filter are economically much more meaningful measures of the business cycle than those based on other simple statistical trend-cycle decomposition techniques, such as the HP or bandpass filter, and should thus be used preferably.
DOI: 10.6084/m9.figshare.12849740.v1
title: Reliable Real-time Output Gap Estimates Based on a Modified Hamilton Filter

description: We propose a simple modification of Hamilton’s (2018) time series filter that yields reliable and economically meaningful real-time output gap estimates. The original filter relies on 8 quarter ahead forecast errors of a simple autoregression of real GDP. While this approach yields a cyclical component that is hardly revised with new incoming data due to the one-sided filtering approach, it does not cover typical business cycle frequencies evenly, but mutes short and amplifies medium length cycles. Further, as the estimated trend contains high frequency noise, it can hardly be interpreted as potential GDP. A simple modification based on the mean of 4 to 12 quarter ahead forecast errors shares the favorable real-time properties of the Hamilton filter, but leads to a much better coverage of typical business cycle frequencies and a smooth estimated trend. Based on output growth and inflation forecasts and a comparison to revised output gap estimates from policy institutions, we find that real-time output gaps based on the modified and the original Hamilton filter are economically much more meaningful measures of the business cycle than those based on other simple statistical trend-cycle decomposition techniques, such as the HP or bandpass filter, and should thus be used preferably.
DOI: 10.6084/m9.figshare.12849746
title: High-Dimensional Dynamic Covariance Matrices With Homogeneous Structure

description: High-dimensional covariance matrices appear in many disciplines. Much literature has devoted to the research in high-dimensional constant covariance matrices. However, constant covariance matrices are not sufficient in applications, for example, in portfolio allocation, dynamic covariance matrices would be more appropriate. As argued in this article, there are two difficulties in the introduction of dynamic structures into covariance matrices: (1) simply assuming each entry of a covariance matrix is a function of time to introduce the dynamic needed would not work; (2) there is a risk of having too many unknowns to estimate due to the high dimensionality. In this article, we propose a dynamic structure embedded with a homogeneous structure. We will demonstrate the proposed dynamic structure makes more sense in applications and avoids, in the meantime, too many unknown parameters/functions to estimate, due to the embedded homogeneous structure. An estimation procedure is also proposed to estimate the proposed high-dimensional dynamic covariance matrices, and asymptotic properties are established to justify the proposed estimation procedure. Intensive simulation studies show the proposed estimation procedure works very well when the sample size is finite. Finally, we apply the proposed high-dimensional dynamic covariance matrices to portfolio allocation. It is interesting to see the resulting portfolio yields much better returns than some commonly used ones.
DOI: 10.6084/m9.figshare.12849746.v2
title: High-Dimensional Dynamic Covariance Matrices With Homogeneous Structure

description: High-dimensional covariance matrices appear in many disciplines. Much literature has devoted to the research in high-dimensional constant covariance matrices. However, constant covariance matrices are not sufficient in applications, for example, in portfolio allocation, dynamic covariance matrices would be more appropriate. As argued in this article, there are two difficulties in the introduction of dynamic structures into covariance matrices: (1) simply assuming each entry of a covariance matrix is a function of time to introduce the dynamic needed would not work; (2) there is a risk of having too many unknowns to estimate due to the high dimensionality. In this article, we propose a dynamic structure embedded with a homogeneous structure. We will demonstrate the proposed dynamic structure makes more sense in applications and avoids, in the meantime, too many unknown parameters/functions to estimate, due to the embedded homogeneous structure. An estimation procedure is also proposed to estimate the proposed high-dimensional dynamic covariance matrices, and asymptotic properties are established to justify the proposed estimation procedure. Intensive simulation studies show the proposed estimation procedure works very well when the sample size is finite. Finally, we apply the proposed high-dimensional dynamic covariance matrices to portfolio allocation. It is interesting to see the resulting portfolio yields much better returns than some commonly used ones.
DOI: 10.25442/hku.12814619
title: Data set for the MPhil thesis titled “Verbal fronting and focus in Igbo”

description: This data set consists of focus constructions in Igbo that were collected through data elicitation. A questionnaire designed to elicit various types of focus constructions in Igbo is also included. It also includes data from Igbo texts and from native-speaker intuition of the author. For the elicited data, the raw anonymized data elicited from five speakers are provided.
DOI: 10.25442/hku.12814619.v1
title: Data set for the MPhil thesis titled “Verbal fronting and focus in Igbo”

description: This data set consists of focus constructions in Igbo that were collected through data elicitation. A questionnaire designed to elicit various types of focus constructions in Igbo is also included. It also includes data from Igbo texts and from native-speaker intuition of the author. For the elicited data, the raw anonymized data elicited from five speakers are provided.
DOI: 10.25442/hku.12756452.v1
title: Anti-tumor effects of PIM1 inhibition in hepatocellular carcinoma

description: Hepatocellular carcinoma (HCC) is the most common malignancy liver cancer. Targeted therapies are the new path for HCC treatment. Under hypoxic microenvironment, PIM1 (a serine/threonine kinase) is overexpressed in HCC. PIM1 induced tumor progression by regulating glycolysis. In this project, the efficacy of PIM1 inhibitor will be investigated in vitro and in vivo. <br><br>SGI-1776 and PIM447 were PIM1 inhibitors which were applied in this study. Both inhibitors were treated to HCC cell lines (MHCC97L and Huh7) under normoxic (20% O2) and hypoxic (1% O2) condition. The expression of PIM1 downstream targets was altered and which was confirmed by using western blotting. MTT assay was used to determine IC50 of PIM1 inhibitors in both HCC cell lines under normoxic and hypoxic conditions. The effect of PIM1 inhibitors on the proliferation and metastasis of HCC was estimated by cell proliferation, cell migration and invasion assays. To examine the effects of PIM1 inhibitors on the glucose uptake and chemosensitivity in HCC, glucose uptake assay and apoptosis assay with Annexin V/PI staining were applied respectively. A subcutaneous injection model using MHCC-97L cells and patient-derived tumor xenograft (PDTX) were applied to investigate the effect of PIM1 inhibitors on the in-vivo tumor growth by oral gavage treatment. To minimize the toxicity of PIM1 inhibitors, PIM1 inhibitors loaded PEGda gel was investigated in cell proliferation assay. <br><br>SGI-1776 and PIM447 treated HCC cells reduced the cell proliferation, migration and invasion in a dose-dependent manner under normoxic and hypoxic conditions. SGI-1776 and PIM447 treatment also sensitized HCC cells to cisplatin and doxorubicin under both conditions. Both PIM1 inhibitors suppressed PKM2 and glucose uptake in vitro. SGI-1776 and PIM447 treatment showed similar activities in HCC cells under normoxic and hypoxic condition. In vivo, tumor growth was inhibited upon administration of SGI-1776 and PIM447 in both MHCC-97L cell line and PDTX mouse model. PIM447 also sensitized cisplatin and doxorubicin in MHCC-97L cells bearing mice. PIM1 inhibitors loaded PEGda gel demonstrated a low releasing rate of PIM1 inhibitors in vitro. PEGda gel may apply in mouse model for minimizing the toxicity of PIM1 inhibitors.<br><br>PIM1 inhibitor showed the efficacy in suppressing HCC progression and glucose metabolism. It also improved chemosensitivity to HCC cells. PEGda gel helps to deliver PIM1 inhibitors to HCC. Therefore, PIM1 inhibitor can be regarded as a potential targeted therapy for HCC.
DOI: 10.25442/hku.12756452
title: Anti-tumor effects of PIM1 inhibition in hepatocellular carcinoma

description: Hepatocellular carcinoma (HCC) is the most common malignancy liver cancer. Targeted therapies are the new path for HCC treatment. Under hypoxic microenvironment, PIM1 (a serine/threonine kinase) is overexpressed in HCC. PIM1 induced tumor progression by regulating glycolysis. In this project, the efficacy of PIM1 inhibitor will be investigated in vitro and in vivo. <br><br>SGI-1776 and PIM447 were PIM1 inhibitors which were applied in this study. Both inhibitors were treated to HCC cell lines (MHCC97L and Huh7) under normoxic (20% O2) and hypoxic (1% O2) condition. The expression of PIM1 downstream targets was altered and which was confirmed by using western blotting. MTT assay was used to determine IC50 of PIM1 inhibitors in both HCC cell lines under normoxic and hypoxic conditions. The effect of PIM1 inhibitors on the proliferation and metastasis of HCC was estimated by cell proliferation, cell migration and invasion assays. To examine the effects of PIM1 inhibitors on the glucose uptake and chemosensitivity in HCC, glucose uptake assay and apoptosis assay with Annexin V/PI staining were applied respectively. A subcutaneous injection model using MHCC-97L cells and patient-derived tumor xenograft (PDTX) were applied to investigate the effect of PIM1 inhibitors on the in-vivo tumor growth by oral gavage treatment. To minimize the toxicity of PIM1 inhibitors, PIM1 inhibitors loaded PEGda gel was investigated in cell proliferation assay. <br><br>SGI-1776 and PIM447 treated HCC cells reduced the cell proliferation, migration and invasion in a dose-dependent manner under normoxic and hypoxic conditions. SGI-1776 and PIM447 treatment also sensitized HCC cells to cisplatin and doxorubicin under both conditions. Both PIM1 inhibitors suppressed PKM2 and glucose uptake in vitro. SGI-1776 and PIM447 treatment showed similar activities in HCC cells under normoxic and hypoxic condition. In vivo, tumor growth was inhibited upon administration of SGI-1776 and PIM447 in both MHCC-97L cell line and PDTX mouse model. PIM447 also sensitized cisplatin and doxorubicin in MHCC-97L cells bearing mice. PIM1 inhibitors loaded PEGda gel demonstrated a low releasing rate of PIM1 inhibitors in vitro. PEGda gel may apply in mouse model for minimizing the toxicity of PIM1 inhibitors.<br><br>PIM1 inhibitor showed the efficacy in suppressing HCC progression and glucose metabolism. It also improved chemosensitivity to HCC cells. PEGda gel helps to deliver PIM1 inhibitors to HCC. Therefore, PIM1 inhibitor can be regarded as a potential targeted therapy for HCC.
DOI: 10.6084/m9.figshare.12849886
title: Effect of the finite width of the temperature transition in diffusive condensation particle counters

description: The fluid streamlines <i>ψ</i> moving near the hot-cold wall junction in diffusive condensation particle counters (DCPCs) experience close to unit saturation ratio (<i>S</i> = 1), being ineffective for nucleation. Nevertheless, when the wall temperature changes discontinuously, the maximal saturation ratio sensed along all near-wall streamlines <i>S<sub>max</sub>(ψ)</i> is well above unity, and is the same for all near-wall streamlines. This property greatly reduces the range of effective values of <i>S<sub>max</sub>(ψ)</i> present within the CPC. When the ratio of heat and mass diffusivities <i>Le = α/D</i> approaches unity, <i>S<sub>max</sub>(ψ)</i> becomes constant also for streamlines far from the wall, enabling in principle the use of DCPCs for basic heterogeneous nucleation studies and for high resolution particle sizing. Here we consider theoretically the near-wall structure of the saturation ratio profile in the more realistic case when the temperature change takes place linearly over an insulating strip of finite length <i>Δ</i> placed between two metallic wall segments held at different uniform temperatures. A thin boundary layer forms then near the wall, over which <i>S<sub>max</sub>(ψ)</i> transitions from unity at the wall to the uniform value expected in the idealized temperature jump case. This boundary layer is unavoidable at all <i>Le</i>, including <i>Le = 1</i>. However, simple scaling laws are provided for its width, showing that it may be relatively thin, and its effects may be removed by using sheath gas. Copyright © 2020 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.12849886.v1
title: Effect of the finite width of the temperature transition in diffusive condensation particle counters

description: The fluid streamlines <i>ψ</i> moving near the hot-cold wall junction in diffusive condensation particle counters (DCPCs) experience close to unit saturation ratio (<i>S</i> = 1), being ineffective for nucleation. Nevertheless, when the wall temperature changes discontinuously, the maximal saturation ratio sensed along all near-wall streamlines <i>S<sub>max</sub>(ψ)</i> is well above unity, and is the same for all near-wall streamlines. This property greatly reduces the range of effective values of <i>S<sub>max</sub>(ψ)</i> present within the CPC. When the ratio of heat and mass diffusivities <i>Le = α/D</i> approaches unity, <i>S<sub>max</sub>(ψ)</i> becomes constant also for streamlines far from the wall, enabling in principle the use of DCPCs for basic heterogeneous nucleation studies and for high resolution particle sizing. Here we consider theoretically the near-wall structure of the saturation ratio profile in the more realistic case when the temperature change takes place linearly over an insulating strip of finite length <i>Δ</i> placed between two metallic wall segments held at different uniform temperatures. A thin boundary layer forms then near the wall, over which <i>S<sub>max</sub>(ψ)</i> transitions from unity at the wall to the uniform value expected in the idealized temperature jump case. This boundary layer is unavoidable at all <i>Le</i>, including <i>Le = 1</i>. However, simple scaling laws are provided for its width, showing that it may be relatively thin, and its effects may be removed by using sheath gas. Copyright © 2020 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.12849974.v1
title: Bioinformatic analysis of brain-specific miRNAs for identification of candidate traumatic brain injury blood biomarkers

description: Detection of brain-specific miRNAs in the peripheral blood could serve as a surrogate marker of traumatic brain injury (TBI). Here, we systematically identified brain-enriched miRNAs, and tested their utility as TBI biomarkers in the acute phase of care. Publically available microarray data generated from 29 postmortem human tissues were used to rank 1,364 miRNAs in terms of their degree of brain-specific expression. Levels of the top six ranked miRNAs were then prospectively measured in serum samples collected from 10 Patients with TBI at hospital admission, as well as from 10 controls. The top six miRNAs identified in our analysis (miR-124-3p, miR-219a-5p, miR-9-5p, miR-9-3p, miR-137, and miR-128-3p) were enriched 70 to 320-fold in brain relative to other tissues, and exhibited dramatically greater brain specificity compared to several miRNAs previously proposed as biomarkers. Furthermore, their levels were elevated in serum from patients with TBI compared to controls, and could collectively discriminate between groups with 90% sensitivity and 100% specificity. Interestingly, subsequent informatic pathway analysis revealed that their target transcripts were enriched for components of signaling pathways active in peripheral organs involved in common post-TBI complications. The six candidate miRNAs identified in this preliminary study have promise as blood biomarkers of TBI, and could also be molecular contributors to systemic physiologic changes commonly observed post-injury.
DOI: 10.6084/m9.figshare.12849974
title: Bioinformatic analysis of brain-specific miRNAs for identification of candidate traumatic brain injury blood biomarkers

description: Detection of brain-specific miRNAs in the peripheral blood could serve as a surrogate marker of traumatic brain injury (TBI). Here, we systematically identified brain-enriched miRNAs, and tested their utility as TBI biomarkers in the acute phase of care. Publically available microarray data generated from 29 postmortem human tissues were used to rank 1,364 miRNAs in terms of their degree of brain-specific expression. Levels of the top six ranked miRNAs were then prospectively measured in serum samples collected from 10 Patients with TBI at hospital admission, as well as from 10 controls. The top six miRNAs identified in our analysis (miR-124-3p, miR-219a-5p, miR-9-5p, miR-9-3p, miR-137, and miR-128-3p) were enriched 70 to 320-fold in brain relative to other tissues, and exhibited dramatically greater brain specificity compared to several miRNAs previously proposed as biomarkers. Furthermore, their levels were elevated in serum from patients with TBI compared to controls, and could collectively discriminate between groups with 90% sensitivity and 100% specificity. Interestingly, subsequent informatic pathway analysis revealed that their target transcripts were enriched for components of signaling pathways active in peripheral organs involved in common post-TBI complications. The six candidate miRNAs identified in this preliminary study have promise as blood biomarkers of TBI, and could also be molecular contributors to systemic physiologic changes commonly observed post-injury.