169 Works

NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

Harald H. H. W. Schmidt, Mahmoud H. Elbatreek, Sepideh Sadegh, Elisa Anastasi, Emre Guney, Cristian Nogales, Tim Kacprowski, Ahmed A. Hassan, Andreas Teubner, Po-Hsun Huang, Chien-Yi Hsu, Paul M. H. Schiffers, Ger M. Janssen, Pamela W. M. Kleikers, Anil Wipat, Jan Baumbach & Jo G. R. De Mey
Hypertension is the most important cause of death and disability in the elderly. In 9 out of 10 cases, the molecular cause, however, is unknown. One mechanistic hypothesis involves impaired endothelium-dependent vasodilation through reactive oxygen species (ROS) formation. Indeed, ROS forming NADPH oxidase (Nox) genes associate with hypertension, yet target validation has been negative. We re-investigate this association by molecular network analysis and identify NOX5, not present in rodents, as a sole neighbor to human...

Experimental comparison of fish mortality and injuries at innovative and conventional small hydropower plants - raw data

Melanie Mueller, Josef Knott, Joachim Pander & Juergen Geist
Resolving the controversy about hydropower is only possible based on reliable data on its ecological effects, particularly fish welfare. Herein, we propose a comprehensive assessment of conventional and innovative hydropower using a data set of 52 250 fish. The effects of hydropower on fish were most harmful at sites with Kaplan turbines, showing £ 83% mortality. Innovative hydropower, often termed ‘fish-friendly’, caused £ 64% mortality. Our findings suggested that the runner peripheral speed, number of...

The evolution, complexity and diversity of models of long-term forest dynamics

Harald Bugmann & Rupert Seidl
1. To assess the impacts of climate change on vegetation from stand to global scales, models of forest dynamics that include tree demography are needed. Such models are now available for 50 years, but the currently existing diversity of model formulations and its evolution over time are poorly documented. This hampers systematic assessments of structural uncertainties in model-based studies. 2. We conducted a meta-analysis of 28 models, focusing on models that were used in the...

Emerging stability of forest productivity by mixing two species buffers temperature destabilizing effect

Miren Del Rio, Ricardo Ruiz‐Peinado, Stig‐Olof Holm, Aris Jansons, Thomas Nord‐Larsen, Kris Verheyen, Andrés Bravo‐Oviedo, Hans Pretzsch, Ricardo Ruiz-Peinado, Hervé Jactel, Lluís Coll, Magnus Löf, Jorge Aldea, Christian Ammer, Admir Avdagić, Ignacio Barbeito, Kamil Bielak, Felipe Bravo, Gediminas Brazaitis, Jakub Cerný, Catherine Collet, Sonia Condés, Lars Drössler, Marek Fabrika, Michael Heym … & Andrés Bravo-Oviedo
The increasing disturbances in monocultures around the world are testimony to their instability under global change. Many studies have claimed that temporal stability of productivity increase with species richness, although the ecological fundaments have mainly been investigated through diversity experiments. To adequately manage forest ecosystems, it is necessary to have a comprehensive understanding of the effect of mixing species on the temporal stability of productivity and the way in which this it is influenced by...

Additional file 1 of Metabolic control analysis enables rational improvement of E. coli l-tryptophan producers but methylglyoxal formation limits glycerol-based production

Kristin Schoppel, Natalia Trachtmann, Emil J. Korzin, Angelina Tzanavari, Georg A. Sprenger & Dirk Weuster-Botz
Additional file 1: Figure S1. Schematic representation of central carbon metabolism and L-tryptophan biosynthesis pathway. Depicted are the metabolites glucose-6-phosphate (G6P), fructose 1,6-bisphosphate (FBP), glyceraldehyde 3-phosphate (GAP), 3-phospho-D-glycerate (3PG), phosphoenolpyruvate (PEP), pyruvate (PYR), 3-phosphohydroxypyruvate (3PHP), O-phospho-L-serine (L-PSer) and L-serine (L-ser) from glycolysis and glycerol metabolism (GLYC & GLYK), 6-phosphoglucono-1,5-lactone (6PG), ribulose 5-phosphate (Ru5P), xylulose 5-phosphate (X5P), ribose 5-phosphate (R5P), sedoheptulose 7-phosphate (S7P), erythrose 4-phosphate (E4P), fructose 6-phosphate (F6P) and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from the pentose-phosphate-pathway...

zOTU-Table_V1V3_Auto-FMT

Hannes Hoelz, Andreas Hiergeist, Dirk Haller, André Gessner, Tobias Schwerd, Maria J. G. T. Vehreschild, Anastasia Tsakmaklis, Jeannine Heetmeyer, Kolja Siebert, Federica De Zen, Deborah Häcker, Amira Metwaly & Klaus Neuhaus
The excel sheet contains zOTU Counts, annotated taxonomy, sample mapping, confidence intervals for the taxonomy and zOTU sequences. 16S rRNA sequencing Samples were prepared for sequencing at the sequencing core facilities in Freising (Core Facility Microbiome; ZIEL - Institute for Food & Health) and Regensburg (Institute for Clinical Microbiology and Hygiene, core facility microbiome). Microbial DNA was isolated from about 150 mg of each fecal sample by bead beating, followed by purification using guanidinium thiocyanate...

zOTU-Table_V1V3_Auto-FMT

Hannes Hoelz, Andreas Hiergeist, Dirk Haller, André Gessner, Tobias Schwerd, Maria J. G. T. Vehreschild, Anastasia Tsakmaklis, Jeannine Heetmeyer, Kolja Siebert, Federica De Zen, Deborah Häcker, Amira Metwaly & Klaus Neuhaus
The excel sheet contains zOTU Counts, annotated taxonomy, sample mapping, confidence intervals for the taxonomy and zOTU sequences. 16S rRNA sequencing Samples were prepared for sequencing at the sequencing core facilities in Freising (Core Facility Microbiome; ZIEL - Institute for Food & Health) and Regensburg (Institute for Clinical Microbiology and Hygiene, core facility microbiome). Microbial DNA was isolated from about 150 mg of each fecal sample by bead beating, followed by purification using guanidinium thiocyanate...

zOTU-Table_V1V3_Auto-FMT

Hannes Hoelz, Andreas Hiergeist, Dirk Haller, André Gessner, Tobias Schwerd, Maria J. G. T. Vehreschild, Anastasia Tsakmaklis, Jeannine Heetmeyer, Kolja Siebert, Federica De Zen, Deborah Häcker, Amira Metwaly & Klaus Neuhaus
The excel sheet contains zOTU Counts, annotated taxonomy, sample mapping, confidence intervals for the taxonomy and zOTU sequences. 16S rRNA sequencing Samples were prepared for sequencing at the sequencing core facilities in Freising (Core Facility Microbiome; ZIEL - Institute for Food & Health) and Regensburg (Institute for Clinical Microbiology and Hygiene, core facility microbiome). Microbial DNA was isolated from about 150 mg of each fecal sample by bead beating, followed by purification using guanidinium thiocyanate...

CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs

Sara Omranian & Zoran Nikoloski
Abstract High-throughput proteomics approaches have resulted in large-scale protein–protein interaction (PPI) networks that have been employed for the prediction of protein complexes. However, PPI networks contain false-positive as well as false-negative PPIs that affect the protein complex prediction algorithms. To address this issue, here we propose an algorithm called CUBCO+ that: (1) employs GO semantic similarity to retain only biologically relevant interactions with a high similarity score, (2) based on link prediction approaches, scores the...

Comparison of allosteric signaling in DnaK and BiP using mutual information between simulated residue conformations

Markus Schneider & Iris Antes
Molecular Dynamics trajectories of the Hsp70 chaperones DnaK and BiP. System configurations include DnaK or BiP bound to ATP, ATP exchanged to ADP, or the NRLLLTG peptide.

Data from: Domain-specific neural networks improve automated bird sound recognition already with small amount of local data

Patrik Lauha, Panu Somervuo, Petteri Lehikoinen, Lisa Geres, Tobias Richter, Sebastian Seibold & Otso Ovaskainen
An automatic bird sound recognition system is a useful tool for collecting data of different bird species for ecological analysis. Together with autonomous recording units (ARUs), such a system provides a possibility to collect bird observations on a scale that no human observer could ever match. During the last decades progress has been made in the field of automatic bird sound recognition, but recognizing bird species from untargeted soundscape recordings remains a challenge. In this...

Additional file 1 of Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Additional file 1. Supplementary material regarding (i) the definition of cancer cases for HCC, GBC, Adv.PrC and Loc.PrC; (ii) the definition and implementation of the data-shared lasso; (iii) the models used to derive point estimates and confidence intervals from the model selected by the data-shared lasso; and (iv) the univariate analysis conducted for comparison.

Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Abstract Background Epidemiological studies of associations between metabolites and cancer risk have typically focused on specific cancer types separately. Here, we designed a multivariate pan-cancer analysis to identify metabolites potentially associated with multiple cancer types, while also allowing the investigation of cancer type-specific associations. Methods We analysed targeted metabolomics data available for 5828 matched case-control pairs from cancer-specific case-control studies on breast, colorectal, endometrial, gallbladder, kidney, localized and advanced prostate cancer, and hepatocellular carcinoma nested...

Additional file 2 of Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition

Marie Breeur, Pietro Ferrari, Laure Dossus, Mazda Jenab, Mattias Johansson, Sabina Rinaldi, Ruth C. Travis, Mathilde His, Tim J. Key, Julie A. Schmidt, Kim Overvad, Anne Tjønneland, Cecilie Kyrø, Joseph A. Rothwell, Nasser Laouali, Gianluca Severi, Rudolf Kaaks, Verena Katzke, Matthias B. Schulze, Fabian Eichelmann, Domenico Palli, Sara Grioni, Salvatore Panico, Rosario Tumino, Carlotta Sacerdote … & Vivian Viallon
Additional file 2: Supplementary tables and figures. Figure S1. Pearson correlation between the 117 original metabolites. Figure S2. Sensitivity analyses of mutually adjusted ORs for the overall associations and cancer type-specific deviations. Figure S3. Sensitivity analysis of mutually adjusted ORs for the overall associations and cancer type-specific deviations with or without excluding hormone users. Figure S4. p-values of tests for departure from linearity and effect modification by BMI. Figure S5. ORs for the overall associations...

Additional file 1 of FoxP3 expression by retinal pigment epithelial cells: transcription factor with potential relevance for the pathology of age-related macular degeneration

Ahmad Samir Alfaar, Lucas Stürzbecher, Maria Diedrichs-Möhring, Marion Lam, Christophe Roubeix, Julia Ritter, Kathrin Schumann, Balasubramaniam Annamalai, Inga-Marie Pompös, Bärbel Rohrer, Florian Sennlaub, Nadine Reichhart, Gerhild Wildner & Olaf Strauß
Additional file 1. The additional file provides statistical comparison of gene expression between wildtype and Cx3cr1GFP/GFP mice at the different time points, control data for human FoxP3 staining, the growth rate of ARPE-19 to compare with Crisp/Cas treated ARPE-19 cells and uncropped dot plots.

CIED-Stack gas concentrations, 2015-2018

Ling Tang, Min Jia, Junai Yang, Ling Li, Xin Bo & Zhifu Mi
The Chinese Industrial Emissions Database (CIED) provides inventory of particulate matter (PM), SO2 and NOX from Chinese industries from 2015 to 2018, based on direct measurements from China’s continuous emission monitoring systems (CEMS) network. This document provides stack gas concentrations for China’s different industrial emission sources.

Additional file 8 of Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei

Conrad L. Ambros & Matthias A. Ehrmann
Additional file 8 Table S1 Examples of genes/putative tasks of annotated proteins within the different phage gene modules and their respective color-coding used in the genome comparison.

Additional file 6 of Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei

Conrad L. Ambros & Matthias A. Ehrmann
Additional file 6 Fig. S3 Neighbor joining tree of the phage terminase (large subunit) gene of as intact predicted prophages in L. sakei strains. Bootstrap values are based on a Jukes-Cantor model (1000 replicates). The phage terminase (large subunit) genes of phages infecting other lactobacilli were included as outgroups.

sj-docx-1-tam-10.1177_17588359221131526 – Supplemental material for Progression-free survival as surrogate endpoint of overall survival in esophageal squamous cell carcinoma: a real-world data and literature-based analysis

Weiming Han, Lan Wang, Chen Li, Junqiang Chen, Wencheng Zhang, Xin Wang, Qingsong Pang, Yidian Zhao, Xinchen Sun, Kaixian Zhang, Gaofeng Li, Ling Li, Xueying Qiao, Miaoling Liu, Yadi Wang, Lei Deng, Wenqing Wang, Nan Bi, Tao Zhang, Wei Deng, Wenjie Ni, Xiao Chang, Zongmei Zhou, Jun Liang, Qinfu Feng … & Zefen Xiao
Supplemental material, sj-docx-1-tam-10.1177_17588359221131526 for Progression-free survival as surrogate endpoint of overall survival in esophageal squamous cell carcinoma: a real-world data and literature-based analysis by Weiming Han, Lan Wang, Chen Li, Junqiang Chen, Wencheng Zhang, Xin Wang, Qingsong Pang, Yidian Zhao, Xinchen Sun, Kaixian Zhang, Gaofeng Li, Ling Li, Xueying Qiao, Miaoling Liu, Yadi Wang, Lei Deng, Wenqing Wang, Nan Bi, Tao Zhang, Wei Deng, Wenjie Ni, Xiao Chang, Zongmei Zhou, Jun Liang, Qinfu Feng, Lvhua...

sj-docx-1-tam-10.1177_17588359221131526 – Supplemental material for Progression-free survival as surrogate endpoint of overall survival in esophageal squamous cell carcinoma: a real-world data and literature-based analysis

Weiming Han, Lan Wang, Chen Li, Junqiang Chen, Wencheng Zhang, Xin Wang, Qingsong Pang, Yidian Zhao, Xinchen Sun, Kaixian Zhang, Gaofeng Li, Ling Li, Xueying Qiao, Miaoling Liu, Yadi Wang, Lei Deng, Wenqing Wang, Nan Bi, Tao Zhang, Wei Deng, Wenjie Ni, Xiao Chang, Zongmei Zhou, Jun Liang, Qinfu Feng … & Zefen Xiao
Supplemental material, sj-docx-1-tam-10.1177_17588359221131526 for Progression-free survival as surrogate endpoint of overall survival in esophageal squamous cell carcinoma: a real-world data and literature-based analysis by Weiming Han, Lan Wang, Chen Li, Junqiang Chen, Wencheng Zhang, Xin Wang, Qingsong Pang, Yidian Zhao, Xinchen Sun, Kaixian Zhang, Gaofeng Li, Ling Li, Xueying Qiao, Miaoling Liu, Yadi Wang, Lei Deng, Wenqing Wang, Nan Bi, Tao Zhang, Wei Deng, Wenjie Ni, Xiao Chang, Zongmei Zhou, Jun Liang, Qinfu Feng, Lvhua...

Progression-free survival as surrogate endpoint of overall survival in esophageal squamous cell carcinoma: a real-world data and literature-based analysis

Weiming Han, Lan Wang, Chen Li, Junqiang Chen, Wencheng Zhang, Xin Wang, Qingsong Pang, Yidian Zhao, Xinchen Sun, Kaixian Zhang, Gaofeng Li, Ling Li, Xueying Qiao, Miaoling Liu, Yadi Wang, Lei Deng, Wenqing Wang, Nan Bi, Tao Zhang, Wei Deng, Wenjie Ni, Xiao Chang, Zongmei Zhou, Jun Liang, Qinfu Feng … & Zefen Xiao
Background:The surrogacy of progression-free survival (PFS) for overall survival (OS) in esophageal squamous cell carcinoma (ESCC) remains unelucidated. This study aimed to determine the validity of PFS as a surrogate endpoint for OS in ESCC patients treated with definitive radiotherapy or definitive chemoradiotherapy (dRT/dCRT), as well as characterize the prognostic factors and survival of such patients.Methods:A total of 3662 patients from 10 cancer centers were enrolled. One-, 2-, and 3-year PFS (PFS12, PFS24, and PSF36,...

Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions

Davide Boldini, Lukas Friedrich, Daniel Kuhn & Stephan A. Sieber
Abstract While in the last years there has been a dramatic increase in the number of available bioassay datasets, many of them suffer from extremely imbalanced distribution between active and inactive compounds. Thus, there is an urgent need for novel approaches to tackle class imbalance in drug discovery. Inspired by recent advances in computer vision, we investigated a panel of alternative loss functions for imbalanced classification in the context of Gradient Boosting and benchmarked them...

Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions

Davide Boldini, Lukas Friedrich, Daniel Kuhn & Stephan A. Sieber
Abstract While in the last years there has been a dramatic increase in the number of available bioassay datasets, many of them suffer from extremely imbalanced distribution between active and inactive compounds. Thus, there is an urgent need for novel approaches to tackle class imbalance in drug discovery. Inspired by recent advances in computer vision, we investigated a panel of alternative loss functions for imbalanced classification in the context of Gradient Boosting and benchmarked them...

Additional file 1 of Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases

Yajing Liu, Angel Angelov, Werner Feiler, Melanie Baudrexl, Vladimir Zverlov, Wolfgang Liebl & Sonja Vanderhaeghen
Additional file 1: Table S1. Bacterial community compositions of the biogas fermenter consortia revealed by 16S rRNA amplicon sequencing. Table S2. Raw data summary of shotgun sequencing and assemblage of positive fosmid clones. Table S3. Detailed information about all the putative CAZymes screened from the metagenomic libraries, including the position of ORFs on the corresponding contigs, the library origin, the KEGG annotation and blastnr identifier of each putative enzyme. Table S4. Information on heterologously expressed...

Additional file 1 of Economic evaluation of implementation science outcomes in low- and middle-income countries: a scoping review

Akash Malhotra, Ryan R. Thompson, Faith Kagoya, Felix Masiye, Peter Mbewe, Mosepele Mosepele, Jane Phiri, Jairos Sambo, Abigail Barker, Drew B. Cameron, Victor G. Davila-Roman, William Effah, Brian Hutchinson, Michael Laxy, Brad Newsome, David Watkins, Hojoon Sohn & David W. Dowdy
Additional file 1. Protocol for scoping review.

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