cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3636990.v1
title: Supplementary Material for: Contribution of IVIM to Conventional Dynamic Contrast-Enhanced and Diffusion-Weighted MRI in Differentiating Benign from Malignant Breast Masses

description: <b><i>Background:</i></b> The aim of this study was to determine whether the indicators obtained from intravoxel incoherent motion (IVIM) imaging can improve the characterization of benign and malignant breast masses compared with conventional dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted magnetic resonance imaging (DW-MRI). <b><i>Patients and Methods:</i></b> This study included 23 benign and 31 malignant breast masses of 48 patients. Main indicators were initial enhancement ratio (IER), time-signal intensity curve (TIC), apparent diffusion coefficient (ADC), tissue diffusivity (D), pseudodiffusivity (D*), and perfusion fraction (f). The discriminative abilities of the different models were compared by means of receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) analysis. <b><i>Results:</i></b> D had the highest AUC (0.980), sensitivity (93.55%), specificity (100%), and diagnostic accuracy (96.36%). Both D and TIC could provide the independent predicted features for malignant breast masses. The combination of D and TIC had an AUC of up to 0.990. <b><i>Conclusion:</i></b> D of IVIM can effectively complement existing conventional DCE-MRI and DW-MRI in differentiating malignant from benign breast masses. IVIM combined with DCE-MRI is a robust means of evaluating breast masses.
DOI: 10.6084/m9.figshare.3635808
title: Authors from the periphery countries choose open access more often (preprint)

description: This is a preprint. The final, published version of this article is here: http://onlinelibrary.wiley.com/doi/10.1002/leap.1093/full<br><br>In this article I analyse attitudes of academic authors toward open access and frequency of choosing open access publication venues by them. I characterize differences between authors based in the periphery countries and the core countries, with regard to choosing so called gold open access as a way of publishing academic articles. The data were obtained with an on-line survey. Emails containing links to the survey were sent to 107,296 scholars listed on the mailing lists belonging to De Gruyter Open, from December 2015 to January 2016. 1012 responses were received. Authors from the periphery countries publish their articles in gold open access more often. They also pay open access publication fees equally often as those based in the core countries. The reasons for that are complex, involving both their preference to publish in open access and the composition of publishing market in the periphery. <br>
DOI: 10.6084/m9.figshare.3635808.v1
title: Authors from the periphery countries choose open access more often

description: In this article I analyse attitudes of academic authors toward open access and frequency of choosing open access publication venues by them. I characterize differences between authors based in the periphery countries and the core countries, with regard to choosing so called gold open access as a way of publishing academic articles. The data were obtained with an on-line survey. Emails containing links to the survey were sent to 107,296 scholars listed on the mailing lists belonging to De Gruyter Open, from December 2015 to January 2016. 1012 responses were received. Authors from the periphery countries publish their articles in gold open access more often. They also pay open access publication fees equally often as those based in the core countries. The reasons for that are complex, involving both their preference to publish in open access and the composition of publishing market in the periphery. <br>
DOI: 10.6084/m9.figshare.3635805
title: What is quantum information? Information symmetry and mechanical motion

description: 2nd PORTUGUESE CONGRESS OF PHILOSOPHYPorto, Portugal: 8-9 September 2016 (14: 30, 8 Sep, room 201)University of Porto - Faculdade de Letras
DOI: 10.6084/m9.figshare.3635805.v3
title: What is quantum information? Information symmetry and mechanical motion

description: 2nd PORTUGUESE CONGRESS OF PHILOSOPHYPorto, Portugal: 8-9 September 2016 (14: 30, 8 Sep, room 201)University of Porto - Faculdade de Letras
DOI: 10.6084/m9.figshare.3635805.v2
title: What is quantum information? Information symmetry and mechanical motion

description: 2nd PORTUGUESE CONGRESS OF PHILOSOPHYPorto, Portugal: 8-9 September 2016 (14: 30, 8 Sep, room 201)University of Porto - Faculdade de Letras
DOI: 10.6084/m9.figshare.3635739
title: PowerPoint Slides for: Genotype/Phenotype Analysis in 67 Chinese Patients with Gitelman's Syndrome

description: <b><i>Background:</i></b> Gitelman's syndrome (GS) is an autosomal recessive renal tubular disorder, which is caused by the mutations in <i>SLC12A3</i>. This study was designed to analyze the characteristics of the genotype and phenotype, and follow-up in the largest group of Chinese patients with GS. <b><i>Methods:</i></b> Sixty-seven patients with GS underwent <i>SLCl2A3</i> analysis, and their clinical characteristics and biochemical findings as well as follow-up were reviewed, aiming to achieve a better description of GS. Additionally, the association of genotype and phenotype was explored. <b><i>Results:</i></b> Forty-one different mutations were identified within these 67 GS patients, including 11 novel mutations and 5 recurrent ones. Typical hypocalciuria and hypomagnesemia were not found in 6 (9%) and 8 (11.9%) patients, respectively. Male patients and those harboring severe mutations in both alleles had significant higher urinary fractional excretion (FE) of potassium, magnesium and chlorine. In addition, there were 2 patients who had chronic kidney disease (estimated glomerular filtration rate &lt;60 ml/min/1.73 m<sup>2</sup>) and 32 patients with abnormal glucose metabolism. <b><i>Conclusions:</i></b> We identified 41 mutations related to GS, containing 11 novel variants and 5 high-frequency ones, which should facilitate earlier and more accurate diagnosis of GS. FE of electrolytes in urine may be more sensitive in the phenotype evaluation and differential diagnosis than corresponding serum electrolytes. Hypokalemia and hypomagnesemia in GS were difficult to correct; however, spironolactone might be helpful for hypokalemia to some degree. Compared with normal people, patients with GS were at higher risk of developing type 2 diabetes.
DOI: 10.6084/m9.figshare.3635739.v1
title: PowerPoint Slides for: Genotype/Phenotype Analysis in 67 Chinese Patients with Gitelman's Syndrome

description: <b><i>Background:</i></b> Gitelman's syndrome (GS) is an autosomal recessive renal tubular disorder, which is caused by the mutations in <i>SLC12A3</i>. This study was designed to analyze the characteristics of the genotype and phenotype, and follow-up in the largest group of Chinese patients with GS. <b><i>Methods:</i></b> Sixty-seven patients with GS underwent <i>SLCl2A3</i> analysis, and their clinical characteristics and biochemical findings as well as follow-up were reviewed, aiming to achieve a better description of GS. Additionally, the association of genotype and phenotype was explored. <b><i>Results:</i></b> Forty-one different mutations were identified within these 67 GS patients, including 11 novel mutations and 5 recurrent ones. Typical hypocalciuria and hypomagnesemia were not found in 6 (9%) and 8 (11.9%) patients, respectively. Male patients and those harboring severe mutations in both alleles had significant higher urinary fractional excretion (FE) of potassium, magnesium and chlorine. In addition, there were 2 patients who had chronic kidney disease (estimated glomerular filtration rate &lt;60 ml/min/1.73 m<sup>2</sup>) and 32 patients with abnormal glucose metabolism. <b><i>Conclusions:</i></b> We identified 41 mutations related to GS, containing 11 novel variants and 5 high-frequency ones, which should facilitate earlier and more accurate diagnosis of GS. FE of electrolytes in urine may be more sensitive in the phenotype evaluation and differential diagnosis than corresponding serum electrolytes. Hypokalemia and hypomagnesemia in GS were difficult to correct; however, spironolactone might be helpful for hypokalemia to some degree. Compared with normal people, patients with GS were at higher risk of developing type 2 diabetes.
DOI: 10.6084/m9.figshare.3635727
title: PowerPoint Slides for: A Double-Blind, Placebo Controlled, Randomized Phase 1 Cross-Over Study with ALLN-177, an Orally Administered Oxalate Degrading Enzyme

description: <b><i>Background:</i></b> Hyperoxaluria may result from increased endogenous production or overabsorption of dietary oxalate in the gastrointestinal tract leading to nephrolithiasis and, in some, to oxalate nephropathy and chronic kidney disease. ALLN-177 is an oral formulation of a recombinant, oxalate specific, microbial enzyme oxalate decarboxylase intended to treat secondary hyperoxaluria by degrading dietary oxalate in the gastrointestinal tract, thereby reducing its absorption and subsequent excretion in the urine. <b><i>Methods:</i></b> This double-blind, placebo controlled, randomized, cross-over, phase 1 study of ALLN-177 evaluated the tolerability of ALLN-177 and its effect on urinary oxalate excretion in 30 healthy volunteers with hyperoxaluria induced by ingestion of a high oxalate, low calcium (HOLC) diet. The primary end point was the difference in the mean 24-hour urinary oxalate excretion during the ALLN-177 treatment period compared with the placebo treatment period. <b><i>Results:</i></b> The daily urinary oxalate excretion increased in the study population from 27.2 ± 9.5 mg/day during screening to 80.8 ± 24.1 mg/day (mean ± SD) on the HOLC diet before introducing ALLN-177 or placebo therapy for 7 days. Compared to placebo, ALLN-177 treatment reduced urinary oxalate by 11.6 ± 2.7 mg/day, p = 0.0002 (least squares mean ± SD). <b><i>Conclusions:</i></b> In healthy volunteers, with diet-induced hyperoxaluria treatment with ALLN-177, when compared to placebo, significantly reduced urinary oxalate excretion by degrading dietary oxalate in the gastrointestinal tract and thereby reducing its absorption. ALLN-177 may represent a new approach for managing secondary hyperoxaluria and its complications.
DOI: 10.6084/m9.figshare.3635727.v1
title: PowerPoint Slides for: A Double-Blind, Placebo Controlled, Randomized Phase 1 Cross-Over Study with ALLN-177, an Orally Administered Oxalate Degrading Enzyme

description: <b><i>Background:</i></b> Hyperoxaluria may result from increased endogenous production or overabsorption of dietary oxalate in the gastrointestinal tract leading to nephrolithiasis and, in some, to oxalate nephropathy and chronic kidney disease. ALLN-177 is an oral formulation of a recombinant, oxalate specific, microbial enzyme oxalate decarboxylase intended to treat secondary hyperoxaluria by degrading dietary oxalate in the gastrointestinal tract, thereby reducing its absorption and subsequent excretion in the urine. <b><i>Methods:</i></b> This double-blind, placebo controlled, randomized, cross-over, phase 1 study of ALLN-177 evaluated the tolerability of ALLN-177 and its effect on urinary oxalate excretion in 30 healthy volunteers with hyperoxaluria induced by ingestion of a high oxalate, low calcium (HOLC) diet. The primary end point was the difference in the mean 24-hour urinary oxalate excretion during the ALLN-177 treatment period compared with the placebo treatment period. <b><i>Results:</i></b> The daily urinary oxalate excretion increased in the study population from 27.2 ± 9.5 mg/day during screening to 80.8 ± 24.1 mg/day (mean ± SD) on the HOLC diet before introducing ALLN-177 or placebo therapy for 7 days. Compared to placebo, ALLN-177 treatment reduced urinary oxalate by 11.6 ± 2.7 mg/day, p = 0.0002 (least squares mean ± SD). <b><i>Conclusions:</i></b> In healthy volunteers, with diet-induced hyperoxaluria treatment with ALLN-177, when compared to placebo, significantly reduced urinary oxalate excretion by degrading dietary oxalate in the gastrointestinal tract and thereby reducing its absorption. ALLN-177 may represent a new approach for managing secondary hyperoxaluria and its complications.
DOI: 10.6084/m9.figshare.3635727.v3
title: PowerPoint Slides for: A Double-Blind, Placebo Controlled, Randomized Phase 1 Cross-Over Study with ALLN-177, an Orally Administered Oxalate Degrading Enzyme

description: <b><i>Background:</i></b> Hyperoxaluria may result from increased endogenous production or overabsorption of dietary oxalate in the gastrointestinal tract leading to nephrolithiasis and, in some, to oxalate nephropathy and chronic kidney disease. ALLN-177 is an oral formulation of a recombinant, oxalate specific, microbial enzyme oxalate decarboxylase intended to treat secondary hyperoxaluria by degrading dietary oxalate in the gastrointestinal tract, thereby reducing its absorption and subsequent excretion in the urine. <b><i>Methods:</i></b> This double-blind, placebo controlled, randomized, cross-over, phase 1 study of ALLN-177 evaluated the tolerability of ALLN-177 and its effect on urinary oxalate excretion in 30 healthy volunteers with hyperoxaluria induced by ingestion of a high oxalate, low calcium (HOLC) diet. The primary end point was the difference in the mean 24-hour urinary oxalate excretion during the ALLN-177 treatment period compared with the placebo treatment period. <b><i>Results:</i></b> The daily urinary oxalate excretion increased in the study population from 27.2 ± 9.5 mg/day during screening to 80.8 ± 24.1 mg/day (mean ± SD) on the HOLC diet before introducing ALLN-177 or placebo therapy for 7 days. Compared to placebo, ALLN-177 treatment reduced urinary oxalate by 11.6 ± 2.7 mg/day, p = 0.0002 (least squares mean ± SD). <b><i>Conclusions:</i></b> In healthy volunteers, with diet-induced hyperoxaluria treatment with ALLN-177, when compared to placebo, significantly reduced urinary oxalate excretion by degrading dietary oxalate in the gastrointestinal tract and thereby reducing its absorption. ALLN-177 may represent a new approach for managing secondary hyperoxaluria and its complications.
DOI: 10.6084/m9.figshare.3635727.v2
title: PowerPoint Slides for: A Double-Blind, Placebo Controlled, Randomized Phase 1 Cross-Over Study with ALLN-177, an Orally Administered Oxalate Degrading Enzyme

description: <b><i>Background:</i></b> Hyperoxaluria may result from increased endogenous production or overabsorption of dietary oxalate in the gastrointestinal tract leading to nephrolithiasis and, in some, to oxalate nephropathy and chronic kidney disease. ALLN-177 is an oral formulation of a recombinant, oxalate specific, microbial enzyme oxalate decarboxylase intended to treat secondary hyperoxaluria by degrading dietary oxalate in the gastrointestinal tract, thereby reducing its absorption and subsequent excretion in the urine. <b><i>Methods:</i></b> This double-blind, placebo controlled, randomized, cross-over, phase 1 study of ALLN-177 evaluated the tolerability of ALLN-177 and its effect on urinary oxalate excretion in 30 healthy volunteers with hyperoxaluria induced by ingestion of a high oxalate, low calcium (HOLC) diet. The primary end point was the difference in the mean 24-hour urinary oxalate excretion during the ALLN-177 treatment period compared with the placebo treatment period. <b><i>Results:</i></b> The daily urinary oxalate excretion increased in the study population from 27.2 ± 9.5 mg/day during screening to 80.8 ± 24.1 mg/day (mean ± SD) on the HOLC diet before introducing ALLN-177 or placebo therapy for 7 days. Compared to placebo, ALLN-177 treatment reduced urinary oxalate by 11.6 ± 2.7 mg/day, p = 0.0002 (least squares mean ± SD). <b><i>Conclusions:</i></b> In healthy volunteers, with diet-induced hyperoxaluria treatment with ALLN-177, when compared to placebo, significantly reduced urinary oxalate excretion by degrading dietary oxalate in the gastrointestinal tract and thereby reducing its absorption. ALLN-177 may represent a new approach for managing secondary hyperoxaluria and its complications.
DOI: 10.6084/m9.figshare.3635721
title: PowerPoint Slides for: Plasma Exchange as an Adjunctive Therapy for Crescentic IgA Nephropathy

description: <b><i>Background:</i></b> Crescentic IgA nephropathy (CreIgAN) has a poor prognosis despite aggressive immunosuppressive therapy. The efficacy of plasma exchange (PE) in CreIgAN is not well defined. <b><i>Methods:</i></b> Twelve patients with severe CreIgAN who received PE as addition to routine immunosuppressive therapy, followed for more than 6 months, were involved. Twelve matched historical controls who received immunosuppressive therapy alone were selected by propensity score matching. Renal survival, plasma IgA-IgG complex and active complement products were assessed. <b><i>Results:</i></b> Nine men and 3 women received a median of 7 PE courses (range 5-10). Their baseline urine protein excretion rate was 5.8 (4.5-8.7) g/day, and their serum creatinine level was 705.3 ± 296.4 μmol/l. During a mean follow-up of 15.6 months (6-51 months), 6 of the 12 PE group patients were free of dialysis, while all the control patients were dialysis dependent (6 of 12 vs. 0 of 12, p = 0.014). In the PE group, dialysis had to be restarted for 1 patient owing to the development of severe pneumonia and pulmonary failure. PE was associated with a higher kidney survival rate (log rank test, p = 0.026) during follow-up. It also significantly decreased plasma IgA-IgG complex levels (pre-PE: 85.3 ± 25.9% vs. post-PE: 38.4 ± 12.4%, p &lt; 0.001) and plasma and urinary active complement product levels, including C3a, C5a and soluble C5b-9. The latter levels remained low until the last follow-up. <b><i>Conclusion:</i></b> This study indicated that PE could increase renal recovery rates in severe CreIgAN.
DOI: 10.6084/m9.figshare.3635721.v1
title: PowerPoint Slides for: Plasma Exchange as an Adjunctive Therapy for Crescentic IgA Nephropathy

description: <b><i>Background:</i></b> Crescentic IgA nephropathy (CreIgAN) has a poor prognosis despite aggressive immunosuppressive therapy. The efficacy of plasma exchange (PE) in CreIgAN is not well defined. <b><i>Methods:</i></b> Twelve patients with severe CreIgAN who received PE as addition to routine immunosuppressive therapy, followed for more than 6 months, were involved. Twelve matched historical controls who received immunosuppressive therapy alone were selected by propensity score matching. Renal survival, plasma IgA-IgG complex and active complement products were assessed. <b><i>Results:</i></b> Nine men and 3 women received a median of 7 PE courses (range 5-10). Their baseline urine protein excretion rate was 5.8 (4.5-8.7) g/day, and their serum creatinine level was 705.3 ± 296.4 μmol/l. During a mean follow-up of 15.6 months (6-51 months), 6 of the 12 PE group patients were free of dialysis, while all the control patients were dialysis dependent (6 of 12 vs. 0 of 12, p = 0.014). In the PE group, dialysis had to be restarted for 1 patient owing to the development of severe pneumonia and pulmonary failure. PE was associated with a higher kidney survival rate (log rank test, p = 0.026) during follow-up. It also significantly decreased plasma IgA-IgG complex levels (pre-PE: 85.3 ± 25.9% vs. post-PE: 38.4 ± 12.4%, p &lt; 0.001) and plasma and urinary active complement product levels, including C3a, C5a and soluble C5b-9. The latter levels remained low until the last follow-up. <b><i>Conclusion:</i></b> This study indicated that PE could increase renal recovery rates in severe CreIgAN.
DOI: 10.6084/m9.figshare.3635718
title: code, dataset, result

description: Complex Detection in Dynamic PPI Network via Edge-Weighted Genes Co-Expression Analysis<br>It includes 2 data sets and java source file for our method
DOI: 10.6084/m9.figshare.3635718.v1
title: src.zip

description: for paper
DOI: 10.6084/m9.figshare.3635709
title: EMAmplitude.java

description: 1234
DOI: 10.6084/m9.figshare.3635298
title: Data for Johnson (2016), Gravel threshold of motion: a state function of sediment transport disequilibrium? ESurf, doi:10.5194/esurf-4-1-2016

description: This figshare item contains matlab mfiles and data files that that allow some figures from my paper to be made; this serves as a data repository for this work.
DOI: 10.6084/m9.figshare.3635298.v1
title: Data for Johnson (2016), Gravel threshold of motion: a state function of sediment transport disequilibrium? ESurf, doi:10.5194/esurf-4-1-2016

description: This figshare item contains matlab mfiles and data files that that allow some figures from my paper to be made; this serves as a data repository for this work.
DOI: 10.6084/m9.figshare.3629055
title: Reverse Sequences for Hepatopancreas

description: Illumina Raw Sequences (R2) for Hepatopancreas of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3629055.v1
title: Reverse Sequences for Hepatopancreas

description: Illumina Raw Sequences (R2) for Hepatopancreas of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628869
title: Forward Sequences for Hepatopancreas

description: Illumina Raw Sequences (R1) for Hepatopancreas of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628869.v1
title: Forward Sequences for Hepatopancreas

description: Illumina Raw Sequences (R1) for Hepatopancreas of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628665
title: Reverse Sequences for Antennal Gland

description: Illumina Raw Sequences (R2) for Antennal Gland of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628665.v1
title: Reverse Sequences for Antennal Gland

description: Illumina Raw Sequences (R2) for Antennal Gland of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628464
title: Forward Sequences for Antennal Gland

description: Illumina Raw Sequences (R1) for Antennal Gland of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628464.v1
title: Forward Sequences for Antennal Gland

description: Illumina Raw Sequences (R1) for Antennal Gland of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628113
title: Reverse Sequences for Gill

description: Illumina Raw Sequences (R2) for Gill of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3628113.v1
title: Reverse Sequences for Gill

description: Illumina Raw Sequences (R2) for Gill of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3627861
title: Forward Sequences for Gill

description: Illumina Raw (R1) Sequences for Gill of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3627504
title: Reverse Raw Reads for PL

description: Illumina Raw Sequences (R2) for <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3627861.v1
title: Forward Sequences for Gill

description: Illumina Raw (R1) Sequences for Gill of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3627504.v1
title: Reverse Raw Reads for PL

description: Illumina Raw Sequences (R2) for <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3626667
title: Forward Raw Reads for PL

description: Illumina Raw Sequences (R1) for <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3626667.v1
title: Forward Raw Reads for PL

description: Illumina Raw Sequences (R1) for <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3625773
title: CO1 Gene Sequences

description: mtCO1 gene sequences of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3625773.v1
title: CO1 Gene Sequences

description: mtCO1 gene sequences of <i>Macrobrachium australiense</i><br>
DOI: 10.6084/m9.figshare.3622086
title: Effects of arginine vasopressin on the urine proteome in rats

description: 1, 2, 3, control group; 4, 5, 6, low dose group; 7, 8, 9, high dose group; -1, -2, -3, three technical replicates of each sample. <br>
DOI: 10.6084/m9.figshare.3622086.v1
title: Effects of arginine vasopressin on the urine proteome in rats

description: 1, 2, 3, control group; 4, 5, 6, low dose group; 7, 8, 9, high dose group; -1, -2, -3, three technical replicates of each sample. <br>