cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3467402.v2
title: Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences: Cracid UCE contigs

description: Ultraconserved element (Faircloth et al. 2012) contigs assembled with Trinity. Raw data is served on NCBI SRA.<br>
DOI: 10.6084/m9.figshare.3467378
title: TCGA: Increased oncoprotein coding region mutations correlate with a greater expression of apoptosis-effector genes and a positive outcome for stomach adenocarcinoma

description: Oncogene mutations are primarily thought to facilitate uncontrolled cell growth. However, overexpression of oncoproteins likely leads to apoptosis in a feed forward mechanism, whereby a certain level of oncoprotein leads to the activation of pro-proliferation effector genes and higher levels lead to activation of pro-apoptotic effector genes. TCGA STAD barcodes having no oncoprotein coding region mutations represented reduced expression of the apoptosis-effector genes compared with barcodes with multiple oncoprotein coding region mutations. Furthermore, STAD barcodes in a “no-subsequent tumor” group, representing 224 samples, and in a “positive outcome” group, had more oncoprotein coding regions mutated, on average, than barcodes of the new tumor and negative outcome groups, respectively. BRAF, CTNNB1, KRAS and MTOR coding region mutations (as a group) had the strongest association with the no-subsequent tumor group. Tumor suppressor coding region mutations were also correlated with no-subsequent tumor. These results are consistent with an oncoprotein-mediated, feed-forward mechanism of apoptosis in patients. Importantly, the no-subsequent tumor group also had more overall mutations. This result leads to considerations of unhealthy cells or cells with more neo-antigens for immune rejection. However, a probabilistic aspect of mutagenesis is also consistent with more oncoprotein and tumor suppressor protein mutations, in cases of more overall mutations, and thus a higher likelihood of activation of feed forward apoptosis pathways.
DOI: 10.6084/m9.figshare.3467402.v1
title: Cracid UCE contigs

description: Ultraconserved element (Faircloth et al. 2012) contigs assembled with Trinity. Raw data is served on NCBI SRA.<br>
DOI: 10.6084/m9.figshare.3467378.v1
title: TCGA: Increased oncoprotein coding region mutations correlate with a greater expression of apoptosis-effector genes and a positive outcome for stomach adenocarcinoma

description: Oncogene mutations are primarily thought to facilitate uncontrolled cell growth. However, overexpression of oncoproteins likely leads to apoptosis in a feed forward mechanism, whereby a certain level of oncoprotein leads to the activation of pro-proliferation effector genes and higher levels lead to activation of pro-apoptotic effector genes. TCGA STAD barcodes having no oncoprotein coding region mutations represented reduced expression of the apoptosis-effector genes compared with barcodes with multiple oncoprotein coding region mutations. Furthermore, STAD barcodes in a “no-subsequent tumor” group, representing 224 samples, and in a “positive outcome” group, had more oncoprotein coding regions mutated, on average, than barcodes of the new tumor and negative outcome groups, respectively. BRAF, CTNNB1, KRAS and MTOR coding region mutations (as a group) had the strongest association with the no-subsequent tumor group. Tumor suppressor coding region mutations were also correlated with no-subsequent tumor. These results are consistent with an oncoprotein-mediated, feed-forward mechanism of apoptosis in patients. Importantly, the no-subsequent tumor group also had more overall mutations. This result leads to considerations of unhealthy cells or cells with more neo-antigens for immune rejection. However, a probabilistic aspect of mutagenesis is also consistent with more oncoprotein and tumor suppressor protein mutations, in cases of more overall mutations, and thus a higher likelihood of activation of feed forward apoptosis pathways.
DOI: 10.6084/m9.figshare.3467216
title: 96well plate

description: 96well tissue culture plate
DOI: 10.6084/m9.figshare.3467201
title: Supplementary Material for: FABP1 and FABP3 Have High Predictive Values for Renal Replacement Therapy in Patients with Acute Kidney Injury

description: <b><i>Background/Aims:</i></b> Early initiation of renal replacement therapy (RRT) is recommended in order to improve the clinical outcome of patients who develop an acute kidney injury (AKI). However, markers that guide an early RRT initiation do not really exist currently. <b><i>Methods:</i></b> Urine and serum samples were prospectively collected from 120 AKI patients. Depending on the necessity of initiating RRT, patients were divided into 2 different groups: dialysis (n = 52) and non-dialysis (n = 68). <b><i>Results:</i></b> Comparative urinary proteomic analyses identified 4 different proteins (fatty acid binding proteins 1 and 3 (FABP1 and FABP3), β-2-microglobulin (B2M), cystatin-M (CST6)) that discriminate AKI patients with high risk for RRT. Western blot analysis confirmed the proteomics data for FABP1 and FABP3 but not for B2M and CST6. Validation analysis confirmed that the FABP1 and FABP3 fulfilled the requirement of functioning as markers for AKI patients with risk to dialysis (p &lt; 0.001). <b><i>Conclusion:</i></b> The release of high amounts of FABP1 and FABP3 in urine of AKI patients could serve as a diagnostic/prognosis marker for RRT initiation in these patients.
DOI: 10.6084/m9.figshare.3467201.v1
title: Supplementary Material for: FABP1 and FABP3 Have High Predictive Values for Renal Replacement Therapy in Patients with Acute Kidney Injury

description: <b><i>Background/Aims:</i></b> Early initiation of renal replacement therapy (RRT) is recommended in order to improve the clinical outcome of patients who develop an acute kidney injury (AKI). However, markers that guide an early RRT initiation do not really exist currently. <b><i>Methods:</i></b> Urine and serum samples were prospectively collected from 120 AKI patients. Depending on the necessity of initiating RRT, patients were divided into 2 different groups: dialysis (n = 52) and non-dialysis (n = 68). <b><i>Results:</i></b> Comparative urinary proteomic analyses identified 4 different proteins (fatty acid binding proteins 1 and 3 (FABP1 and FABP3), β-2-microglobulin (B2M), cystatin-M (CST6)) that discriminate AKI patients with high risk for RRT. Western blot analysis confirmed the proteomics data for FABP1 and FABP3 but not for B2M and CST6. Validation analysis confirmed that the FABP1 and FABP3 fulfilled the requirement of functioning as markers for AKI patients with risk to dialysis (p &lt; 0.001). <b><i>Conclusion:</i></b> The release of high amounts of FABP1 and FABP3 in urine of AKI patients could serve as a diagnostic/prognosis marker for RRT initiation in these patients.
DOI: 10.6084/m9.figshare.3467090
title: Can LEDs help with art conservation? – Impact of different light spectra on paint pigment degradation

description: The impact of the spectral composition of light on the discoloration of paint pigments has been investigated for the case of lead chromate sulfate, an unstable yellow pigment used by Vincent van Gogh and other painters. With LEDification, museum lighting is moving from using halogen to LED lamps. LED light sources have a significantly different spectral composition than halogen lamps. To understand the impact of these differences on pigment stability, the wavelength dependence of pigment discoloration was determined. Contrary to the expectation that lower wavelength photons induce more damage than higher wavelength ones, UV (394 nm), blue, and cyan light all lead to similar levels of discoloration of a pigment for the same level of radiant power. By understanding this wavelength dependence, it becomes possible to create white light LED lamps with a spectral composition tuned to minimize the degradation effect. An existing LED solution with a modified emission indeed resulted in 30% less color change in the experiment than halogen. Furthermore, a method is proposed to optimize the LED spectra by tuning to the properties of each specific artifact. Simulations show that this can reduce the damage of the light source by 45% in specific cases.
DOI: 10.6084/m9.figshare.3467090.v1
title: Can LEDs help with art conservation? – Impact of different light spectra on paint pigment degradation

description: The impact of the spectral composition of light on the discoloration of paint pigments has been investigated for the case of lead chromate sulfate, an unstable yellow pigment used by Vincent van Gogh and other painters. With LEDification, museum lighting is moving from using halogen to LED lamps. LED light sources have a significantly different spectral composition than halogen lamps. To understand the impact of these differences on pigment stability, the wavelength dependence of pigment discoloration was determined. Contrary to the expectation that lower wavelength photons induce more damage than higher wavelength ones, UV (394 nm), blue, and cyan light all lead to similar levels of discoloration of a pigment for the same level of radiant power. By understanding this wavelength dependence, it becomes possible to create white light LED lamps with a spectral composition tuned to minimize the degradation effect. An existing LED solution with a modified emission indeed resulted in 30% less color change in the experiment than halogen. Furthermore, a method is proposed to optimize the LED spectra by tuning to the properties of each specific artifact. Simulations show that this can reduce the damage of the light source by 45% in specific cases.
DOI: 10.6084/m9.figshare.3466979
title: Supplementary Material for: Development and Validation of a Simple Diagnostic Method to Detect Gain and Loss of Function Defects in Fibroblast Growth Factor-23

description: <b><i>Background:</i></b> Fibroblast growth factor-23 (FGF23) is a bone-derived hormone that regulates the homeostasis of phosphate and vitamin D. Three substitutions in the hormone are reported to cause autosomal dominant hypophosphatemic rickets and seven substitutions to cause autosomal recessive hyperphosphatemic familial tumoral calcinosis (HFTC). Both disorders are rare in the general population and occur most often in the Eastern Mediterranean region and Africa. None of the mutations could be identified using standard restriction fragment length polymorphism. The only technique currently available to confirm the clinical diagnosis is DNA sequencing. <b><i>Methods:</i></b> Using a tri-primer ARMS-PCR, in vitro site-directed mutagenesis and DNA sequencing, we developed, verified and validated a rapid and reliable diagnostic test for the ten mutations in <i>FGF23</i>. <b><i>Results:</i></b> We generated a test for all ten mutations and confirmed each test by DNA sequencing. We increased the specificity of the test by introducing a mismatch at position -2 in the 3′-terminus of the reverse primer of the normal and the mutant sequences. Finally, using DNA sequencing, we validated the technique for FGF23/S129F substitution by testing samples from 80 individuals from two unrelated Arab families harboring HFTC. <b><i>Conclusions:</i></b> This inexpensive and specific method could be adopted where DNA sequencing is not available or affordable.
DOI: 10.6084/m9.figshare.3466979.v1
title: Supplementary Material for: Development and Validation of a Simple Diagnostic Method to Detect Gain and Loss of Function Defects in Fibroblast Growth Factor-23

description: <b><i>Background:</i></b> Fibroblast growth factor-23 (FGF23) is a bone-derived hormone that regulates the homeostasis of phosphate and vitamin D. Three substitutions in the hormone are reported to cause autosomal dominant hypophosphatemic rickets and seven substitutions to cause autosomal recessive hyperphosphatemic familial tumoral calcinosis (HFTC). Both disorders are rare in the general population and occur most often in the Eastern Mediterranean region and Africa. None of the mutations could be identified using standard restriction fragment length polymorphism. The only technique currently available to confirm the clinical diagnosis is DNA sequencing. <b><i>Methods:</i></b> Using a tri-primer ARMS-PCR, in vitro site-directed mutagenesis and DNA sequencing, we developed, verified and validated a rapid and reliable diagnostic test for the ten mutations in <i>FGF23</i>. <b><i>Results:</i></b> We generated a test for all ten mutations and confirmed each test by DNA sequencing. We increased the specificity of the test by introducing a mismatch at position -2 in the 3′-terminus of the reverse primer of the normal and the mutant sequences. Finally, using DNA sequencing, we validated the technique for FGF23/S129F substitution by testing samples from 80 individuals from two unrelated Arab families harboring HFTC. <b><i>Conclusions:</i></b> This inexpensive and specific method could be adopted where DNA sequencing is not available or affordable.
DOI: 10.6084/m9.figshare.3466946
title: PLOS ONE repository data.xlsx

description: Data extracted from Cochrane Reviews and Crossover trials for use in the publication:<br>Nolan SJ, Hambleton I, Dwan K. The use and reporting of the cross-over study design in clinical trials and systematic reviews: a systematic assessment. PLOS ONE (accepted)
DOI: 10.6084/m9.figshare.3466946.v2
title: PLOS ONE repository data.xlsx

description: Data extracted from Cochrane Reviews and Crossover trials for use in the publication:<br>Nolan SJ, Hambleton I, Dwan K. The use and reporting of the cross-over study design in clinical trials and systematic reviews: a systematic assessment. PLOS ONE (accepted)
DOI: 10.6084/m9.figshare.3466946.v1
title: PLOS ONE repository data.xlsx

description: Data extracted from Cochrane Reviews and Crossover trials for use in the publication:<br>Nolan SJ, Hambleton I, Dwan K. The use and reporting of the cross-over study design in clinical trials and systematic reviews: a systematic assessment. PLOS ONE (accepted)
DOI: 10.6084/m9.figshare.3466871
title: Supplementary Material for: Lobular Breast Cancer and Abdominal Metastases: A Retrospective Review and Impact on Survival

description: <b><i>Background:</i></b> The predominant breast cancer subtypes, invasive lobular carcinoma (ILC) and invasive ductal carcinoma (IDC), have similar recurrence and survival rates but differing patterns of metastatic recurrence. <b><i>Methods:</i></b> A retrospective review of breast cancers treated at an academic medical center from 1999 to 2012 was performed. Demographic, pathologic, treatment, and follow-up data were collected for 179 ILC and 358 IDC patients (1:2 stage-matched). The median follow-up was 4.7 years. <b><i>Results:</i></b> The baseline characteristics were similar in the two groups. ILC was more likely to be hormone-receptor-positive/HER2-negative and mammographically occult. The number of surgical resections, breast conservation rate, systemic treatment, and taxane use was similar between the groups. The overall recurrence rate was the same. ILC recurred more often in the abdominal cavity (24.3% in ILC vs. 4.1% in IDC, p = 0.001). The disease-free survival and overall survival were equal. On multivariate analysis, age, stage of disease, hormone receptor status, and systemic therapy were associated with survival, but histology was not. <b><i>Conclusions:</i></b> Compared to ductal breast cancers, lobular breast cancers recur more often in the abdominal cavity. Both ILC and IDC have comparable surgical and medical treatment outcomes and survival. Our data suggest that enhanced surveillance and imaging might be useful in ILC.
DOI: 10.6084/m9.figshare.3466871.v1
title: Supplementary Material for: Lobular Breast Cancer and Abdominal Metastases: A Retrospective Review and Impact on Survival

description: <b><i>Background:</i></b> The predominant breast cancer subtypes, invasive lobular carcinoma (ILC) and invasive ductal carcinoma (IDC), have similar recurrence and survival rates but differing patterns of metastatic recurrence. <b><i>Methods:</i></b> A retrospective review of breast cancers treated at an academic medical center from 1999 to 2012 was performed. Demographic, pathologic, treatment, and follow-up data were collected for 179 ILC and 358 IDC patients (1:2 stage-matched). The median follow-up was 4.7 years. <b><i>Results:</i></b> The baseline characteristics were similar in the two groups. ILC was more likely to be hormone-receptor-positive/HER2-negative and mammographically occult. The number of surgical resections, breast conservation rate, systemic treatment, and taxane use was similar between the groups. The overall recurrence rate was the same. ILC recurred more often in the abdominal cavity (24.3% in ILC vs. 4.1% in IDC, p = 0.001). The disease-free survival and overall survival were equal. On multivariate analysis, age, stage of disease, hormone receptor status, and systemic therapy were associated with survival, but histology was not. <b><i>Conclusions:</i></b> Compared to ductal breast cancers, lobular breast cancers recur more often in the abdominal cavity. Both ILC and IDC have comparable surgical and medical treatment outcomes and survival. Our data suggest that enhanced surveillance and imaging might be useful in ILC.
DOI: 10.6084/m9.figshare.3466853
title: AlfaxaloneNWRresponses

description: Please refer to the accompanying readme text files for information.
DOI: 10.6084/m9.figshare.3466853.v1
title: AlfaxaloneNWRresponses

description: Please refer to the accompanying readme text files for information.
DOI: 10.6084/m9.figshare.3466844
title: Capacity Vs B for E=1.5J

description: Capacity Vs Bx for E=1.5J, L=25, D=-25 E. The second dataset shows the capacity as a function of Bz when Bx=sqrt(-2DE).
DOI: 10.6084/m9.figshare.3466844.v1
title: Capacity Vs B for E=1.5J

description: Capacity Vs Bx for E=1.5J, L=25, D=-25 E. The second dataset shows the capacity as a function of Bz when Bx=sqrt(-2DE).
DOI: 10.6084/m9.figshare.3466835
title: Capacity Vs B/E

description: Capacity as a function of B, for L=25, D=-25E, E=0.5J. Second data set shows the capacity as a function of D when B_x=sqrt(-2DE)
DOI: 10.6084/m9.figshare.3466835.v1
title: Capacity Vs B/E

description: Capacity as a function of B, for L=25, D=-25E, E=0.5J. Second data set shows the capacity as a function of D when B_x=sqrt(-2DE)
DOI: 10.6084/m9.figshare.3466829
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - TW5 (3/3)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3466829.v1
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - TW5 (3/3)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3466826
title: Capacity and Gap vs Bx/E

description: Capacity (2nd column) and Gap (3rd column) vs B/E (first column) for S=1, L=6, D=-25E, and either E=0.5J or E=1.5J as a function of Bx/E
DOI: 10.6084/m9.figshare.3466826.v1
title: Capacity and Gap vs Bx/E

description: Capacity (2nd column) and Gap (3rd column) vs B/E (first column) for S=1, L=6, D=-25E, and either E=0.5J or E=1.5J as a function of Bx/E
DOI: 10.6084/m9.figshare.3466811
title: Capacity Vs E, for either D=-7E or D=-15E

description: Capacity Vs E, for either D=-7E or D=-15E, FM and AFM chains, and different values of the spin: S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466811.v1
title: Capacity Vs E, for either D=-7E or D=-15E

description: Capacity Vs E, for either D=-7E or D=-15E, FM and AFM chains, and different values of the spin: S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466793
title: Capacity Vs Length, D=-5

description: Capacity vs Length, for D=-5, B0=100 and different values of S: S=1, S=3/2
DOI: 10.6084/m9.figshare.3466793.v1
title: Capacity Vs Length, D=-5

description: Capacity vs Length, for D=-5, B0=100 and different values of S: S=1, S=3/2
DOI: 10.6084/m9.figshare.3466787
title: Capacity Vs Length D=-1.5

description: Capacity vs Length, for D=-1.5, B0=100 and different values of S: S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466787.v1
title: Capacity Vs Length D=-1.5

description: Capacity vs Length, for D=-1.5, B0=100 and different values of S: S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466781
title: Capacity Vs Length, D=-0.5

description: Capacity vs Length, for D=-0.5, B0=100 and different values of S: S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466781.v1
title: Capacity Vs Length, D=-0.5

description: Capacity vs Length, for D=-0.5, B0=100 and different values of S: S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466769
title: Capacity Vs Length D=0

description: Capacity vs Length, for D=0, B0=100 and different values of S: S=1/2, S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466769.v1
title: Capacity Vs Length D=0

description: Capacity vs Length, for D=0, B0=100 and different values of S: S=1/2, S=1, S=3/2 and S=2
DOI: 10.6084/m9.figshare.3466742
title: Facial features of abstract virtual characters.

description: This dataset is connected to the paper: <br>Do I trust you, abstract creature?: A study on personality perception of abstractvirtual faces. Ferstl Y., Kokkinara E., McDonnell R., Proceeding of Symposium of Applied Perception 2016
DOI: 10.6084/m9.figshare.3466742.v1
title: Facial features of abstract virtual characters.

description: This dataset is connected to the paper: <br>Do I trust you, abstract creature?: A study on personality perception of abstractvirtual faces. Ferstl Y., Kokkinara E., McDonnell R., Proceeding of Symposium of Applied Perception 2016