cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5230468
title: Permutation testing for non-imaging data using FSL randomise

description: The <i>randomise_non_imaging</i> script is designed to take advantage of the functionalities of FSL randomise (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise/) to perform GLM-based non-parametric permutation testing using non-imaging data. This can be done fairly easily with other programs, but using randomise could be convenient to FSL users, who are accustomed to creating the necessary input files. <br>How to make it work<br><b>System requirements:</b>This scripts requires FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL) as well as python (including the numpy (http://www.numpy.org/) and nipy (http://nipy.org/) packages), and is meant to be used in Linux systems. The necessary python packages can be easily obtained by installing Anaconda (https://www.continuum.io/downloads).<br><br><b>Add alias and route to .bashrc:</b>After unzipping <i>randomise_non_imaging.zip</i>, we recommend adding an alias to the user's .bashrc as an easy way to call the script from any terminal. The path to the folder containing the <i>parameter2nifti.py</i> script should also be specified as <i>route_NIR </i>in the .bashrc:<br><i>alias randomise_non_imaging='bash <b>/full/path/to/your/folder/</b>randomise_non_imaging.sh'<br></i><i>export route_NIR=<b>/full/path/to/your/folder/</b></i><br><b>Input files:</b>Three basic input files are required: 1. Dependent variable matrix: text file containing the variables to be tested, consisting of one column per variable and one row for each observation. This is equivalent to the image input in randomise – and will in fact be converted to image format so it can be fed into the program 2. Design matrix (<i>.mat</i>) 3. Contrast matrix (<i>.con</i>)<br>Some options require additional input files: 1. F tests: requires <i>.fts </i>files (with the same root name as the design and contrast files) 2. Block permutation: requires exchangeability block labels <i>.grp</i> file (with the same root name as the design and contrast files)<br><b>Output (text) files:</b><br>1. P value file: named <i>(output)_p_all_contrasts</i>2. Stats file: named <i>(output)_stat_all_contrasts</i>3. F test p value file: <i>(output)_p_F_test</i>4. F test stats file: <i>(output)_Fstat</i>5. Corrected p value file: <i>(output)_corrp_all_contrasts</i>6. Corrected F test p value file: <i>(output)_corrp_F_test</i><br><b>Usage instructions are given here:</b> <i>https://cjneurolab.org/2017/07/21/permutation-testing-for-non-imaging-data-using-fsl-randomise/</i><br>
DOI: 10.6084/m9.figshare.5230417
title: Supplementary Material for: Distinct Involvement of the Sonic Hedgehog Signaling Pathway in Gastric Adenocarcinoma of Fundic Gland Type and Conventional Gastric Adenocarcinoma

description: <b><i>Background/Aims:</i></b> Gastric adenocarcinoma of fundic gland type (GAFG), which is a rare variant of gastric cancer, is reportedly associated with both Wnt/β-catenin signaling activation and guanine nucleotide binding protein, alpha stimulating complex (<i>GNAS</i>) mutations. This study aimed to elucidate potential roles of the Sonic hedgehog (Shh) signaling pathway in GAFG. <b><i>Methods:</i></b> We performed immunostaining for β-catenin and Shh signal-associated proteins, including Patched (Ptch), Smoothened (Smo), and Glioma-associated oncogene-1 (Gli1), and the direct sequencing of <i>GNAS</i>/<i>BRAF</i>/<i>KRAS</i> in 27 GAFGs, and compared them with 30 conventional gastric adenocarcinomas (CGAs). <b><i>Results:</i></b> GAFGs exhibited significantly lower immunoreactivity scores for Ptch, Smo, and Gli1 than CGAs. Moreover, while the Ptch score was significantly lower in the GAFG tumor areas than in the non-neoplastic areas adjacent to GAFG, the score was significantly higher in the CGA tumor areas than in the non-neoplastic areas. Similar trends were observed in the scores for Smo and Gli1. β-Catenin expression and <i>GNAS</i> mutations were found in 22 (81%) and 8 (30%) of the 27 GAFGs respectively. Gli1 expression was significantly associated with mutations in <i>GNAS</i>. <b><i>Conclusion:</i></b> GAFG and CGA exhibited distinct Ptch, Smo, and Gli1 expression patterns. Downregulation of the Shh signaling pathway, as well as activation of the Wnt/β-catenin signaling pathway, may therefore be associated with tumorigenesis in GAFG.
DOI: 10.6084/m9.figshare.5230417.v1
title: Supplementary Material for: Distinct Involvement of the Sonic Hedgehog Signaling Pathway in Gastric Adenocarcinoma of Fundic Gland Type and Conventional Gastric Adenocarcinoma

description: <b><i>Background/Aims:</i></b> Gastric adenocarcinoma of fundic gland type (GAFG), which is a rare variant of gastric cancer, is reportedly associated with both Wnt/β-catenin signaling activation and guanine nucleotide binding protein, alpha stimulating complex (<i>GNAS</i>) mutations. This study aimed to elucidate potential roles of the Sonic hedgehog (Shh) signaling pathway in GAFG. <b><i>Methods:</i></b> We performed immunostaining for β-catenin and Shh signal-associated proteins, including Patched (Ptch), Smoothened (Smo), and Glioma-associated oncogene-1 (Gli1), and the direct sequencing of <i>GNAS</i>/<i>BRAF</i>/<i>KRAS</i> in 27 GAFGs, and compared them with 30 conventional gastric adenocarcinomas (CGAs). <b><i>Results:</i></b> GAFGs exhibited significantly lower immunoreactivity scores for Ptch, Smo, and Gli1 than CGAs. Moreover, while the Ptch score was significantly lower in the GAFG tumor areas than in the non-neoplastic areas adjacent to GAFG, the score was significantly higher in the CGA tumor areas than in the non-neoplastic areas. Similar trends were observed in the scores for Smo and Gli1. β-Catenin expression and <i>GNAS</i> mutations were found in 22 (81%) and 8 (30%) of the 27 GAFGs respectively. Gli1 expression was significantly associated with mutations in <i>GNAS</i>. <b><i>Conclusion:</i></b> GAFG and CGA exhibited distinct Ptch, Smo, and Gli1 expression patterns. Downregulation of the Shh signaling pathway, as well as activation of the Wnt/β-catenin signaling pathway, may therefore be associated with tumorigenesis in GAFG.
DOI: 10.6084/m9.figshare.5230396
title: Supplementary Material for: TPOAb and Thyroid Function Are Not Associated with Breast Cancer Outcome: Evidence from a Large-Scale Study Using Data from the Taxotere as Adjuvant Chemotherapy Trial (TACT, CRUK01/001)

description: <b><i>Background:</i></b> Small-scale studies correlated the presence of thyroid autoimmunity with both improved or worsened breast cancer outcome. <b><i>Objectives:</i></b> We aimed to clarify this association in a large cohort using the phase III, randomized, controlled Taxotere as Adjuvant Chemotherapy Trial (TACT, CRUK01/001). <b><i>Methods:</i></b> TACT women &gt;18 years old with node-positive or high-risk node-negative early breast cancer (pT1–3a, pN0–1, M0), with stored plasma (<i>n</i> = 1,974), taken 15.5 (median; IQR 7.0–24.0) months after breast surgery were studied. Patients had also received chemotherapy (100%), radiotherapy (1,745/1,974; 88.4%), hormonal therapy (1,378/ 1,974; 69.8%), or trastuzumab (48/1,974; 2.4%). History of thyroid diseases and/or related treatments was not available. The prognostic significance of autoantibodies to thyroid peroxidase (TPOAb; positive ≥6 kIU/L), free-thyroxine and thyrotropin (combined: euthyroid, hypothyroid, hyperthyroid) was evaluated for disease-free survival (DFS), overall-survival (OS), and time-to-recurrence (TTR), with Cox regression models in univariate and multivariable analyses. The extended median follow-up was 97.5 months. <b><i>Results:</i></b> No difference in DFS was found by TPOAb status (unadjusted hazard ratio [HR]: 0.97, 95%CI: 0.78–1.19; <i>p</i> = 0.75) and/or thyroid function (unadjusted HR [hypothyroid vs. euthyroid]: 1.15, 95% CI: 0.79–1.68; <i>p</i> = 0.46; unadjusted HR [hyperthyroid vs. euthyroid]: 1.14, 95% CI: 0.82–1.61; <i>p</i> = 0.44). Similar results were obtained for OS, TTR, multivariable analyses, when TPOAb titre by tertiles was considered, and in a subgroup of 123 patients with plasma collected before adjuvant treatments. <b><i>Conclusions:</i></b> No evidence for a prognostic role of TPOAb and/or thyroid function in moderate-to-high-risk early breast cancer was found in the largest and longest observational study to date.
DOI: 10.6084/m9.figshare.5230432.v2
title: Rapid Woodfuel Assessment around the refugee, returnee and autochthonous communities of Goré, Chad

description: The dataset contains tree-level forest inventory data from 12 sample plots in Chad. The data have been collected on a 12 m radius circular plot. All stumps and trees with dbh &gt;= 10 cm have been measured. Information regarding plots location and land uses are contained in a second spreadsheet (“plot_data”).
DOI: 10.6084/m9.figshare.5230432.v1
title: Rapid Woodfuel Assessment around the refugee camps of Goré, Chad.

description: The dataset contains tree-level forest inventory data from 12 sample plots in Chad. The data have been collected on a 12 m radius circular plot. All stumps and trees with dbh &gt;= 10 cm have been measured. Information regarding plots location and land uses are contained in a second spreadsheet (“plot_data”).
DOI: 10.6084/m9.figshare.5230309
title: Rapid monitoring of beer-quality attributes based on UV-Vis spectral data

description: This work aimed to determinate eight beer properties using UV-Vis spectra in combination with principal component regression (PCR) or artificial neural network (ANN) models. A statistical experimental design was performed to generate the calibration data. First, principal component analysis (PCA) was applied to the original spectral data, and the scores in significant PCs were utilized to calibrate both models. PCR showed poor correlation for beer parameters (R<sup>2</sup> &lt; 0.61). The ANNs showed satisfactory correlations (R<sup>2</sup> = 0.74–0.92) and low relative error considering a variable range (&lt; 9%) for most of the beer-quality attributes, but vicinal diketones (R<sup>2</sup> = 0.56, = 16.69%). Once implemented, this method would be fast and low cost.
DOI: 10.6084/m9.figshare.5230309.v2
title: Rapid monitoring of beer-quality attributes based on UV-Vis spectral data

description: This work aimed to determinate eight beer properties using UV-Vis spectra in combination with principal component regression (PCR) or artificial neural network (ANN) models. A statistical experimental design was performed to generate the calibration data. First, principal component analysis (PCA) was applied to the original spectral data, and the scores in significant PCs were utilized to calibrate both models. PCR showed poor correlation for beer parameters (R<sup>2</sup> &lt; 0.61). The ANNs showed satisfactory correlations (R<sup>2</sup> = 0.74–0.92) and low relative error considering a variable range (&lt; 9%) for most of the beer-quality attributes, but vicinal diketones (R<sup>2</sup> = 0.56, = 16.69%). Once implemented, this method would be fast and low cost.
DOI: 10.6084/m9.figshare.5230309.v1
title: Rapid monitoring of beer quality attributes based on UV-Vis spectral data

description: This work aimed to determinate eight beer properties using UV-Vis spectrums in combination with principal component regression (PCR) or artificial neural network (ANN) models. A statistical experimental design was performed to generate the calibration data. Firstly, principal component analysis was applied to original spectral data, the scores in significant PCs were utilized to calibrate both models. PCR showed poor correlation for beer parameters (R<sup>2</sup>&lt;0.61). The ANNs showed satisfactory correlations (R<sup>2</sup>=0.74-0.92) and low relative error considering variable range (&lt;9%) for most of the beer quality attributes, but vicinal diketones (R<sup>2</sup>=0.56, =16.69%). Once implemented, this method would be fast and low cost.
DOI: 10.5281/zenodo.4010606
title: Dataset for "Impact of Dust Shortwave Absorbability on the East Asian Summer Monsoon"

description: Dataset for "Impact of Dust Shortwave Absorbability on the East Asian Summer Monsoon"
DOI: 10.6073/pasta/e048414b480a2a1359192f5c8d30dcd1
title: Time series of dissolved methane and carbon dioxide concentrations for Falling Creek Reservoir and Beaverdam Reservoir in southwestern Virginia, USA during 2015-2019

description: Depth profiles of carbon dioxide and methane concentrations were sampled during the ice-free period from 2015 to 2019 in two drinking water reservoirs in southwestern Virginia, USA: Beaverdam Reservoir (Vinton, Virginia) and Falling Creek Reservoir (Vinton, Virginia). Both reservoirs are owned and operated by the Western Virginia Water Authority as primary or secondary drinking water sources for Roanoke, Virginia. The dataset consists of depth profiles of dissolved greenhouse gas (carbon dioxide, methane) samples measured at the deepest site of each reservoir adjacent to the dam. Additional samples were collected at a gauged weir on Falling Creek Reservoir's primary inflow tributary as well as surface samples from a wetland adjacent to Falling Creek Reservoir. At Beaverdam Reservoir, additional samples were collected at the outflow below the dam. The samples were collected approximately fortnightly from March-April, weekly from May-October, and monthly in November at Falling Creek Reservoir and Beaverdam Reservoir.
DOI: 10.6084/m9.figshare.5229913
title: P15194_tandem mass spectra.zip

description: And I will provide tandem mass spectra of a single unique peptide to identify proteins
DOI: 10.6084/m9.figshare.5229898
title: c-fos Immunohistochemistry Protocol

description: <b>Introduction</b>Many studies on memory and learning utilize the immediate early gene c-Fos as an indicator of recent synaptic activity. By quantifying c-Fos positive neurons, we can compare activity across different populations in the brain, and analyze co-labelled neurons with other useful cell markers such as BrdU and Doublecortin.Our lab recently devised an amplification protocol for c-Fos stains that specifically increases the intensity of the signal via a Biotin-Streptavidin-Rhodamine complex (see below). We have demonstrated this amplification protocol is effective over a wide range of primary antibody dilutions, with strong signaling from 1:250 to 1:5000 dilution. Basically, our amplification protocol is a fluorescent dream come true. But don’t just take our word for it, check it out for yourself. Dilutions and amplification conditions are stated in the image filenames.<b>Protocol</b>Day 1:<br>1) 3 x 5 min wash in PBS<br>2) 30 min wash 10% PBS-Triton X (TX) with 3% horse serum<br>3) Add primary antibody for 3-day incubation period (tested range of 1:250 to 1:5000 dilution of c-Fos antibody (Santa Cruz, sc-52-G) in 10% PBS-TX w/ 3% horse serum)Day 2:<br>1) 3 x 5 min wash in PBS-TX<br>2) 1 hour at room temp Secondary Antibody (biotinylated anti-goat 1:250, Jackson Immuno #705-065-147, in 10% PBS-TX w/ 3% horse serum)<br>3) 3 x 5 min wash in PBS<br>4) 30 min Blocking Solution at 5%<br>a) To make blocking solution:<br>- 40 mL PBS<br>- 0.2g blocking powder (Perkin Elmer, FP1020)<br>- Warm to dissolve then cool to room temp before use<br>5) 1:100 Streptavidin Horseradish Peroxidase (Perkin Elmer, NEL750) in Blocking Solution for 1 hour<br>6) 3 x 5 min wash in PBS<br>7) 30 min 1:2000 NHS-Rhodamine (Fisher, PI-46406), in PBS w/ 1:20,000 H2O2<br>8) 2 x 5 min wash in PBS<br>9) 1 x 5 min incubation 1:1000 DAPI in PBS<br>10) 4 x 5 min wash in PBSStaining Recommendation: Incubate any additional primary antibodies separately from amplification Day 2 after adding the Rhodamine (step 7) and completing 3 subsequent PBS washes.
DOI: 10.6084/m9.figshare.5229913.v1
title: P15194_tandem mass spectra.zip

description: And I will provide tandem mass spectra of a single unique peptide to identify proteins
DOI: 10.6084/m9.figshare.5229844
title: NGeo2017_plots.m

description: The code in NGeo2017_plots.m will generate the plots in the main body of the paper Linz et al. 2017 "The strength of the meridional overturning circulation of the stratosphere". The N2O data set starts in late 2004 and is derived from the GOZCARDS data product and the Mauna Loa N2O time series. The tropical heights were determined using the MIPAS temperature and pressure. WACCM SF6 age is a shorter time series than WACCM ideal age because the earlier years were removed so as to avoid extrapolating the reference time series backwards in time. The ERA-I timeseries of overturning circulation strength is also included.<br>
DOI: 10.6084/m9.figshare.5229802
title: Bone Marrow Wnt10b Expression Flow Cytometry

description: Analysis of antibody for the intracellular detection of Wnt10b in bone marrow immune cells by flow cytometry. <b></b>
DOI: 10.6084/m9.figshare.5229844.v1
title: NGeo2017_plots.m

description: The code in NGeo2017_plots.m will generate the plots in the main body of the paper Linz et al. 2017 "The strength of the meridional overturning circulation of the stratosphere". The N2O data set starts in late 2004 and is derived from the GOZCARDS data product and the Mauna Loa N2O time series. The tropical heights were determined using the MIPAS temperature and pressure. WACCM SF6 age is a shorter time series than WACCM ideal age because the earlier years were removed so as to avoid extrapolating the reference time series backwards in time. The ERA-I timeseries of overturning circulation strength is also included.<br>
DOI: 10.6084/m9.figshare.5226496
title: New, previously unreported correlations between latent Toxoplasma gondii infection and excessive ethanol consumption

description: A number of world literature reports indicate that a latent <i>Toxoplasma gondii</i> infection leads to development of central nervous system disorders, which in turn may lead to altered behavior in the affected individuals. <i>T. gondii </i>infection has been observed to play the greatest role in drivers, suicides, and psychiatric patients. Studies conducted for this manuscript involve a different, never before really reported correlation between latent <i>T. gondii</i> infection and ethanol abuse. A total of 538 decedents with a known cause of death were included in the study. These individuals were divided into three groups: the risky behavior group, inconclusively risky behavior group, and control group. The criterion for this division was the likely effect of the individual’s behavior on the mechanism and cause of his/her death. The material used for analyses were blood samples collected during routine medico-legal examinations in these cases. The blood samples were used to measure anti-<i>Toxoplasma</i> IgG antibodies with an enzyme-linked immunosorbent assay (ELISA). Moreover, the following data were recorded for each decedent: sex, age, circumstances of death, cause of death, time from death to autopsy, and (if provided) substance abuse status (alcohol, illicit drugs). In those cases where blood alcohol level or toxicology tests were requested by the Prosecutor’s Office, their results were also included in our analysis. Test results demonstrated a strong correlation between chronic <i>Toxoplasma gondii</i> infestation and engaging in risky behaviors leading to death. Moreover, analyses demonstrated a positive correlation between the presence of anti-<i>T. gondii</i> IgG antibodies and psychoactive substance (especially ethanol) abuse, however, the causal relationship remains unclear. Due to the fact that alcohol abuse constitutes a significant social problem, searching for eliminable risk factors for dependence is extremely important. Our analyses provided new important information on the possible effects of latent <i>T. gondii</i> infection in humans.
DOI: 10.6084/m9.figshare.5226517
title: Screen Shot 2017-07-18 at 11.25.44 AM.png

description: ESIP Discovery Cluster
DOI: 10.6084/m9.figshare.5226517.v1
title: Screen Shot 2017-07-18 at 11.25.44 AM.png

description: ESIP Discovery Cluster
DOI: 10.6084/m9.figshare.5226319
title: fsh.csv

description: Survey
DOI: 10.6084/m9.figshare.5226328
title: EnergyPlus Input Data Files used to test HVAC systems in two buildings in eight different climate regions of Portugal

description: This is a set of EnergyPlus v8.7.0 Input Data Files (IDFs) used to test several HVAC systems in two buildings in eight different climate regions of Portugal.
DOI: 10.6084/m9.figshare.5226496.v2
title: New, previously unreported correlations between latent Toxoplasma gondii infection and excessive ethanol consumption

description: A number of world literature reports indicate that a latent <i>Toxoplasma gondii</i> infection leads to development of central nervous system disorders, which in turn may lead to altered behavior in the affected individuals. <i>T. gondii </i>infection has been observed to play the greatest role in drivers, suicides, and psychiatric patients. Studies conducted for this manuscript involve a different, never before really reported correlation between latent <i>T. gondii</i> infection and ethanol abuse. A total of 538 decedents with a known cause of death were included in the study. These individuals were divided into three groups: the risky behavior group, inconclusively risky behavior group, and control group. The criterion for this division was the likely effect of the individual’s behavior on the mechanism and cause of his/her death. The material used for analyses were blood samples collected during routine medico-legal examinations in these cases. The blood samples were used to measure anti-<i>Toxoplasma</i> IgG antibodies with an enzyme-linked immunosorbent assay (ELISA). Moreover, the following data were recorded for each decedent: sex, age, circumstances of death, cause of death, time from death to autopsy, and (if provided) substance abuse status (alcohol, illicit drugs). In those cases where blood alcohol level or toxicology tests were requested by the Prosecutor’s Office, their results were also included in our analysis. Test results demonstrated a strong correlation between chronic <i>Toxoplasma gondii</i> infestation and engaging in risky behaviors leading to death. Moreover, analyses demonstrated a positive correlation between the presence of anti-<i>T. gondii</i> IgG antibodies and psychoactive substance (especially ethanol) abuse, however, the causal relationship remains unclear. Due to the fact that alcohol abuse constitutes a significant social problem, searching for eliminable risk factors for dependence is extremely important. Our analyses provided new important information on the possible effects of latent <i>T. gondii</i> infection in humans.
DOI: 10.6084/m9.figshare.5226250
title: Friction behaviour of polymeric material

description: The understanding of the friction behaviour of the human skin is indispensable in order to optimize surfaces and materials in contact with the skin. The coefficient of friction for different materials contacting against the skin is mainly influenced by the nature of the materials, mechanical contact parameters and physiological skin conditions. The aim of the present research work was to study the grip effect of two different polymeric materials by producing different textured patterns using a 3D printing micro-fabrication technique. It was found that a difference in friction amplitude exists between the two different polymeric materials and that positive texturing showed higher coefficient of friction than negative texturing (that decreases as the textured pattern area density increases).
DOI: 10.6084/m9.figshare.5226319.v1
title: fsh.csv

description: Survey