cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6703760.v1
title: Supplementary Material for: Comparison of Preterm and Term Wharton’s Jelly-Derived Mesenchymal Stem Cell Properties in Different Oxygen Tensions

description: Mesenchymal stem cells (MSCs) have shown promise as therapeutic agents in treating morbidities associated with premature birth. MSCs derived from the human umbilical cord are easy to isolate and have low immunogenicity and a robust ability to secrete paracrine factors. To date, there are no studies evaluating preterm versus term umbilical cord tissue-derived MSCs. Therefore, our aim was twofold: (1) to compare stem cell properties in preterm versus term MSCs and (2) to examine the impact of oxygen tension on stem cell behavior. Umbilical cord tissue was obtained from 5 preterm and 5 term neonates. The cells were isolated and characterized as MSCs in accordance with the International Society for Cellular Therapy. We exposed MSCs to different oxygen tensions to examine the impact of environmental factors on cell performance. We studied the following stem cell properties: (i) motility, (ii) proliferation, (iii) senescence, (iv) cell viability, (v) colony-forming unit efficiency, and (vi) inflammatory cytokine expression. Under normoxia (21% O<sub>2</sub>), cells from preterm and term infants had similar properties. Under hypoxic conditions (1% O<sub>2</sub>), term MSCs had better cell proliferation; however, cells exposed to hyperoxia (90% O<sub>2</sub>) had the slowest motility and lowest cell viability (<i>p</i> &lt; 0.05). There was no difference in the expression of senescence or cytokine expression between the groups. The term cells demonstrated more colony-forming efficiency than the preterm cells. In sum, our preliminary findings suggest that MSCs derived from term and preterm umbilical cords have similar characteristics, offering the potential of future autologous/allogeneic MSC transplants in neonates.
DOI: 10.6084/m9.figshare.6703457
title: Shared Silence (Coriolanus Online 2016)

description: Shared moment of silence using telepresence system and highlights of this games session
DOI: 10.6084/m9.figshare.6703457.v2
title: Shared Silence (Coriolanus Online 2016)

description: Shared moment of silence using telepresence system and highlights of this games session
DOI: 10.6084/m9.figshare.12890993.v1
title: Bashar H. Malkawi, Middle East Librarian Association Conference 2020

description: People around the world have faced unusual challenges touching nearly every aspect of their lives due to the COVID-19 outbreak and its rapid spread. The 2020 MELA Program offers presentations that engage with the impact of such challenges on libraries and other cultural institutions providing service to users of collections centered around the study of the Middle East. Crises such as the current pandemic profoundly change how information professionalsmust do their work, usually requiring adaptations in a matter of weeks, to last for nobody can say how long. At present, while stay-at-home orders have kept users away from physical collections maintained on campuses and in various repositories, librarians and archivists have responded rapidly and nimbly to maintain the visibility and accessibility of collections and library services to everyone who uses them. The crisis has also created an opportunity for all of us to reexamine how best to respond to user needs, as well as how to continue creatively engaging with them.
DOI: 10.6084/m9.figshare.12890993
title: Bashar H. Malkawi, Middle East Librarian Association Conference 2020

description: People around the world have faced unusual challenges touching nearly every aspect of their lives due to the COVID-19 outbreak and its rapid spread. The 2020 MELA Program offers presentations that engage with the impact of such challenges on libraries and other cultural institutions providing service to users of collections centered around the study of the Middle East. Crises such as the current pandemic profoundly change how information professionalsmust do their work, usually requiring adaptations in a matter of weeks, to last for nobody can say how long. At present, while stay-at-home orders have kept users away from physical collections maintained on campuses and in various repositories, librarians and archivists have responded rapidly and nimbly to maintain the visibility and accessibility of collections and library services to everyone who uses them. The crisis has also created an opportunity for all of us to reexamine how best to respond to user needs, as well as how to continue creatively engaging with them.
DOI: 10.6084/m9.figshare.6703355
title: Vilhelmsen2018CimbicidaeMatrix

description: Data matrix used for analyses for Vilhelmsen, L. (in press). Giant sawflies and their kin: morphological phylogeny of<br>Cimbicidae (Hymenoptera), Systematic Entomology xx: xxx-xxx.<br>
DOI: 10.6084/m9.figshare.6703355.v1
title: Vilhelmsen2018CimbicidaeMatrix

description: Data matrix used for analyses for Vilhelmsen, L. (in press). Giant sawflies and their kin: morphological phylogeny of<br>Cimbicidae (Hymenoptera), Systematic Entomology xx: xxx-xxx.<br>
DOI: 10.6084/m9.figshare.11542539
title: suppl_datafile_table1.xlsx

description: <b><i>Supporting Table 1</i></b><b>. <i>Coverage. </i></b>Table showing the amount of coverage per group (# of reads) and the percentage of uniquely mapped reads.<b></b>
DOI: 10.6084/m9.figshare.12890567.v1
title: H&E-stained sections

description: 5X objective images merged using photoshop<br>Larynges were sectioned in four series where A = H&E, B = Masson's Trichrome, C = Verhoeff van Gieson, and D = Alcian Blue. Each slide contained 6 sections<br>Numbers before the letter (e.g. 3A) refer to the slide number. Lower numbers contain sections that are more caudal (towards the trachea).<br>The numbers after the letter (e.g. #A_2) refer to the section number on the slide.
DOI: 10.6084/m9.figshare.11542533
title: suppl_datafile_table3.xlsx

description: <b><i>Supporting Table 3. Cytokine Genes. </i></b>List of differentially expressed cytokine genes from the DAVID Cytokine-Cytokine Receptor Pathway. For reference, the protein product and Ensembl IDs are included. Both log2 fold change values and adjusted p-values are included.
DOI: 10.6084/m9.figshare.6701543
title: Supplementary Material for: Late Cochlear Implantation in Early-Deafened Adults: A Detailed Analysis of Auditory and Self-Perceived Benefits

description: <b><i>Objectives:</i></b> It is known that early-deafened cochlear implant (CI) users are a very heterogeneously performing group. To gain more insight into this population, this study investigated (1) postoperative changes in auditory performance over time based on various outcome measures, focusing on poor performers, (2) self-perceived outcomes, (3) relations between auditory and self-perceived outcomes, and (4) preimplantation factors predicting postoperative outcomes. <b><i>Methods:</i></b> Outcomes were assessed prospectively in a group of 27 early-deafened, late-implanted CI users, up to 3 years after implantation. Outcome measures included open-set word and sentence recognition, closed-set word recognition, speech tracking and a questionnaire on self-perceived outcomes. Additionally, the relative influence of 8 preimplantation factors on CI outcome was assessed with linear regression analyses. <b><i>Results:</i></b> Significant improvements were found for auditory performance measures and most of the questionnaire domains. Significant changes of the closed-set word test, speech tracking and questionnaire were also found for a subgroup of poor performers. Correlations between auditory and self-perceived outcomes were weak and nonsignificant. Preoperative word recognition and preoperative hearing thresholds, both for the implanted ear, were significant predictors of postoperative outcome in the multivariable regression model, explaining 63.5% of the variation. <b><i>Conclusions:</i></b> Outcome measurement in this population should be adjusted to the patients’ individual performance level and include self-perceived benefit. There is still a need for more knowledge regarding predictors of CI outcomes in this group, but the current study suggests the importance of the preoperative performance of the ear to be implanted.
DOI: 10.6084/m9.figshare.6701012
title: Supplementary Material for: Long-Term Immune Alterations Accompanying Chronic Posttraumatic Stress Disorder following Exposure to Suicide Bomb Terror Incidents during Childhood

description: <b><i>Background and Aim:</i></b> Long-term immune alterations have been proposed to play a mechanistic role in posttraumatic stress disorder (PTSD) as well as in its associated increase in medical morbidity and mortality. Better characterization of altered immune function may help identify diagnostic and prognostic biomarkers and potentially targets for preventive intervention. <b><i>Methods:</i></b> As part of an ongoing study, we conducted a preliminary case-control comparison of resting immune inflammatory profiles between terror victims treated in childhood at the emergency department over the previous decade, who developed chronic PTSD upon long-term follow-up, and healthy controls. <b><i>Results:</i></b> Our preliminary results in a subsample of this ongoing study support and extend elevated resting levels of granulocyte colony-stimulating factor, interleukin-4, and regulated on activation, normal T cell expressed and secreted in childhood onset chronic PTSD. <b><i>Conclusion:</i></b> Chronic immune alterations may participate in inflammatory activation and signal to the CNS through the neurovascular unit, as well as modulate the neuroendocrine axis. Better characterization and understanding of these preliminary findings may point to diagnostic and prognostic biomarkers and potentially elucidate mechanistic involvement of immune activation in PTSD.
DOI: 10.6084/m9.figshare.6701012.v1
title: Supplementary Material for: Long-Term Immune Alterations Accompanying Chronic Posttraumatic Stress Disorder following Exposure to Suicide Bomb Terror Incidents during Childhood

description: <b><i>Background and Aim:</i></b> Long-term immune alterations have been proposed to play a mechanistic role in posttraumatic stress disorder (PTSD) as well as in its associated increase in medical morbidity and mortality. Better characterization of altered immune function may help identify diagnostic and prognostic biomarkers and potentially targets for preventive intervention. <b><i>Methods:</i></b> As part of an ongoing study, we conducted a preliminary case-control comparison of resting immune inflammatory profiles between terror victims treated in childhood at the emergency department over the previous decade, who developed chronic PTSD upon long-term follow-up, and healthy controls. <b><i>Results:</i></b> Our preliminary results in a subsample of this ongoing study support and extend elevated resting levels of granulocyte colony-stimulating factor, interleukin-4, and regulated on activation, normal T cell expressed and secreted in childhood onset chronic PTSD. <b><i>Conclusion:</i></b> Chronic immune alterations may participate in inflammatory activation and signal to the CNS through the neurovascular unit, as well as modulate the neuroendocrine axis. Better characterization and understanding of these preliminary findings may point to diagnostic and prognostic biomarkers and potentially elucidate mechanistic involvement of immune activation in PTSD.
DOI: 10.6084/m9.figshare.6699068
title: S wave velocity and attenuation at Imperial College site

description: The boundary layer in Stokes' second problem is used to esimate dynamic permeability at the Imperial College site. <br><br>The results showed that (1) S wave in the borehole site is largely controlled by siltstone with porosity of 0.6; <br>(2) Theoretical estimation is consistent with measured permeability of S wave at the sonic band. <br>
DOI: 10.6084/m9.figshare.6699068.v1
title: S wave velocity and attenuation at Imperial College site

description: The boundary layer in Stokes' second problem is used to esimate dynamic permeability at the Imperial College site. <br><br>The results showed that (1) S wave in the borehole site is largely controlled by siltstone with porosity of 0.6; <br>(2) Theoretical estimation is consistent with measured permeability of S wave at the sonic band. <br>
DOI: 10.6084/m9.figshare.6698780
title: Hand shape decoding (rock–paper–scissors)

description: This is fMRI data from a human subject who changed shape of his right hand (rock-, paper-, or scissor-shape). The dataset includes preprocessed BOLD signals of voxels in cerebellum (CB), primary motor cortex (M1), and supplementary motor area (SMA).
DOI: 10.6084/m9.figshare.6697076
title: Portal Project Teaching Database - excerpt

description: This is an excerpt from the dataset available on Figshare https://doi.org/10.6084/m9.figshare.1314459.v9The Portal Project Teaching Database is a simplified version of the Portal Project Database designed for teaching. It provides a real world example of life-history, population, and ecological data, with sufficient complexity to teach many aspects of data analysis and management, but with many complexities removed to allow students to focus on the core ideas and skills being taught.<br>
DOI: 10.6084/m9.figshare.6697076.v1
title: Portal Project Teaching Database - exceprt

description: This is an excerpt from the dataset available on Figshare https://doi.org/10.6084/m9.figshare.1314459.v9The Portal Project Teaching Database is a simplified version of the Portal Project Database designed for teaching. It provides a real world example of life-history, population, and ecological data, with sufficient complexity to teach many aspects of data analysis and management, but with many complexities removed to allow students to focus on the core ideas and skills being taught.<br>
DOI: 10.6084/m9.figshare.6696749
title: Fully Bayesian logistic regression with hyper-LASSO priors for high-dimensional feature selection

description: Feature selection arises in many areas of modern science. For example, in genomic research, we want to find the genes that can be used to separate tissues of different classes (e.g. cancer and normal). One approach is to fit regression/classification models with certain penalization. In the past decade, hyper-LASSO penalization (priors) have received increasing attention in the literature. However, fully Bayesian methods that use Markov chain Monte Carlo (MCMC) for regression/classification with hyper-LASSO priors are still in lack of development. In this paper, we introduce an MCMC method for learning multinomial logistic regression with hyper-LASSO priors. Our MCMC algorithm uses Hamiltonian Monte Carlo in a restricted Gibbs sampling framework. We have used simulation studies and real data to demonstrate the superior performance of hyper-LASSO priors compared to LASSO, and to investigate the issues of choosing heaviness and scale of hyper-LASSO priors.
DOI: 10.6084/m9.figshare.6696749.v1
title: Fully Bayesian logistic regression with hyper-LASSO priors for high-dimensional feature selection

description: Feature selection arises in many areas of modern science. For example, in genomic research, we want to find the genes that can be used to separate tissues of different classes (e.g. cancer and normal). One approach is to fit regression/classification models with certain penalization. In the past decade, hyper-LASSO penalization (priors) have received increasing attention in the literature. However, fully Bayesian methods that use Markov chain Monte Carlo (MCMC) for regression/classification with hyper-LASSO priors are still in lack of development. In this paper, we introduce an MCMC method for learning multinomial logistic regression with hyper-LASSO priors. Our MCMC algorithm uses Hamiltonian Monte Carlo in a restricted Gibbs sampling framework. We have used simulation studies and real data to demonstrate the superior performance of hyper-LASSO priors compared to LASSO, and to investigate the issues of choosing heaviness and scale of hyper-LASSO priors.
DOI: 10.6084/m9.figshare.6695369
title: Poliovirus induces autophagic signaling independent of the ULK1 complex

description: Poliovirus (PV), like many positive-strand RNA viruses, subverts the macroautophagy/autophagy pathway to promote its own replication. Here, we investigate whether the virus uses the canonical autophagic signaling complex, consisting of the ULK1/2 kinases, ATG13, RB1CC1, and ATG101, to activate autophagy. We find that the virus sends autophagic signals independent of the ULK1 complex, and that the members of the autophagic complex are not required for normal levels of viral replication. We also show that the SQSTM1/p62 receptor protein is not degraded in a conventional manner during infection, but is likely cleaved in a manner similar to that shown for coxsackievirus B3. This means that SQSTM1, normally used to monitor autophagic degradation, cannot be used to accurately monitor degradation during poliovirus infection. In fact, autophagic degradation may be affected by the loss of SQSTM1 at the same time as autophagic signals are being sent. Finally, we demonstrate that ULK1 and ULK2 protein levels are greatly reduced during PV infection, and ATG13, RB1CC1, and ATG101 protein levels are reduced as well. Surprisingly, autophagic signaling appears to increase as ULK1 levels decrease. Overexpression of wild-type or dominant-negative ULK1 constructs does not affect virus replication, indicating that ULK1 degradation may be a side effect of the ULK1-independent signaling mechanism used by PV, inducing complex instability. This demonstration of ULK1-independent autophagic signaling is novel and leads to a model by which the virus is signaling to generate autophagosomes downstream of ULK1, while at the same time, cleaving cargo receptors, which may affect cargo loading and autophagic degradative flux. Our data suggest that PV has a finely-tuned relationship with the autophagic machinery, generating autophagosomes without using the primary autophagy signaling pathway. <b>Abbreviations:</b> ACTB - actin beta; ATG13 - autophagy related 13; ATG14 - autophagy related 14; ATG101 - autophagy related 101; BECN1 - beclin 1; CVB3 - coxsackievirus B3; DMV - double-membraned vesicles; EM - electron microscopy; EMCV - encephalomyocarditis virus; EV-71 - enterovirus 71; FMDV - foot and mouth disease virus; GFP - green fluorescent protein; MAP1LC3B/LC3B - microtubule associated protein 1 light chain 3 beta; MOI - multiplicity of infection; MTOR - mechanistic target of rapamycin kinase; PIK3C3 - phosphatidylinositol 3-kinase catalytic subunit type 3; PRKAA2 - protein kinase AMP-activated catalytic subunit alpha 2; PSMG1 - proteasome assembly chaperone 1; PSMG2 - proteasome assembly chaperone 2PV - poliovirus; RB1CC1 - RB1 inducible coiled-coil 1; SQSTM1 - sequestosome 1; ULK1 - unc-51 like autophagy activating kinase 1; ULK2 - unc-51 like autophagy activating kinase 2; WIPI1 - WD repeat domain, phosphoinositide interacting 1
DOI: 10.6084/m9.figshare.6695369.v2
title: Poliovirus induces autophagic signaling independent of the ULK1 complex

description: Poliovirus (PV), like many positive-strand RNA viruses, subverts the macroautophagy/autophagy pathway to promote its own replication. Here, we investigate whether the virus uses the canonical autophagic signaling complex, consisting of the ULK1/2 kinases, ATG13, RB1CC1, and ATG101, to activate autophagy. We find that the virus sends autophagic signals independent of the ULK1 complex, and that the members of the autophagic complex are not required for normal levels of viral replication. We also show that the SQSTM1/p62 receptor protein is not degraded in a conventional manner during infection, but is likely cleaved in a manner similar to that shown for coxsackievirus B3. This means that SQSTM1, normally used to monitor autophagic degradation, cannot be used to accurately monitor degradation during poliovirus infection. In fact, autophagic degradation may be affected by the loss of SQSTM1 at the same time as autophagic signals are being sent. Finally, we demonstrate that ULK1 and ULK2 protein levels are greatly reduced during PV infection, and ATG13, RB1CC1, and ATG101 protein levels are reduced as well. Surprisingly, autophagic signaling appears to increase as ULK1 levels decrease. Overexpression of wild-type or dominant-negative ULK1 constructs does not affect virus replication, indicating that ULK1 degradation may be a side effect of the ULK1-independent signaling mechanism used by PV, inducing complex instability. This demonstration of ULK1-independent autophagic signaling is novel and leads to a model by which the virus is signaling to generate autophagosomes downstream of ULK1, while at the same time, cleaving cargo receptors, which may affect cargo loading and autophagic degradative flux. Our data suggest that PV has a finely-tuned relationship with the autophagic machinery, generating autophagosomes without using the primary autophagy signaling pathway. <b>Abbreviations:</b> ACTB - actin beta; ATG13 - autophagy related 13; ATG14 - autophagy related 14; ATG101 - autophagy related 101; BECN1 - beclin 1; CVB3 - coxsackievirus B3; DMV - double-membraned vesicles; EM - electron microscopy; EMCV - encephalomyocarditis virus; EV-71 - enterovirus 71; FMDV - foot and mouth disease virus; GFP - green fluorescent protein; MAP1LC3B/LC3B - microtubule associated protein 1 light chain 3 beta; MOI - multiplicity of infection; MTOR - mechanistic target of rapamycin kinase; PIK3C3 - phosphatidylinositol 3-kinase catalytic subunit type 3; PRKAA2 - protein kinase AMP-activated catalytic subunit alpha 2; PSMG1 - proteasome assembly chaperone 1; PSMG2 - proteasome assembly chaperone 2PV - poliovirus; RB1CC1 - RB1 inducible coiled-coil 1; SQSTM1 - sequestosome 1; ULK1 - unc-51 like autophagy activating kinase 1; ULK2 - unc-51 like autophagy activating kinase 2; WIPI1 - WD repeat domain, phosphoinositide interacting 1