cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5789469
title: Supplementary Material for: Unravelling Pathophysiology of Crystalline Nephropathy in Ceftriaxone-Associated Acute Kidney Injury: A Cellular Proteomic Approach

description: <b><i>Background:</i></b> Previous studies showed that ceftriaxone can cause acute kidney injury (AKI) in the pediatric population. This study proposed a cellular model of crystalline nephropathy in ceftriaxone-associated AKI and explored the related pathophysiology by using a proteomic approach. <b><i>Methods:</i></b> Ceftriaxone was crystallized with calcium in artificial urine. Madin-Darby Canine Kidney (MDCK) cells, a model of distal renal tubular cell, were cultured in the absence (untreated control) or presence of ceftriaxone crystals for 48-h (<i>n</i> = 5 each). MDCK cells were harvested and subsequently analyzed by proteomic analysis. Protein bioinformatics (i.e., STRING and Reactome) was used to predict functional alterations, and subsequently validated by Western blotting and cellular studies. <i>p &lt;</i> 0.05 was considered statistically significant. <b><i>Results:</i></b> Phase-contrast microscopy showed increased intracellular vesiculation and cell enlargement as a result of ceftriaxone crystal exposure. Proteome analysis revealed a total of 20 altered proteins (14 increased, 5 decreased and 1 absent) in ceftriaxone crystal-treated MDCK cells as compared to untreated cells (<i>p</i> &lt; 0.05). Protein bioinformatics and validation studies supported heat stress response mediated by heat shock protein 70 (Hsp70) and downregulation of annexin A1 as the proposed pathophysiology of crystalline nephropathy in ceftriaxone-associated AKI, in which impaired proliferation and wound healing of crystal-induced distal tubular cells were outcomes. <b><i>Conclusions:</i></b> This study, for the first time, used the in vitro model of crystalline nephropathy to investigate the underlying pathophysiology of ceftriaxone-associated AKI, which should be investigated in vivo for potential clinical benefits in the future.
DOI: 10.6084/m9.figshare.5789442
title: Covariate Selection in High-Dimensional Generalized Linear Models With Measurement Error

description: In many problems involving generalized linear models, the covariates are subject to measurement error. When the number of covariates <i>p</i> exceeds the sample size <i>n</i>, regularized methods like the lasso or Dantzig selector are required. Several recent papers have studied methods which correct for measurement error in the lasso or Dantzig selector for linear models in the <i>p</i> &gt; <i>n</i> setting. We study a correction for generalized linear models, based on Rosenbaum and Tsybakov’s matrix uncertainty selector. By not requiring an estimate of the measurement error covariance matrix, this generalized matrix uncertainty selector has a great practical advantage in problems involving high-dimensional data. We further derive an alternative method based on the lasso, and develop efficient algorithms for both methods. In our simulation studies of logistic and Poisson regression with measurement error, the proposed methods outperform the standard lasso and Dantzig selector with respect to covariate selection, by reducing the number of false positives considerably. We also consider classification of patients on the basis of gene expression data with noisy measurements. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5789442.v1
title: Covariate Selection in High-Dimensional Generalized Linear Models With Measurement Error

description: In many problems involving generalized linear models, the covariates are subject to measurement error. When the number of covariates <i>p</i> exceeds the sample size <i>n</i>, regularized methods like the lasso or Dantzig selector are required. Several recent papers have studied methods which correct for measurement error in the lasso or Dantzig selector for linear models in the <i>p</i> &gt; <i>n</i> setting. We study a correction for generalized linear models, based on Rosenbaum and Tsybakov’s matrix uncertainty selector. By not requiring an estimate of the measurement error covariance matrix, this generalized matrix uncertainty selector has a great practical advantage in problems involving high-dimensional data. We further derive an alternative method based on the lasso, and develop efficient algorithms for both methods. In our simulation studies of logistic and Poisson regression with measurement error, the proposed methods outperform the standard lasso and Dantzig selector with respect to covariate selection, by reducing the number of false positives considerably. We also consider classification of patients on the basis of gene expression data with noisy measurements. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5789349
title: Data for "Adaptive avoidance of cuckoo catfish parasitism by cichlids"

description: data for analysis reported in the paper:<br>Blažek R., Polačik M., Smith, C., Honza, M., Meyer, A., Reichard M. (2018) Success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their cichlid hosts. Science Advances, 4, eaar4380.<br>
DOI: 10.6084/m9.figshare.5789349.v2
title: Data for "Adaptive avoidance of cuckoo catfish parasitism by cichlids"

description: data for analysis reported in the paper:<br>Blažek R., Polačik M., Smith, C., Honza, M., Meyer, A., Reichard M. (2018) Success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their cichlid hosts. Science Advances, 4, eaar4380.<br>
DOI: 10.6084/m9.figshare.5789349.v1
title: Data for "Adaptive avoidance of cuckoo catfish parasitism by cichlids"

description: data for analysis reported in the paper
DOI: 10.6084/m9.figshare.5789172
title: Distribution area of the two floral morphs of <i>Nigella damascena</i> L. (Ranunculaceae): a diachronic study using herbarium specimens collected in France

description: Perianth dimorphism in <i>Nigella damascena</i> (Ranunculaceae) has been documented for four centuries, and its genetic basis started to be studied almost a century ago. Based on herbarium collections, we reconstructed the evolution of the distribution area of the wild-type (perianth composed of a calyx and nectariferous petals) and mutant (apetalous) floral morphs in mainland France over the last two centuries. We showed that the collection localities of the wild-type morph are mostly concentrated in the southern coastal areas of France, whereas the collection localities of the mutant morph were less numerous but more scattered in France. The collection effort of both morphs peaked in the second half of the nineteenth century and continuously decreased afterwards. Results are interpreted taking into account the biases in the constitution of a herbarium collection. Knowledge about the spatial distribution and the frequency of occurrence of wild-type and mutant populations through time will help botanists and evolutionary biologists investigate the origin and ecological grounds for the maintenance and propagation of the apetalous morph in the wild.
DOI: 10.6084/m9.figshare.5789172.v1
title: Distribution area of the two floral morphs of <i>Nigella damascena</i> L. (Ranunculaceae): a diachronic study using herbarium specimens collected in France

description: Perianth dimorphism in <i>Nigella damascena</i> (Ranunculaceae) has been documented for four centuries, and its genetic basis started to be studied almost a century ago. Based on herbarium collections, we reconstructed the evolution of the distribution area of the wild-type (perianth composed of a calyx and nectariferous petals) and mutant (apetalous) floral morphs in mainland France over the last two centuries. We showed that the collection localities of the wild-type morph are mostly concentrated in the southern coastal areas of France, whereas the collection localities of the mutant morph were less numerous but more scattered in France. The collection effort of both morphs peaked in the second half of the nineteenth century and continuously decreased afterwards. Results are interpreted taking into account the biases in the constitution of a herbarium collection. Knowledge about the spatial distribution and the frequency of occurrence of wild-type and mutant populations through time will help botanists and evolutionary biologists investigate the origin and ecological grounds for the maintenance and propagation of the apetalous morph in the wild.
DOI: 10.6084/m9.figshare.5789100
title: Supplementary Material for: The Combined Effects of Genetic Variation in the CNDP1 and CNDP2 Genes and Dietary Carbohydrate and Carotene Intake on Obesity Risk

description: <b><i>Background/Aims:</i></b> It is possible that carnosinase (CNDP1) and cellular nonspecific dipeptidase (CNDP2) have important roles in protecting cells and tissues against the damage of oxidative stress. Oxidative stress and subsequent inflammation are key factors in the development of common chronic metabolic diseases, such as obesity. We aimed to investigate the combined effects of genetic variations in <i>CNDP1</i> and <i>CNDP2</i> and dietary carbohydrate and carotene intake on obesity risk. <b><i>Methods:</i></b> A total of 1,059 Japanese men were randomly selected from participants who visited a medical center for routine medical checkups. We analyzed the relationships between the genotypes of 4 single-nucleotide polymorphisms (SNPs) (rs12605520, rs7244647, rs4891558, and rs17089368) in the <i>CNDP1/CNDP2 </i>locus and body mass index or prevalence of obesity/overweight taking into account dietary carbohydrate and carotene intake. <b><i>Results:</i></b> We found that 2 SNPs (rs7244647 in <i>CNDP1</i> and rs4891558 in <i>CNDP2</i>) were associated with obesity risk. In addition, these associations were observed only in the group with high carbohydrate and low carotene intake but not in the group with low carbohydrate and high carotene intake. <b><i>Conclusions:</i></b> Our findings indicate that the combination of genetic variations in <i>CNDP1 </i>and<i> CNDP2</i> and dietary carbohydrate/carotene intake modulate obesity risk.
DOI: 10.6084/m9.figshare.5789097
title: Supplementary Material for: The IL20 Genetic Polymorphism Is Associated with Altered Clinical Outcome in Septic Shock

description: Background: The IL10 family of genes includes crucial immune regulators. We tested the hypothesis that single nucleotide polymorphisms (SNPs) in IL10 , IL19 , IL20 , and IL24 of the IL10 family gene cluster alter the clinical outcome of septic shock. Methods: Patients with septic shock ( n = 1,193) were genotyped for 13 tag SNPs of IL10 , IL19 , IL20 , and IL24 . IL20 gene expression was measured in genotyped lymphoblastoid cells in vitro. Cardiac surgical ICU patients ( n = 981) were genotyped for IL20 rs2981573 A/G. The primary outcome variable was 28-day mortality. Results: Patients with the G allele of IL20 rs2981573 had a significantly increased hazard of death over the 28-day period compared to patients with the A allele in the septic shock cohort (adjusted hazard ratio 1.27; 95% confidence interval 1.10–1.47; p = 8.0 × 10 –4 ). Patients with the GG genotype had more organ dysfunction ( p &lt; 0.05). The GG genotype was associated with increased IL20 gene expression in stimulated lymphoblastoid cells in vitro ( p &lt; 0.05). The cardiac surgical ICU patients with the GG genotype had an increased length of ICU stay ( p = 0.032). Conclusions: The GG genotype of IL20 rs2981573 SNP was associated with increased IL20 gene expression and increased adverse outcomes in patients with septic shock and following cardiac surgery. <br>
DOI: 10.6084/m9.figshare.5789097.v1
title: Supplementary Material for: The IL20 Genetic Polymorphism Is Associated with Altered Clinical Outcome in Septic Shock

description: Background: The IL10 family of genes includes crucial immune regulators. We tested the hypothesis that single nucleotide polymorphisms (SNPs) in IL10 , IL19 , IL20 , and IL24 of the IL10 family gene cluster alter the clinical outcome of septic shock. Methods: Patients with septic shock ( n = 1,193) were genotyped for 13 tag SNPs of IL10 , IL19 , IL20 , and IL24 . IL20 gene expression was measured in genotyped lymphoblastoid cells in vitro. Cardiac surgical ICU patients ( n = 981) were genotyped for IL20 rs2981573 A/G. The primary outcome variable was 28-day mortality. Results: Patients with the G allele of IL20 rs2981573 had a significantly increased hazard of death over the 28-day period compared to patients with the A allele in the septic shock cohort (adjusted hazard ratio 1.27; 95% confidence interval 1.10–1.47; p = 8.0 × 10 –4 ). Patients with the GG genotype had more organ dysfunction ( p &lt; 0.05). The GG genotype was associated with increased IL20 gene expression in stimulated lymphoblastoid cells in vitro ( p &lt; 0.05). The cardiac surgical ICU patients with the GG genotype had an increased length of ICU stay ( p = 0.032). Conclusions: The GG genotype of IL20 rs2981573 SNP was associated with increased IL20 gene expression and increased adverse outcomes in patients with septic shock and following cardiac surgery. <br>
DOI: 10.6084/m9.figshare.5789079
title: DatabaseVariability.xlsx

description: Data from "Durán et al. Ecology - Under review"<br>There are two spreadsheets with data. The spreadsheet "Data" contains the data used in the different analyses presented in the article. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found.
DOI: 10.6084/m9.figshare.5789079.v1
title: DatabaseVariability.xlsx

description: Data from "Durán et al. Ecology - Under review"<br>There are two spreadsheets with data. The spreadsheet "Data" contains the data used in the different analyses presented in the article. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found.
DOI: 10.6084/m9.figshare.5789073
title: Application of a semi-automated vocal fingerprinting approach to monitor Bornean gibbon females in an experimentally fragmented landscape in Sabah, Malaysia

description: Vocal individuality has been documented in a variety of mammalian species and it has been proposed that this individuality can be used as a vocal fingerprint to monitor individuals. Here we provide and test a classification method using Mel-frequency cepstral coefficients (MFCCs) to extract features from Bornean gibbon female calls. Our method is semi-automated as it requires manual pre-processing to identify and extract calls from the original recordings. We compared two methods of MFCC feature extraction: (1) averaging across all time windows and (2) creating a standardized number of time windows for each call. We analysed 376 calls from 33 gibbon females and, using linear discriminant analysis, found that we were able to improve female identification accuracy from 95.7% with spectrogram features to 98.4% accuracy when averaging MFCCs across time windows, and 98.9% accuracy when using a standardized number of windows. We divided our data randomly into training and test data-sets, and tested the accuracy of support vector machine (SVM) predictions over 100 iterations. We found that we could predict female identity in the test data-set with a 98.8% accuracy. Using SVM on our entire data-set, we were able to predict female identity with 99.5% accuracy (validated by leave-one-out cross-validation). Lastly, we used the method presented here to classify four females recorded during three or more recording seasons using SVM with limited success. We provide evidence that MFCC feature extraction is effective for distinguishing between female Bornean gibbons, and make suggestions for future vocal fingerprinting applications.
DOI: 10.6084/m9.figshare.5789073.v1
title: Application of a semi-automated vocal fingerprinting approach to monitor Bornean gibbon females in an experimentally fragmented landscape in Sabah, Malaysia

description: Vocal individuality has been documented in a variety of mammalian species and it has been proposed that this individuality can be used as a vocal fingerprint to monitor individuals. Here we provide and test a classification method using Mel-frequency cepstral coefficients (MFCCs) to extract features from Bornean gibbon female calls. Our method is semi-automated as it requires manual pre-processing to identify and extract calls from the original recordings. We compared two methods of MFCC feature extraction: (1) averaging across all time windows and (2) creating a standardized number of time windows for each call. We analysed 376 calls from 33 gibbon females and, using linear discriminant analysis, found that we were able to improve female identification accuracy from 95.7% with spectrogram features to 98.4% accuracy when averaging MFCCs across time windows, and 98.9% accuracy when using a standardized number of windows. We divided our data randomly into training and test data-sets, and tested the accuracy of support vector machine (SVM) predictions over 100 iterations. We found that we could predict female identity in the test data-set with a 98.8% accuracy. Using SVM on our entire data-set, we were able to predict female identity with 99.5% accuracy (validated by leave-one-out cross-validation). Lastly, we used the method presented here to classify four females recorded during three or more recording seasons using SVM with limited success. We provide evidence that MFCC feature extraction is effective for distinguishing between female Bornean gibbons, and make suggestions for future vocal fingerprinting applications.
DOI: 10.6084/m9.figshare.5789031
title: Parasites of importance for human health on edible fruits and vegetables in Nigeria: a systematic review and meta-analysis of published data

description: Contamination of edible fruits and vegetables is now a global public health issue despite their health benefits as non-pharmacological prophylaxis against chronic diseases. Studies that will harness the extent of parasitic contaminations will ensure public health protection. Here, the prevalence and distribution of parasites of importance for human health on fruits and vegetables in Nigeria were determined through a systematic review and meta-analysis of published data. The random-effects model was used to determine pooled prevalence estimate (PPE). Heterogeneity was evaluated by the Cochran’s Q-test. Parasites overall PPE of 32.4% (95% CI: 0.73, 0.91) was observed from 19 eligible studies reported across 13 Nigerian states. Sub-groups PPEs ranged between 3.5% (95% CI: 0.45, 1.86) and 58.5% (95% CI: 1.40, 4.09). A high degree of heterogeneity 97.53% (95% CI: 0.30, 0.46, <i>P</i>: 0.000) was observed within studies and sub-groups. <i>Cryptosporidium</i> species were the most prevalent, while <i>Ancylostoma duodenale</i> and <i>Ascaris lumbricoides</i> had the widest geographical distribution. Pineapple (Prev: 41.3%, 95% CI: 0.40, 0.75) and lettuce (Prev: 51.5%, 95% CI: 0.37, 0.68) recorded the highest level of parasitic contamination. Parasites of importance for human health are prevalent on edible fruits and vegetables in Nigeria. Prevalence estimates were highest in the South-eastern region and during the most recent decade. Adequate washing of fruits and vegetables, on-farm irrigation of vegetables using good sources of water and adequate hygiene by food handlers will help the general public to maximize the health benefits associated with the intake of fruits and vegetables while minimizing the risk of acquiring parasitic infections.
DOI: 10.6084/m9.figshare.5789031.v1
title: Parasites of importance for human health on edible fruits and vegetables in Nigeria: a systematic review and meta-analysis of published data

description: Contamination of edible fruits and vegetables is now a global public health issue despite their health benefits as non-pharmacological prophylaxis against chronic diseases. Studies that will harness the extent of parasitic contaminations will ensure public health protection. Here, the prevalence and distribution of parasites of importance for human health on fruits and vegetables in Nigeria were determined through a systematic review and meta-analysis of published data. The random-effects model was used to determine pooled prevalence estimate (PPE). Heterogeneity was evaluated by the Cochran’s Q-test. Parasites overall PPE of 32.4% (95% CI: 0.73, 0.91) was observed from 19 eligible studies reported across 13 Nigerian states. Sub-groups PPEs ranged between 3.5% (95% CI: 0.45, 1.86) and 58.5% (95% CI: 1.40, 4.09). A high degree of heterogeneity 97.53% (95% CI: 0.30, 0.46, <i>P</i>: 0.000) was observed within studies and sub-groups. <i>Cryptosporidium</i> species were the most prevalent, while <i>Ancylostoma duodenale</i> and <i>Ascaris lumbricoides</i> had the widest geographical distribution. Pineapple (Prev: 41.3%, 95% CI: 0.40, 0.75) and lettuce (Prev: 51.5%, 95% CI: 0.37, 0.68) recorded the highest level of parasitic contamination. Parasites of importance for human health are prevalent on edible fruits and vegetables in Nigeria. Prevalence estimates were highest in the South-eastern region and during the most recent decade. Adequate washing of fruits and vegetables, on-farm irrigation of vegetables using good sources of water and adequate hygiene by food handlers will help the general public to maximize the health benefits associated with the intake of fruits and vegetables while minimizing the risk of acquiring parasitic infections.
DOI: 10.6084/m9.figshare.5789007
title: Collective Knowledge repository with reproducible experimental results from collaborative program autotuning on Raspberry Pi (program reactions to most efficient compiler optimizations)

description: Optimization results to demonstrate compiler autotuning, crowd-tuning and machine learning on RPi3 via customizable Collective Knowledge workflow framework with a portable package manager.<br><br>These results in the Collective Knowledge format help prototype a common and reproducible optimization methodology to support Artifact evaluation and Pareto-efficient co-design competitions of the whole software and hardware stack for emerging workloads such as deep learning in terms of speed, accuracy, energy and costs:<br>* http://cKnowledge.org/request<br>* http://cTuning.org/ae<br><br>Interactive CK report: http://cKnowledge.org/rpi-crowd-tuning<br><br>ArXiv report: https://arxiv.org/abs/1801.08024<br><br>
DOI: 10.6084/m9.figshare.5789007.v1
title: Collective Knowledge repository with reproducible experimental results from collaborative program autotuning on Raspberry Pi (program reactions to most efficient compiler optimizations)

description: Optimization results to demonstrate compiler autotuning, crowd-tuning and machine learning on RPi3 via customizable Collective Knowledge workflow framework with a portable package manager.<br><br>These results in the Collective Knowledge format help prototype a common and reproducible optimization methodology to support Artifact evaluation and Pareto-efficient co-design competitions of the whole software and hardware stack for emerging workloads such as deep learning in terms of speed, accuracy, energy and costs:<br>* http://cKnowledge.org/request<br>* http://cTuning.org/ae<br><br>