417 Works

Data from: Influence of different data cleaning solutions of point-occurrence records on downstream macroecological diversity models

Petra Fuehrding-Potschkat & Stefanie M. Ickert-Bond
Digital point-occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time-consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. This study examined the extent to which cleaned data from six pipelines using data cleaning tools...

Additional file 1 of Accuracy of intraoral real-time navigation versus static, CAD/CAM-manufactured pilot drilling guides in dental implant surgery: an in vitro study

Robert Stünkel, Alexander-Nicolai Zeller, Thomas Bohne, Florian Böhrnsen, Edris Wedi, David Raschke & Philipp Kauffmann
Additional file 1: Fig. S1. A) Schematic illustration of spatial offsets from implant planning. Analysis shows deviations in drilling depth, oro-vestibular as well as mesio-distal direction and angulation. B) Section of the Treatment Evaluation Tool in coDiagnostix®. Planning is shown in blue. Red shows the actual implant position. C) Mandible model used for the in vitro testing with pilot drilling guide in situ. D) DENACAM system used for the in vitro testing. E) Major findings...

Visinin-like protein 1 levels in blood and CSF as emerging markers for Alzheimer’s and other neurodegenerative diseases

Steffen Halbgebauer, Petra Steinacker, Daniel Riedel, Patrick Oeckl, Sarah Anderl-Straub, Jolina Lombardi, Christine A. F. von Arnim, Magdalena Nagl, Armin Giese, Albert C. Ludolph & Markus Otto
Abstract Background Visinin-like protein 1 (VILIP-1) belongs to the group of emerging biomarkers with the potential to support the early diagnosis of Alzheimer’s disease (AD). However, studies investigating the differential diagnostic potential in cerebrospinal fluid (CSF) are rare and are not available for blood. Methods We set up a novel, sensitive single molecule array (Simoa) assay for the detection of VILIP-1 in CSF and serum. In total, paired CSF and serum samples from 234 patients...

Additional file 3 of Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

Gordon Wiegleb, Susanne Reinhardt, Andreas Dahl & Nico Posnien
Additional file 3: Table S3. Results of automatic cluster annotation and assignment to combined clusters.

Additional file 4 of Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

Gordon Wiegleb, Susanne Reinhardt, Andreas Dahl & Nico Posnien
Additional file 4: Table S4. List of marker genes for each cluster in scRNAseq analysis.

No seasonal curtailment of the Eurasian Skylark’s (Alauda arvensis) breeding season in German heterogeneous farmland

Manuel Püttmanns, Franziska Lehmann, Fabian Willert, Jasmin Heinz, Antje Kieburg, Tim Filla, Niko Balkenhol, Matthias Waltert & Eckhard Gottschalk
The lack of suitable nesting sites is one key driver behind the farmland bird crisis in Europe. Winter cereals become impenetrable for ground-breeding birds like the Eurasian Skylark (Alauda arvensis), curtailing breeding time. Stable Skylark populations depend on multiple breeding attempts per year; thus, the widespread cultivation of winter cereals has strongly contributed to their tremendous decline. Crop diversification is thought to be a potential measure to counteract this development. Therefore, we explored how individual...

Significant performance enhancement of UV-Vis self-powered CsPbBr3 quantum dot-based photodetectors induced by ligand modification and P3HT embedding

Meng Wang, Dehai Liang, Wen Ma, Qionghua Mo, Zhigang Zang, Qingkai Qian & wensi cai
In this work, we report a novel strategy in improving the performance of UV-Vis self-powered CsPbBr₃ quantum dots (QDs) photodetectors (PDs) by ligand modification and P3HT embedding. Compared with those based on pure QDs, modified PDs show a shorten of response time by nearly 10 times, and an increase of maximum responsivity and specific detectivity for nearly 45 and 97 times, respectively. Such PDs also show a high stability with 90% of the initial photocurrent...

Additional file 8 of Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

Gordon Wiegleb, Susanne Reinhardt, Andreas Dahl & Nico Posnien
Additional file 8: Table S8. List of top 3000 variable genes for scRNAseq and snRNAseq data, respectively.

Additional file 9 of Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

Gordon Wiegleb, Susanne Reinhardt, Andreas Dahl & Nico Posnien
Additional file 9: Table S9. Top 3000 variable genes and GO enrichment results for scRNAseq, snRNAseq and shared.

Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

Gordon Wiegleb, Susanne Reinhardt, Andreas Dahl & Nico Posnien
Abstract Background Recent technological advances opened the opportunity to simultaneously study gene expression for thousands of individual cells on a genome-wide scale. The experimental accessibility of such single-cell RNA sequencing (scRNAseq) approaches allowed gaining insights into the cell type composition of heterogeneous tissue samples of animal model systems and emerging models alike. A major prerequisite for a successful application of the method is the dissociation of complex tissues into individual cells, which often requires large...

Additional file 3 of Monitoring and management of chronic kidney disease in ambulatory care – analysis of clinical and claims data from a population-based study

Gesine Weckmann, Janine Wirkner, Elisa Kasbohm, Carolin Zimak, Annekathrin Haase, Jean-François Chenot, Carsten Oliver Schmidt & Sylvia Stracke
Additional file 3: Supplemental Table 2. Billing and coding according to KDIGO glomerular filtration rate categorization for the observation period 2008 – 2012.

Additional file 4 of Monitoring and management of chronic kidney disease in ambulatory care – analysis of clinical and claims data from a population-based study

Gesine Weckmann, Janine Wirkner, Elisa Kasbohm, Carolin Zimak, Annekathrin Haase, Jean-François Chenot, Carsten Oliver Schmidt & Sylvia Stracke
Additional file 4: Supplemental Table 3. Billing and coding according to KDIGO albuminuria categorization* for the observation period 2008 – 2012.

Additional file 1 of Dementia risk prediction in individuals with mild cognitive impairment: a comparison of Cox regression and machine learning models

Meng Wang, Matthew Greenberg, Nils D. Forkert, Thierry Chekouo, Gabriel Afriyie, Zahinoor Ismail, Eric E. Smith & Tolulope T. Sajobi
Supplementary Material 1

Supplementary material from \"The road to recovery: a synthesis of outcomes from ecosystem restoration in tropical and sub-tropical Asian forests\"

Lindsay F. Banin, Elizabeth H. Raine, Lucy M. Rowland, Robin L. Chazdon, Stuart W. Smith, Nur Estya Binte Rahman, Adam Butler, Christopher Philipson, Grahame G. Applegate, E. Petter Axelsson, Sugeng Budiharta, Siew Chin Chua, Mark E. J. Cutler, Stephen Elliott, Elva Gemita, Elia Godoong, Laura L. B. Graham, Robin M. Hayward, Andy Hector, Ulrik Ilstedt, Joel Jensen, Srinivasan Kasinathan, Christopher J. Kettle, Daniel Lussetti, Benjapan Manohan … & David F. R. P. Burslem
Current policy is driving renewed impetus to restore forests to return ecological function, protect species, sequester carbon and secure livelihoods. Here we assess the contribution of tree planting to ecosystem restoration in tropical and sub-tropical Asia; we synthesize evidence on mortality and growth of planted trees at 176 sites and assess structural and biodiversity recovery of co-located actively restored and naturally regenerating forest plots. Mean mortality of planted trees was 18% 1 year after planting,...

Regularization approaches in clinical biostatistics: A review of methods and their applications

Sarah Friedrich, Andreas Groll, Katja Ickstadt, Thomas Kneib, Markus Pauly, Jörg Rahnenführer & Tim Friede
A range of regularization approaches have been proposed in the data sciences to overcome overfitting, to exploit sparsity or to improve prediction. Using a broad definition of regularization, namely controlling model complexity by adding information in order to solve ill-posed problems or to prevent overfitting, we review a range of approaches within this framework including penalization, early stopping, ensembling and model averaging. Aspects of their practical implementation are discussed including available R-packages and examples are...

Empfehlungen für transformative Zeitschriftenverträge mit Publikationsdienstleistern: Handreichung der Schwerpunktinitiative „Digitale Information“ der Allianz der deutschen Wissenschaftsorganisationen vor dem Hintergrund der Umsetzung der Open-Access-Strategie 2021–2025 der Allianz der deutschen Wissenschaftsorganisationen

, Heinz Pampel, Roland Bertelmann, Kristine Hillenkötter, Bernhard Mittermaier, Dirk Pieper, Hildegard Schäffler, Stefanie Seeh & Marco Tullney

Additional file 4 of Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer

Peng Song, Ying Li, Feng Wang, Lingxiao Pu, Linsen Bao, Hengfei Gao, Chuandong Zhu, Meng Wang & Liang Tao
Additional file 4: Figure S3. Volcano plot showing the log2 fold change of 517 significantly differentially expressed miRNAs in CRC patients from the TCGA database.

Additional file 5 of Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer

Peng Song, Ying Li, Feng Wang, Lingxiao Pu, Linsen Bao, Hengfei Gao, Chuandong Zhu, Meng Wang & Liang Tao
Additional file 5: Figure S4. Prediction of 6 miRNAs (miR-29b-3p, miR-4677-3p, miR-144-3p, miR-30b-5p, miR-30e-5p and miR-374b-5p) targeting LIFR-AS1 in CRC.

Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer

Peng Song, Ying Li, Feng Wang, Lingxiao Pu, Linsen Bao, Hengfei Gao, Chuandong Zhu, Meng Wang & Liang Tao
Abstract Background Aberrant DNA methylation is an epigenetic marker that has been linked to the pathogenesis of colorectal cancer (CRC). Long noncoding RNAs (lncRNAs) have been increasingly identified to be associated with tumorigenic processes of CRC. Identifying epigenetically dysregulated lncRNAs and characterizing their effects during carcinogenesis are focuses of cancer research. Methods Differentially methylated loci and expressed lncRNAs were identified by integrating DNA methylome and transcriptome analyses using The Cancer Genome Atlas database. Bisulfite sequencing...

Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer

Peng Song, Ying Li, Feng Wang, Lingxiao Pu, Linsen Bao, Hengfei Gao, Chuandong Zhu, Meng Wang & Liang Tao
Abstract Background Aberrant DNA methylation is an epigenetic marker that has been linked to the pathogenesis of colorectal cancer (CRC). Long noncoding RNAs (lncRNAs) have been increasingly identified to be associated with tumorigenic processes of CRC. Identifying epigenetically dysregulated lncRNAs and characterizing their effects during carcinogenesis are focuses of cancer research. Methods Differentially methylated loci and expressed lncRNAs were identified by integrating DNA methylome and transcriptome analyses using The Cancer Genome Atlas database. Bisulfite sequencing...

Additional file 1 of Monitoring and management of chronic kidney disease in ambulatory care – analysis of clinical and claims data from a population-based study

Gesine Weckmann, Janine Wirkner, Elisa Kasbohm, Carolin Zimak, Annekathrin Haase, Jean-François Chenot, Carsten Oliver Schmidt & Sylvia Stracke
Additional file 1: Supplement1. SHIP study and detailed description of data sources.

Additional file 2 of Monitoring and management of chronic kidney disease in ambulatory care – analysis of clinical and claims data from a population-based study

Gesine Weckmann, Janine Wirkner, Elisa Kasbohm, Carolin Zimak, Annekathrin Haase, Jean-François Chenot, Carsten Oliver Schmidt & Sylvia Stracke
Additional file 2: Supplemental Table 1. Comparison of baseline characteristics of participants with and without linked claims data.

DIGIS: Digital Geochemistry Infrastructure for GEOROC 2.0

Marthe Klöcking , Bärbel Sarbas , Wolfram Horstmann , Stefan Möller-McNett , Jens Nieschulze , Caroline Sporleder , Matthias Willbold & Gerhard Wörner
GEOROC is a leading open-access source of geochemical and isotopic datasets and has facilitated thousands of peer-reviewed publications and new avenues of geochemical research. The new Digital Geochemistry Infrastructure (DIGIS) concept of GEOROC 2.0, an integral part of the NFDI4Earth initiative, will continue and enhance the existing data collection by generating a connected platform that meets future challenges of digital data-based research and provides advanced service to the community. Our approach is to (1) realign...

Sediment routing systems and provenance analysis

Laura Stutenbecker , Hilmar von Eynatten , Luca Caracciolo & Guido Meinhold
The composition of clastic sediments or sedimentary rocks is a result of source area properties, sediment generation and transport processes as well as post-depositional changes. Deciphering the provenance of clastic deposits can therefore provide valuable insights into tectonic, geomorphic, climatic and anthropogenic factors and processes shaping sedimentary systems over different temporal and spatial scales. This session welcomes contributions that investigate (1) the provenance of clastic deposits by analyzing compositional (e.g. mineralogical, geochemical) properties, (2) the...

Data from: Biogeographic, climatic and spatial drivers differentially affect α-, β- and γ-diversities on oceanic archipelagos

Juliano Sarmento Cabral, Patrick Weigelt, Walter Daniel Kissling & Holger Kreft
Island biogeographic studies traditionally treat single islands as units of analysis. This ignores the fact that most islands are spatially nested within archipelagos. Here, we took a fundamentally different approach and focused on entire archipelagos using species richness of vascular plants on 23 archipelagos worldwide and their 174 constituent islands. We assessed differential effects of biogeographic factors (area, isolation, age, elevation), current and past climate (temperature, precipitation, seasonality, climate change velocity) and intra-archipelagic spatial structure...

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