cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5254480.v1
title: Kaposi's Sarcoma-Associated Herpesvirus Infection Promotes Differentiation and Polarization of Monocytes into Tumor-Associated Macrophages

description: Tumor associated macrophages (TAMs) promote angiogenesis, tumor invasion and metastasis, and suppression of anti-tumor immunity. These myeloid cells originate from monocytes, which differentiate into TAMs upon exposure to the local tumor microenvironment. We previously reported that Kaposi's sarcoma-associated herpes virus (KSHV) infection of endothelial cells induces the cytokine angiopoietin-2 (Ang-2) to promote migration of monocytes into tumors. Here we report that KSHV infection of endothelial cells induces additional cytokines including interleukin-6 (IL-6), interleukin-10 (IL-10), and interleukin-13 (IL-13) that drive monocytes to differentiate and polarize into TAMs. The KSHV-induced TAMs not only express TAM-specific markers such as CD-163 and legumain (LGMN) but also display a gene expression profile with characteristic features of viral infection. More importantly, KSHV-induced TAMs enhance tumor growth in nude mice. These results are consistent with the strong presence of TAMs in Kaposi's sarcoma (KS) tumors. Therefore, KSHV infection of endothelial cells generates a local microenvironment that not only promotes the recruitment of monocytes but also induces their differentiation and polarization into TAMs. These findings reveal a new mechanism of KSHV contribution to KS tumor development.
DOI: 10.6084/m9.figshare.5250457
title: Sinusoid Data

description: Data should be locate within subfolder named 'sinwave' within main script folder (also found within this project folder)<br>Contains function-generated pure-tone sinusoid data for analysis of the frequency-recording capabilities of the OpenBCI device (see project description for file details)
DOI: 10.6084/m9.figshare.5254441.v2
title: Online Supplement, Supp and Graham et al. study on environmental correlates of hummingbird migration

description: Online Supplement to Supp and Graham et al. study, "Alternate migration scenarios provide novel insights into environmental associations for migrating hummingbird populations in North America". Data and code.<br>The code and data in this supplement allow for the analyses and figures to be fully replicated using eBird citizen science datasets for hummingbird observation and remotely sensed datasets from movebank for environment. Details on the code and files can be found in the Supplement_text file in the zipped folder.
DOI: 10.6084/m9.figshare.5254441.v1
title: Online Supplement to Supp and Graham et al. study, "Alternate migration scenarios provide novel insights into environmental associations for migrating hummingbird populations in North America". Data and code.

description: The code and data in this supplement allow for the analyses and figures to be fully replicated using eBird citizen science datasets for hummingbird observation and remotely sensed datasets from movebank for environment. Details on the code and files can be found in the Supplement_text file in the zipped folder.
DOI: 10.6084/m9.figshare.5249929
title: Trade-offs in sustainability impacts of introducing cascade use of wood

description: The aim of this study was to analyse the sustainability impacts of allocating material from energy use to material use by adding cascaded wood into production of wood products. A case study is presented, where we analyse sustainability impacts of cascade use alternatives compared to the non-cascade use practice in particleboard production within the province of North Karelia, Finland. Direct impacts are captured using sustainability indicators representing environmental, economic and social aspects of sustainability. Results show that introducing cascaded wood can increase carbon storage in wood products, employment and production costs. Energy use and GHG emissions increase as well, when the total industrial activity during the lifetime of wood increases. We conclude that cascade use can improve resource efficiency as it enables the use of wood multiple times before combustion; however, the amount of waste wood for energy generation decreases locally, and alternative sources of energy need to be identified.
DOI: 10.6084/m9.figshare.5249932
title: Comparative efficacy of vasoconstrictor therapies for type 1 hepatorenal syndrome: a network meta-analysis

description: <b>Introduction</b>: The outcome of a comparative efficacy and safety of vasoconstrictor therapies for treatment of patients with type 1 hepatorenal syndrome (HRS-1) remain inconclusive. <b>Areas covered</b>: We searched literature databases for randomized controlled trials (RCTs) until 31 January 2016, and included ten eligible RCTs. In conclusion, terlipressin was the most efficacious vasoconstrictor drug for HRS-1, but had a higher probability of causing AEs. Norepinephrine was an attractive alternative to terlipressin and associated with less AEs. <b>Expert commentary</b>: To date, most previous traditional meta-analyses included trials with a limited population and compared terlipressin alone or with albumin against no intervention or albumin. Since different HRS types have different diagnoses and show different responses to vasoconstrictors, it may be questionable to combine data from patients with type 1 and type 2 HRS, which has been reported for most previous meta-analyses. Thus, performing a high-quality network meta-analysis of the existing literature is a valuable way to interrogate published data and to draw conclusions which may inform on the best interventional strategy.
DOI: 10.6084/m9.figshare.5249932.v1
title: Comparative efficacy of vasoconstrictor therapies for type 1 hepatorenal syndrome: a network meta-analysis

description: <b>Introduction</b>: The outcome of a comparative efficacy and safety of vasoconstrictor therapies for treatment of patients with type 1 hepatorenal syndrome (HRS-1) remain inconclusive. <b>Areas covered</b>: We searched literature databases for randomized controlled trials (RCTs) until 31 January 2016, and included ten eligible RCTs. In conclusion, terlipressin was the most efficacious vasoconstrictor drug for HRS-1, but had a higher probability of causing AEs. Norepinephrine was an attractive alternative to terlipressin and associated with less AEs. <b>Expert commentary</b>: To date, most previous traditional meta-analyses included trials with a limited population and compared terlipressin alone or with albumin against no intervention or albumin. Since different HRS types have different diagnoses and show different responses to vasoconstrictors, it may be questionable to combine data from patients with type 1 and type 2 HRS, which has been reported for most previous meta-analyses. Thus, performing a high-quality network meta-analysis of the existing literature is a valuable way to interrogate published data and to draw conclusions which may inform on the best interventional strategy.
DOI: 10.6084/m9.figshare.5249914
title: Main Folder Files

description: The main dataset and associated scripts for extracting results within the associated manuscript (refer to the project description for a description of each file)
DOI: 10.6084/m9.figshare.5249929.v1
title: Trade-offs in sustainability impacts of introducing cascade use of wood

description: The aim of this study was to analyse the sustainability impacts of allocating material from energy use to material use by adding cascaded wood into production of wood products. A case study is presented, where we analyse sustainability impacts of cascade use alternatives compared to the non-cascade use practice in particleboard production within the province of North Karelia, Finland. Direct impacts are captured using sustainability indicators representing environmental, economic and social aspects of sustainability. Results show that introducing cascaded wood can increase carbon storage in wood products, employment and production costs. Energy use and GHG emissions increase as well, when the total industrial activity during the lifetime of wood increases. We conclude that cascade use can improve resource efficiency as it enables the use of wood multiple times before combustion; however, the amount of waste wood for energy generation decreases locally, and alternative sources of energy need to be identified.
DOI: 10.6084/m9.figshare.5249914.v1
title: Main Folder Files

description: The main dataset and associated scripts for extracting results within the associated manuscript (refer to the project description for a description of each file)
DOI: 10.6084/m9.figshare.5249653
title: Integrating RMap with the Open Science Framework

description: This material was used in a breakout session at ESIP Summer 2017 meeting. The session provided an introduction to both RMap and OSF followed by a walk through of 3 proposed new features that integrate RMap functionality into the OSF user interface.
DOI: 10.6084/m9.figshare.5249548
title: Variation in Particle Size, Moisture Content and Supplements for Improvement of Cotton Stalks’ Lignin Degradation by <i>Phlebia radiata</i> and Saccharification

description: Particle size, moisture content and media supplements were studied for delignification of cotton stalks by <i>Phlebia radiata</i> MTCC 2791 in solid-state fermentation. Highest lignin degradation of 31.02 ± 1.27% (w/w) with cellulose loss of 14.39 ± 0.53% (w/w) observed in cotton stalks having particle size 5 mm and 75% moisture content, after 40 days. Supplements Cu<sup>2+</sup>, Mn<sup>2+</sup> and veratryl alcohol (VA) enhanced the lignolytic enzymes production and the lignin degradation. Supplements Mn<sup>2+</sup> at 1 mM with lignin degradation 36.58 ± 0.28% (w/w), high selectivity value (SV) 2.81; Cu<sup>2+</sup> at 0.5 mM with lignin degradation 31.75 ± 1.74% (w/w), SV 2.56; VA 0.5 mM with lignin degradation 33.96 ± 0.54% (w/w), SV 2.30 were optimal for pretreatment. The glucose yield increased to 113.22 ± 3.79 mg/g from 40 days pretreated cotton stalks with Mn<sup>2+</sup> (1 mM) supplements, more than twofolds higher from untreated cotton stalks. Strong linear correlation of <i>R</i><sup>2</sup> = 0.956 between lignin degradation and glucose yield was observed.
DOI: 10.6084/m9.figshare.5249551
title: Contour absent & present .Rdata

description: The datasets (Rdata) for the contour-absent and contour-present conditions in the paper:<br>Van Humbeeck, N., Meghanathan, R. N., Wagemans, J., van Leeuwen, C., Nikolaev, A. R. (2018) Presaccadic EEG activity predicts visual saliency in free-viewing contour integration. Psychophysiology, e13267. https://doi.org/10.1111/psyp.13267<br>
DOI: 10.6084/m9.figshare.5249653.v1
title: Integrating RMap with the Open Science Framework

description: This material was used in a breakout session at ESIP Summer 2017 meeting. The session provided an introduction to both RMap and OSF followed by a walk through of 3 proposed new features that integrate RMap functionality into the OSF user interface.
DOI: 10.6084/m9.figshare.5249548.v1
title: Variation in Particle Size, Moisture Content and Supplements for Improvement of Cotton Stalks’ Lignin Degradation by <i>Phlebia radiata</i> and Saccharification

description: Particle size, moisture content and media supplements were studied for delignification of cotton stalks by <i>Phlebia radiata</i> MTCC 2791 in solid-state fermentation. Highest lignin degradation of 31.02 ± 1.27% (w/w) with cellulose loss of 14.39 ± 0.53% (w/w) observed in cotton stalks having particle size 5 mm and 75% moisture content, after 40 days. Supplements Cu<sup>2+</sup>, Mn<sup>2+</sup> and veratryl alcohol (VA) enhanced the lignolytic enzymes production and the lignin degradation. Supplements Mn<sup>2+</sup> at 1 mM with lignin degradation 36.58 ± 0.28% (w/w), high selectivity value (SV) 2.81; Cu<sup>2+</sup> at 0.5 mM with lignin degradation 31.75 ± 1.74% (w/w), SV 2.56; VA 0.5 mM with lignin degradation 33.96 ± 0.54% (w/w), SV 2.30 were optimal for pretreatment. The glucose yield increased to 113.22 ± 3.79 mg/g from 40 days pretreated cotton stalks with Mn<sup>2+</sup> (1 mM) supplements, more than twofolds higher from untreated cotton stalks. Strong linear correlation of <i>R</i><sup>2</sup> = 0.956 between lignin degradation and glucose yield was observed.
DOI: 10.6084/m9.figshare.5249551.v1
title: contour_absent_data.Rdata

description: The dataset (Rdata) for the contour-absent condition for the paper “Presaccadic EEG activity predicts visual saliency in free-viewing contour integration” by Nathalie Van Humbeeck, Radha Nila Meghanathan, Johan Wagemans, Cees van Leeuwen, Andrey R. Nikolaev
DOI: 10.6084/m9.figshare.5249551.v2
title: Contour absent & present .Rdata

description: The datasets (Rdata) for the contour-absent and contour-present conditions for the paper “Presaccadic EEG activity predicts visual saliency in free-viewing contour integration” by Nathalie Van Humbeeck, Radha Nila Meghanathan, Johan Wagemans, Cees van Leeuwen, Andrey R. Nikolaev
DOI: 10.6084/m9.figshare.5249551.v3
title: Contour absent & present .Rdata

description: The datasets (Rdata) for the contour-absent and contour-present conditions for the paper “Presaccadic EEG activity predicts visual saliency in free-viewing contour integration” by Nathalie Van Humbeeck, Radha Nila Meghanathan, Johan Wagemans, Cees van Leeuwen, Andrey R. Nikolaev
DOI: 10.6084/m9.figshare.5249383
title: Supplementary Material for: A Novel Evaluation for Predicting Aortic Complicated Lesions Using Calcification on Chest X-ray

description: <b><i>Background:</i></b> The aorta is a significant source of cerebral thromboembolisms. Aortic complicated lesions (ACLs) are key findings on transesophageal echocardiography (TEE) for assessing aortic sources of emboli to the brain. TEE is sometimes avoided due to its invasiveness. However, few reports have examined alternative methods for predicting ACLs. We investigated relationships between aortic arch calcification (AAC) on chest X-ray and ACLs. <b><i>Methods:</i></b> Participants comprised 300 patients with acute ischemic stroke or transient ischemic attack who underwent TEE for the evaluation of the aortic arch and heart. A postero-anterior plain chest X-ray in the recumbent position was evaluated on admission for each patient. AAC was evaluated using 4 grades (0-3) and “AAC thickness” defined as the distance from the inner margin of the most distant AAC to the outer margin of the aortic vessel wall. ACLs were defined by intima-media thickness (IMT) ≥4.0 mm or presence of ulcerated or mobile plaques. Carotid maximum IMT on ultrasonography was also evaluated. Comparison of the diagnostic ability to predict ACL was performed between AAC grades and AAC thickness or AAC thickness and carotid maximum IMT using the Delong method. <b><i>Results:</i></b> ACLs were identified in 71 patients (23.7%), including ACLs with ulcerated plaques in 24 (8.0%) and ACLs with mobile plaques in 9 (3.0%). Plaque thickness was greater in higher AAC grades or higher quartiles of AAC thickness (<i>p</i> for trend &lt;0.001 each). The Cochran-Armitage test showed that both higher AAC grade and higher quartile of AAC thickness were significantly associated with the presence of ACLs, as well as the presence of ulcerated or mobile plaques (<i>p</i> for trend &lt; 0.001 each). Receiver-operating characteristic (ROC) analysis showed optimal cut-off values for AAC thickness of 5.6 mm for ACLs and 6.0 mm for ulcerated or mobile plaques. Multivariate logistic regression revealed a higher grade of AAC (grades 2-3) and AAC thickness (≥6 mm) as significantly associated with ACLs and ulcerated or mobile plaques (<i>p</i> &lt; 0.001 each). ROC curve comparisons showed that AAC thickness offered a better marker of ACLs than AAC grade (<i>p</i> = 0.019), although no significant difference was evident between AAC thickness and carotid maximum IMT (<i>p</i> = 0.567). <b><i>Conclusions:</i></b> AAC on chest X-ray, evaluated by both AAC grade and AAC thickness to the outer aortic vessel wall, was significantly associated with ACLs on TEE. AAC thickness was suggested as more useful than AAC grade and equivalent to carotid IMT in predicting ACLs.
DOI: 10.6084/m9.figshare.5249551.v4
title: Contour absent & present .Rdata

description: The datasets (Rdata) for the contour-absent and contour-present conditions for the paper “Presaccadic EEG activity predicts visual saliency in free-viewing contour integration” by Nathalie Van Humbeeck, Radha Nila Meghanathan, Johan Wagemans, Cees van Leeuwen, Andrey R. Nikolaev
DOI: 10.6084/m9.figshare.5249380
title: Discovery of thalicthuberine as a novel antimitotic agent from nature that disrupts microtubule dynamics and induces apoptosis in prostate cancer cells

description: We report for the first time the mechanism of action of the natural product thalicthuberine (TH) in prostate and cervical cancer cells. TH induced a strong accumulation of LNCaP cells in mitosis, severe mitotic spindle defects, and asymmetric cell divisions, ultimately leading to mitotic catastrophe accompanied by cell death through apoptosis. However, unlike microtubule-binding drugs (vinblastine and paclitaxel), TH did not directly inhibit tubulin polymerization when tested in a cell-free system, whereas it reduced cellular microtubule polymer mass in LNCaP cells. This suggests that TH indirectly targets microtubule dynamics through inhibition of a critical regulator or tubulin-associated protein. Furthermore, TH is not a major substrate for P-glycoprotein (Pgp), which is responsible for multidrug resistance in numerous cancers, providing a rationale to further study TH in cancers with Pgp-mediated treatment resistance. The identification of TH's molecular target in future studies will be of great value to the development of TH as potential treatment of multidrug-resistant tumors.
DOI: 10.6084/m9.figshare.5249551.v5
title: Contour absent & present .Rdata

description: The datasets (Rdata) for the contour-absent and contour-present conditions for the paper “Presaccadic EEG activity predicts visual saliency in free-viewing contour integration” by Nathalie Van Humbeeck, Radha Nila Meghanathan, Johan Wagemans, Cees van Leeuwen, Andrey R. Nikolaev
DOI: 10.6084/m9.figshare.5249380.v2
title: Discovery of thalicthuberine as a novel antimitotic agent from nature that disrupts microtubule dynamics and induces apoptosis in prostate cancer cells

description: We report for the first time the mechanism of action of the natural product thalicthuberine (TH) in prostate and cervical cancer cells. TH induced a strong accumulation of LNCaP cells in mitosis, severe mitotic spindle defects, and asymmetric cell divisions, ultimately leading to mitotic catastrophe accompanied by cell death through apoptosis. However, unlike microtubule-binding drugs (vinblastine and paclitaxel), TH did not directly inhibit tubulin polymerization when tested in a cell-free system, whereas it reduced cellular microtubule polymer mass in LNCaP cells. This suggests that TH indirectly targets microtubule dynamics through inhibition of a critical regulator or tubulin-associated protein. Furthermore, TH is not a major substrate for P-glycoprotein (Pgp), which is responsible for multidrug resistance in numerous cancers, providing a rationale to further study TH in cancers with Pgp-mediated treatment resistance. The identification of TH's molecular target in future studies will be of great value to the development of TH as potential treatment of multidrug-resistant tumors.
DOI: 10.6084/m9.figshare.5249380.v1
title: Discovery of Thalicthuberine as a Novel Antimitotic Agent from Nature that Disrupts Microtubule Dynamics and Induces Apoptosis in Prostate Cancer Cells

description: We report for the first time the mechanism of action of the natural product thalicthuberine (TH) in prostate and cervical cancer cells. TH induced a strong accumulation of LNCaP cells in mitosis, severe mitotic spindle defects and asymmetric cell divisions, ultimately leading to mitotic catastrophe accompanied by cell death through apoptosis. However, unlike microtubule-binding drugs (vinblastine and paclitaxel), TH did not directly inhibit tubulin polymerization when tested in a cell-free system, whereas it reduced cellular microtubule polymer mass in LNCaP cells. This suggests that TH indirectly targets microtubule dynamics through inhibition of a critical regulator or tubulin-associated protein. Furthermore, TH is not a major substrate for P-glycoprotein (Pgp), which is responsible for multidrug resistance in numerous cancers, providing a rationale to further study TH in cancers with Pgp-mediated treatment resistance. The identification of TH's molecular target in future studies will be of great value to the development of TH as potential treatment of multidrug resistant tumors.
DOI: 10.6084/m9.figshare.5249551.v6
title: Contour absent & present .Rdata

description: The datasets (Rdata) for the contour-absent and contour-present conditions for the paper “Presaccadic EEG activity predicts visual saliency in free-viewing contour integration” by Nathalie Van Humbeeck, Radha Nila Meghanathan, Johan Wagemans, Cees van Leeuwen, Andrey R. Nikolaev
DOI: 10.6084/m9.figshare.5249356
title: Step-wise laser excitation of the 4s<i>n</i>f <sup>3</sup>F Rydberg states of neutral zinc

description: The new experimental results on the effective quantum numbers and term energies of the highly excited odd-parity 4s4d <sup>3</sup>D<sub>1,2,3</sub> →4s<i>n</i>f <sup>3</sup>F<sub>2,3,4</sub> Rydberg transitions of zinc have been presented. The experiment was performed using the three dye lasers simultaneously pumped by the second harmonic (532 nm) of the Q-switched Nd:YAG laser. The new observation includes the 4s<i>n</i>f <sup>3</sup>F<sub>3</sub> (12 ≤<i>n</i> ≤ 50) series excited from the 4s4d <sup>3</sup>D<sub>2</sub> intermediate level. In addition, the 4s<i>n</i>f <sup>3</sup>F<sub>2</sub> (12 ≤<i>n</i> ≤ 28) and 4s<i>n</i>f<sup>3</sup>F<sub>4</sub> (12 ≤<i>n</i> ≤ 33) series are observed from the thermally populated 4s4d <sup>3</sup>D<sub>1,3</sub> fine structure components. The ionization potential of zinc has been determined from the unperturbed 4s<i>n</i>f <sup>3</sup>F<sub>3</sub> series as 75769.31 ± 0.15 cm<sup>−1</sup>, which is in excellent agreement with the previously reported value.
DOI: 10.6084/m9.figshare.5249335
title: Supplementary Material for: Changes in White Matter Integrity following Intensive Voice Treatment (LSVT LOUD®) in Children with Cerebral Palsy and Motor Speech Disorders

description: Preliminary evidence suggests that intensive voice and speech treatment based on activity-dependent neuroplasticity principles holds promise for affecting positive change in children with cerebral palsy (CP) and motor speech disorders. Diffusion tensor imaging (DTI) allows researchers to make inferences about the integrity of white matter tracks and provides a sensitive measure of neuroplasticity. Previous treatment studies looking at the effects of training on white matter integrity have shown positive results, but these studies have been limited to gross motor function. Eight children with motor speech disorders and CP (3 females; age 8-16 years) and an age- and sex-matched group of typically developing (TD) children participated. Each child with CP completed a full dose of LSVT LOUD® and a 12-week maintenance program. Participants attended 3 recording sessions: before and after treatment, and after the maintenance period. TD children were tested at the same 3 time points. Recording sessions for both groups of children included measures of white matter integrity using DTI and acoustic measures of voice and speech. Fractional anisotropy (FA) was measured for 2 motor tracts and 5 association tracts. In children with CP, we observed an increase in FA in several motor and association tracts immediately following treatment and 12 weeks after treatment. Acoustic data on untrained tasks were correlated with changes in FA detected immediately following treatment and after the 12-week maintenance program. These findings suggest that long-term practice of skills attained during the treatment phase enhances white matter tract integrity in speech production networks.