cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14553750
title: PCA results for Dopamine and Rotenone 24h and 96h

description: This dataset contains the results for the mitochondrial mobility under treatment of dopamine 24h and 96h, and rotenone 24 and 96h. First two columns PC1 and PC2 are the principal components, followed by the treatment concentration and the image filename from which the data was extracted.
DOI: 10.6084/m9.figshare.14553750.v1
title: PCA results for Dopamine and Rotenone 24h and 96h

description: This dataset contains the results for the mitochondrial mobility under treatment of dopamine 24h and 96h, and rotenone 24 and 96h. First two columns PC1 and PC2 are the principal components, followed by the treatment concentration and the image filename from which the data was extracted.
DOI: 10.5281/zenodo.4662023
title: High-throughput characterization of photocrosslinker-bearing ion channel variants to map residues critical for function and pharmacology

description: Contains a read_me file and data related to the publication: High-throughput characterization of photocrosslinker-bearing ion channel variants to map residues critical for function and pharmacology
description: Søren Friis is a full-time employee of Nanion Technologies. The other authors declare no competing interests. We acknowledge the Lundbeck Foundation (R139-2012-12390 to SAP and R218-2016-1490 to NB), the Boehringer Ingelheim Fond (to NB) and the University of Copenhagen for financial support.
DOI: 10.6084/m9.figshare.14553771
title: Supplementary Material for: Noninvasive Home Mechanical Ventilation in Adult Myotonic Dystrophy Type 1: A Systematic Review

description: <b><i>Introduction:</i></b> Chronic hypercapnic respiratory failure induces considerable morbidity and mortality in patients with myotonic dystrophy type 1 (DM1). This study systematically reviews the effects of noninvasive home mechanical ventilation (HMV) on gas exchange, quality of life, survival, and compliance in DM1 patients. <b><i>Methods:</i></b> A systematic Medline and Embase search was performed (January 1995 to January 2020). Records were screened for eligibility criteria, data were extracted from included studies, and risk of bias was assessed. We present findings mainly using a narrative synthesis. <b><i>Results:</i></b> Twenty-eight relevant full-text articles were screened for eligibility criteria. Nine studies were included. Randomized controlled trials were not found. Studies had either an observational (<i>n</i> = 8) or interventional (<i>n</i> = 1) design. In the pooled data analysis, HMV showed to improve mean oxygen saturation with 4.8% and decreased mean carbon dioxide values with 3 mm Hg. Compliance varied widely between studies, from no use to more than 12 h per day. Quality of life was not studied extensively, but some studies reported positive effects of HMV on symptoms of chronic respiratory failure. HMV may improve survival in DM1 patients with chronic hypercapnic respiratory failure. <b><i>Conclusion:</i></b> This review shows that HMV can improve gas exchange and relieve symptoms with a possible survival benefit in DM1 patients with chronic hypercapnic respiratory failure. Future studies should focus on developing strategies to optimize the timing of HMV initiation and to promote compliance.
DOI: 10.6084/m9.figshare.14553771.v1
title: Supplementary Material for: Noninvasive Home Mechanical Ventilation in Adult Myotonic Dystrophy Type 1: A Systematic Review

description: <b><i>Introduction:</i></b> Chronic hypercapnic respiratory failure induces considerable morbidity and mortality in patients with myotonic dystrophy type 1 (DM1). This study systematically reviews the effects of noninvasive home mechanical ventilation (HMV) on gas exchange, quality of life, survival, and compliance in DM1 patients. <b><i>Methods:</i></b> A systematic Medline and Embase search was performed (January 1995 to January 2020). Records were screened for eligibility criteria, data were extracted from included studies, and risk of bias was assessed. We present findings mainly using a narrative synthesis. <b><i>Results:</i></b> Twenty-eight relevant full-text articles were screened for eligibility criteria. Nine studies were included. Randomized controlled trials were not found. Studies had either an observational (<i>n</i> = 8) or interventional (<i>n</i> = 1) design. In the pooled data analysis, HMV showed to improve mean oxygen saturation with 4.8% and decreased mean carbon dioxide values with 3 mm Hg. Compliance varied widely between studies, from no use to more than 12 h per day. Quality of life was not studied extensively, but some studies reported positive effects of HMV on symptoms of chronic respiratory failure. HMV may improve survival in DM1 patients with chronic hypercapnic respiratory failure. <b><i>Conclusion:</i></b> This review shows that HMV can improve gas exchange and relieve symptoms with a possible survival benefit in DM1 patients with chronic hypercapnic respiratory failure. Future studies should focus on developing strategies to optimize the timing of HMV initiation and to promote compliance.
DOI: 10.13012/b2idb-4677176_v1
title: Use of legumes and yeast as novel dietary protein sources in extruded canine diets

description: - The objective of this study was to evaluate macronutrient apparent total tract digestibility (ATTD), gastrointestinal tolerance, and fermentative end-products in extruded, canine diets. <br>- Five diets were formulated to be isocaloric and isonitrogenous with either garbanzo beans (GBD), green lentils (GLD), peanut flour (PFD), dried yeast (DYD), or poultry by-product meal (CON) as the primary protein sources. Ten adult, intact, female beagles (mean age: 4.2 ± 1.1 yr, mean 28 weight: 11.9 ± 1.3 kg) were used in a replicated, 5x5 Latin square design with 14 d periods. Total DNA from fresh fecal samples was extracted using Mo-Bio PowerSoil kits (MO BIO Laboratories, Inc., Carlsbad, CA). Amplification of the 292 bp-fragment of V4 region from the 16S rRNA gene was completed using a Fluidigm Access Array (Fluidigm Corporation, South San Francisco, CA). Paired-end Illumina sequencing was performed on a MiSeq using v3 reagents (Illumina Inc., San Diego, CA) at the Roy J. Carver Biotechnology Center at the University of Illinois. <br>- Filenames are composed of animal name identifier, diet (CON=control; DY= dried yeast; GB= garbanzo beans; GL= green lentils; PF= peanut flour) and period replicate number (P1, P2, P3, P4, and P5).
DOI: 10.13012/b2idb-2580847_v1
title: White and Red Sorghum as Primary Carbohydrate Sources in Extruded Diets of Felines

description: - The research objectives were to evaluate the effect of dietary supplementation of white (WSH) and red (RSH) sorghum grains on gastrointestinal health of felines through the determination of apparent total tract macronutrient digestibility (ATTD), fecal characteristics, fermentative end-products, and microbiota, compared with a traditional corn-based diet (Control). <br>- Nine, intact, male domestic shorthaired cats (average age: 0.8 ± 0.00 yr; average weight: 4.5 ± 0.23 kg) were used in a triplicated 3 × 3 Latin square design. Total DNA from fresh fecal samples was extracted using Mo-Bio PowerSoil kits (MO BIO Laboratories, Inc., Carlsbad, CA). Amplification of the 292 bp-fragment of V4 region from the 16S rRNA gene was completed using a Fluidigm Access Array (Fluidigm Corporation, South San Francisco, CA). Paired-end Illumina sequencing was performed on a MiSeq using v3 reagents (Illumina Inc., San Diego, CA) at the Roy J. Carver Biotechnology Center at the University of Illinois. <br>- Filenames are composed of animal name identifier, supplement (C=control; RS=red sorghum grain; WS= white sorghum grain) and period replicate number (P1, P2 and P3).
DOI: 10.5281/zenodo.4742011
title: Physical activity interventions and nutrition-based interventions for children and adolescents with type 1 diabetes mellitus

description: 1. Baseline characteristics of participants 2. Description of studies 3. Data extraction_Excel
DOI: 10.17632/7w4cb4mdd4.1
title: Allele frequency data for SNPs on a combined-species SNP array for European seabass and gilthead seabream

description: SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits, and for incorporating genetic markers to expedite genetic gain in selective breeding programmes. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are two primary fish species of importance for Mediterranean aquaculture. The aim of our study was to design a combined-species, 60K SNP array for the European seabass and the gilthead seabream, and to test its performance on farmed and wild populations from multiple locations throughout the Mediterranean. The data presented here are part of the validation process of the abovementioned platform and represents the allele frequencies of the SNPs on the array that were genotyped across 23 European seabass and 26 gilthead seabream populations sampled mainly from the Mediterranean Sea. The data comprises two text files, one for each fish species. Each file contains seven tab separated columns that indicate: chromosome/scaffold ID (1st column), position of the SNP (2nd column), SNP ID (3rd column), reference allele (4th column), alternate allele (5th column), the number of individuals successfully genotyped (6th column) and the average allele frequency of the SNP (7th column). The data shows that the majority of the SNPs on the platform are highly polymorphic across the sampled European seabass and gilthead seabream populations. The allele frequency information can be used to generate low-density panels to perform genetic research in both fish species.
DOI: 10.6084/m9.figshare.14554146
title: Supplementary Material for: Incremental Value of Renal Dysfunction Addition to the CHA2DS2-Vasc Score for Mortality Prediction in Patients with Acute Coronary Syndrome

description: <b><i>Introduction:</i></b> This study analyzes the usefulness of the CHA2DS2-VASc score for mortality prediction in patients with acute coronary syndromes (ACSs) and evaluates if the addition of renal functional status could improve its predictive accuracy. <b><i>Methods:</i></b> CHA2DS2-VASc score was calculated by using both the original scoring system and adding renal functional status using 3 alternative renal dysfunction definitions (CHA2DS2-VASc-R1: eGFR &lt;60 mL/min/1.73 mq = 1 point; CHA2DS2-VASc-R2: eGFR &lt;60 mL/min/1.73 mq = 2 points; and CHA2DS2-VASc-R3: eGFR &lt;60 mL/min/1.73 mq = 1 point, &lt;30 mL/min/1.73 mq = 2 points). Inhospital mortality (IHM) and post-discharge mortality (PDM) were recorded, and discrimination of the various risk models was evaluated. Finally, the net reclassification index (NRI) was calculated to compare the mortality risk classification of the modified risk models with that of the original score. <b><i>Results:</i></b> Nine hundred and eight ACS patients (median age 68 years, 30% female, 51% ST-elevation) composed the study population. Of the 871 patients discharged, 865 (99%) completed a 12-month follow-up. The IHM rate was 4.1%. The CHA2DS2-VASc score demonstrated a good discriminative performance for IHM (C-statistic 0.75). Although all the eGFR-modified risk models showed higher C-statistics than the original model, a statistically significant difference was observed only for CHA2DS2-VASc-R3. The PDM rate was 4.5%. The CHA2DS2-VASc C-statistic for PDM was 0.75, and all the modified risk models showed significantly higher C-statistics values than the original model. The NRI analysis showed similar results. <b><i>Conclusions:</i></b> CHA2DS2-VASc score demonstrated a good predictive accuracy for IHM and PDM in ACS patients. The addition of renal dysfunction to the original score has the potential to improve identification of patients at the risk of death.
DOI: 10.6084/m9.figshare.14554146.v1
title: Supplementary Material for: Incremental Value of Renal Dysfunction Addition to the CHA2DS2-Vasc Score for Mortality Prediction in Patients with Acute Coronary Syndrome

description: <b><i>Introduction:</i></b> This study analyzes the usefulness of the CHA2DS2-VASc score for mortality prediction in patients with acute coronary syndromes (ACSs) and evaluates if the addition of renal functional status could improve its predictive accuracy. <b><i>Methods:</i></b> CHA2DS2-VASc score was calculated by using both the original scoring system and adding renal functional status using 3 alternative renal dysfunction definitions (CHA2DS2-VASc-R1: eGFR &lt;60 mL/min/1.73 mq = 1 point; CHA2DS2-VASc-R2: eGFR &lt;60 mL/min/1.73 mq = 2 points; and CHA2DS2-VASc-R3: eGFR &lt;60 mL/min/1.73 mq = 1 point, &lt;30 mL/min/1.73 mq = 2 points). Inhospital mortality (IHM) and post-discharge mortality (PDM) were recorded, and discrimination of the various risk models was evaluated. Finally, the net reclassification index (NRI) was calculated to compare the mortality risk classification of the modified risk models with that of the original score. <b><i>Results:</i></b> Nine hundred and eight ACS patients (median age 68 years, 30% female, 51% ST-elevation) composed the study population. Of the 871 patients discharged, 865 (99%) completed a 12-month follow-up. The IHM rate was 4.1%. The CHA2DS2-VASc score demonstrated a good discriminative performance for IHM (C-statistic 0.75). Although all the eGFR-modified risk models showed higher C-statistics than the original model, a statistically significant difference was observed only for CHA2DS2-VASc-R3. The PDM rate was 4.5%. The CHA2DS2-VASc C-statistic for PDM was 0.75, and all the modified risk models showed significantly higher C-statistics values than the original model. The NRI analysis showed similar results. <b><i>Conclusions:</i></b> CHA2DS2-VASc score demonstrated a good predictive accuracy for IHM and PDM in ACS patients. The addition of renal dysfunction to the original score has the potential to improve identification of patients at the risk of death.
DOI: 10.6084/m9.figshare.14554089
title: Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma

description: Stage 4S neuroblastoma, as defined by theInternational Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of theSK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in modulating TME, thus facilitating the progression of neuroblastoma.
DOI: 10.6084/m9.figshare.14554089.v1
title: Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma

description: Stage 4S neuroblastoma, as defined by theInternational Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of theSK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in modulating TME, thus facilitating the progression of neuroblastoma.
DOI: 10.6084/m9.figshare.12191118
title: Amelioration from the ocular irritant Capsaicin: development and assessment of a Capsazepine <i>in situ</i> gel system for ocular delivery

description: Defense personnel utilize capsaicin-based ocular sprays as non-lethal agents for law implementation during instances of mob violence. This study involves the capsaicin antagonist Capsazepine and the investigation of whether Capsazepine’s antagonistic approach can be favorably utilized for defense utilization to block capsaicin-initiated pain and inflammation via the ocular pathway. Ocular capsazepine <i>in situ</i> gels were prepared with polymers Pluronic F-127 and Chitosan; optimized formulation was quantified in ocular tissues chromatographically and by <i>in vivo</i> live ocular imaging; anti-inflammatory efficacy was determined by eye irritation testing, corneal and retinal imaging, ocular prostaglandin estimation, and by viability and proliferation testing using human ocular cell lines, etc. A physicochemically stable Capsazepine <i>in situ</i> gel was formulated which showed little ocular irritation, considerable transcorneal permeation; was precisely quantified in ocular tissues by gas chromatography and <i>in vivo</i> live ocular imaging; showed anti-inflammatory properties against capsaicin by eye imaging experiments, prostaglandin declination and showed acceptable cytocompatibility when studied using human ocular cell lines. The fabricated <i>in situ</i> Capsazepine gel system might be promising for ocular delivery as it appears a pharmacologically potent and safe development, suitable for utilization in the ocular clinical therapy, provided there is additional research to substantiate it.
DOI: 10.6084/m9.figshare.12191118.v1
title: Amelioration from the ocular irritant Capsaicin: development and assessment of a Capsazepine <i>in situ</i> gel system for ocular delivery

description: Defense personnel utilize capsaicin-based ocular sprays as non-lethal agents for law implementation during instances of mob violence. This study involves the capsaicin antagonist Capsazepine and the investigation of whether Capsazepine’s antagonistic approach can be favorably utilized for defense utilization to block capsaicin-initiated pain and inflammation via the ocular pathway. Ocular capsazepine <i>in situ</i> gels were prepared with polymers Pluronic F-127 and Chitosan; optimized formulation was quantified in ocular tissues chromatographically and by <i>in vivo</i> live ocular imaging; anti-inflammatory efficacy was determined by eye irritation testing, corneal and retinal imaging, ocular prostaglandin estimation, and by viability and proliferation testing using human ocular cell lines, etc. A physicochemically stable Capsazepine <i>in situ</i> gel was formulated which showed little ocular irritation, considerable transcorneal permeation; was precisely quantified in ocular tissues by gas chromatography and <i>in vivo</i> live ocular imaging; showed anti-inflammatory properties against capsaicin by eye imaging experiments, prostaglandin declination and showed acceptable cytocompatibility when studied using human ocular cell lines. The fabricated <i>in situ</i> Capsazepine gel system might be promising for ocular delivery as it appears a pharmacologically potent and safe development, suitable for utilization in the ocular clinical therapy, provided there is additional research to substantiate it.
DOI: 10.6084/m9.figshare.14554188
title: Supplementary Material for: Plasma Amino Acids and Risk of Impaired Lower-Extremity Function and Role of Dietary Intake: A Nested Case-Control Study in Older Adults

description: <b><i>Introduction:</i></b> Amino acids are key elements in the regulation of the aging process which entails a progressive loss of muscle mass. The health effects of plasma amino acids can be influenced by dietary intake. This study assessed the prospective association between amino acid species and impaired lower-extremity function (ILEF) in older adults, exploring the role of diet on this association. <b><i>Methods:</i></b> This is a case-control design comprising 43 incident cases of ILEF and 85 age- and sex-matched controls. Plasma concentrations of 20 amino acid species were measured at baseline using liquid chromatography-tandem mass spectrometry, and incident cases of ILEF were measured after 2 years by means of the Short Physical Performance Battery. Conditional logistic regression models were used to assess longitudinal relationships. <b><i>Results:</i></b> After adjusting for potential confounders, higher levels of tryptophan were associated with a decreased 2-year risk of ILEF (OR per 1-SD increase = 0.64, 95% CI = [0.42, 0.97]), while glutamine and total essential amino acids were linked to higher ILEF risk (OR = 1.57, 95% CI = [1.01, 2.45]; OR = 1.89, 95% CI = [1.18, 3.03], respectively). Those with a lower adherence to a Mediterranean diet, a higher BMI, a higher consumption of red meat, and a lower consumption of nuts and legumes had an increased risk of ILEF associated with higher levels of essential amino acids. <b><i>Discussion/Conclusion:</i></b> Some amino acid species could serve as risk markers for physical function decline in older adults, and healthy diet might attenuate the excess risk of ILEF linked to essential amino acids.